1
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He M, Zong X, Xu B, Qi W, Huang W, Djekidel MN, Zhang Y, Pagala VR, Li J, Hao X, Guy C, Bai L, Cross R, Li C, Peng J, Feng Y. Dynamic Foxp3-chromatin interaction controls tunable Treg cell function. J Exp Med 2024; 221:e20232068. [PMID: 38935023 PMCID: PMC11211070 DOI: 10.1084/jem.20232068] [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: 11/10/2023] [Revised: 04/11/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Nuclear factor Foxp3 determines regulatory T (Treg) cell fate and function via mechanisms that remain unclear. Here, we investigate the nature of Foxp3-mediated gene regulation in suppressing autoimmunity and antitumor immune response. Contrasting with previous models, we find that Foxp3-chromatin binding is regulated by Treg activation states, tumor microenvironment, and antigen and cytokine stimulations. Proteomics studies uncover dynamic proteins within Foxp3 proximity upon TCR or IL-2 receptor signaling in vitro, reflecting intricate interactions among Foxp3, signal transducers, and chromatin. Pharmacological inhibition and genetic knockdown experiments indicate that NFAT and AP-1 protein Batf are required for enhanced Foxp3-chromatin binding in activated Treg cells and tumor-infiltrating Treg cells to modulate target gene expression. Furthermore, mutations at the Foxp3 DNA-binding domain destabilize the Foxp3-chromatin association. These representative settings delineate context-dependent Foxp3-chromatin interaction, suggesting that Foxp3 associates with chromatin by hijacking DNA-binding proteins resulting from Treg activation or differentiation, which is stabilized by direct Foxp3-DNA binding, to dynamically regulate Treg cell function according to immunological contexts.
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Affiliation(s)
- Minghong He
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Xinying Zong
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Wenjie Qi
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Wenjun Huang
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | | | - Yang Zhang
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Vishwajeeth R. Pagala
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jun Li
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Xiaolei Hao
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Clifford Guy
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Lu Bai
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Richard Cross
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Junmin Peng
- Department of Structure Biology and Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Yongqiang Feng
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN, USA
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2
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Szeto ACH, Clark PA, Ferreira ACF, Heycock M, Griffiths EL, Jou E, Mannion J, Luan SL, Storrar S, Knolle MD, Kozik P, Jolin HE, Fallon PG, McKenzie ANJ. Mef2d potentiates type-2 immune responses and allergic lung inflammation. Science 2024; 384:eadl0370. [PMID: 38935708 DOI: 10.1126/science.adl0370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 05/02/2024] [Indexed: 06/29/2024]
Abstract
Innate lymphoid cells (ILCs) and adaptive T lymphocytes promote tissue homeostasis and protective immune responses. Their production depends on the transcription factor GATA3, which is further elevated specifically in ILC2s and T helper 2 cells to drive type-2 immunity during tissue repair, allergic disorders, and anti-helminth immunity. The control of this crucial up-regulation is poorly understood. Using CRISPR screens in ILCs we identified previously unappreciated myocyte-specific enhancer factor 2d (Mef2d)-mediated regulation of GATA3-dependent type-2 lymphocyte differentiation. Mef2d-deletion from ILC2s and/or T cells specifically protected against an allergen lung challenge. Mef2d repressed Regnase-1 endonuclease expression to enhance IL-33 receptor production and IL-33 signaling and acted downstream of calcium-mediated signaling to translocate NFAT1 to the nucleus to promote type-2 cytokine-mediated immunity.
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Affiliation(s)
| | - Paula A Clark
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | | | - Morgan Heycock
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | | | - Eric Jou
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | | | - Shi-Lu Luan
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Sophie Storrar
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Martin D Knolle
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
- Cambridge University Hospitals, Cambridge, CB2 0QQ, UK
| | - Patrycja Kozik
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Helen E Jolin
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
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3
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de Jesus M, Settle AH, Vorselen D, Gaetjens TK, Galiano M, Romin Y, Lee E, Wong YY, Fu TM, Santosa E, Winer BY, Tamzalit F, Wang MS, Santella A, Bao Z, Sun JC, Shah P, Theriot JA, Abel SM, Huse M. Single-cell topographical profiling of the immune synapse reveals a biomechanical signature of cytotoxicity. Sci Immunol 2024; 9:eadj2898. [PMID: 38941478 DOI: 10.1126/sciimmunol.adj2898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 06/05/2024] [Indexed: 06/30/2024]
Abstract
Immune cells have intensely physical lifestyles characterized by structural plasticity and force exertion. To investigate whether specific immune functions require stereotyped mechanical outputs, we used super-resolution traction force microscopy to compare the immune synapses formed by cytotoxic T cells with contacts formed by other T cell subsets and by macrophages. T cell synapses were globally compressive, which was fundamentally different from the pulling and pinching associated with macrophage phagocytosis. Spectral decomposition of force exertion patterns from each cell type linked cytotoxicity to compressive strength, local protrusiveness, and the induction of complex, asymmetric topography. These features were validated as cytotoxic drivers by genetic disruption of cytoskeletal regulators, live imaging of synaptic secretion, and in silico analysis of interfacial distortion. Synapse architecture and force exertion were sensitive to target stiffness and size, suggesting that the mechanical potentiation of killing is biophysically adaptive. We conclude that cellular cytotoxicity and, by implication, other effector responses are supported by specialized patterns of efferent force.
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Affiliation(s)
- Miguel de Jesus
- Louis V. Gerstner, Jr., Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander H Settle
- Louis V. Gerstner, Jr., Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daan Vorselen
- Cell Biology and Immunology Group, Wageningen University & Research, Wageningen, Netherlands
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Thomas K Gaetjens
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA
| | - Michael Galiano
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yevgeniy Romin
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Esther Lee
- Immunology & Molecular Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY, USA
| | - Yung Yu Wong
- Louis V. Gerstner, Jr., Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tian-Ming Fu
- Department of Electrical and Computer Engineering, Princeton University, Princeton, NJ, USA
| | - Endi Santosa
- Immunology & Molecular Pathogenesis Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY, USA
| | - Benjamin Y Winer
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fella Tamzalit
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mitchell S Wang
- Pharmacology Program, Weill Cornell Medicine Graduate School of Medical Sciences, New York, NY, USA
| | - Anthony Santella
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhirong Bao
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pavak Shah
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Julie A Theriot
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Steven M Abel
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA
| | - Morgan Huse
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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4
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Dwivedi D, Dumontier D, Sherer M, Lin S, Mirow AMC, Qiu Y, Xu Q, Liebman SA, Joseph D, Datta SR, Fishell G, Pouchelon G. Metabotropic signaling within somatostatin interneurons controls transient thalamocortical inputs during development. Nat Commun 2024; 15:5421. [PMID: 38926335 PMCID: PMC11208423 DOI: 10.1038/s41467-024-49732-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: 12/18/2023] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
During brain development, neural circuits undergo major activity-dependent restructuring. Circuit wiring mainly occurs through synaptic strengthening following the Hebbian "fire together, wire together" precept. However, select connections, essential for circuit development, are transient. They are effectively connected early in development, but strongly diminish during maturation. The mechanisms by which transient connectivity recedes are unknown. To investigate this process, we characterize transient thalamocortical inputs, which depress onto somatostatin inhibitory interneurons during development, by employing optogenetics, chemogenetics, transcriptomics and CRISPR-based strategies in mice. We demonstrate that in contrast to typical activity-dependent mechanisms, transient thalamocortical connectivity onto somatostatin interneurons is non-canonical and involves metabotropic signaling. Specifically, metabotropic-mediated transcription, of guidance molecules in particular, supports the elimination of this connectivity. Remarkably, we found that this process impacts the development of normal exploratory behaviors of adult mice.
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Affiliation(s)
- Deepanjali Dwivedi
- Harvard Medical School, Department of Neurobiology, Boston, MA, USA
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA, USA
| | | | - Mia Sherer
- Harvard Medical School, Department of Neurobiology, Boston, MA, USA
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA, USA
| | - Sherry Lin
- Harvard Medical School, Department of Neurobiology, Boston, MA, USA
| | - Andrea M C Mirow
- Harvard Medical School, Department of Neurobiology, Boston, MA, USA
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, Harbor, NY, USA
| | - Yanjie Qiu
- Harvard Medical School, Department of Neurobiology, Boston, MA, USA
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA, USA
| | - Qing Xu
- Harvard Medical School, Department of Neurobiology, Boston, MA, USA
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA, USA
- Center for Genomics & Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Samuel A Liebman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, Harbor, NY, USA
| | - Djeckby Joseph
- Cold Spring Harbor Laboratory, Cold Spring Harbor, Harbor, NY, USA
| | - Sandeep R Datta
- Harvard Medical School, Department of Neurobiology, Boston, MA, USA
| | - Gord Fishell
- Harvard Medical School, Department of Neurobiology, Boston, MA, USA.
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA, USA.
| | - Gabrielle Pouchelon
- Harvard Medical School, Department of Neurobiology, Boston, MA, USA.
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA, USA.
- Cold Spring Harbor Laboratory, Cold Spring Harbor, Harbor, NY, USA.
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5
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Chen X, Cai Q, Zhou J, Pleasure SJ, Schulman H, Zhang M, Nicoll RA. CaMKII autophosphorylation is the only enzymatic event required for synaptic memory. Proc Natl Acad Sci U S A 2024; 121:e2402783121. [PMID: 38889145 PMCID: PMC11214084 DOI: 10.1073/pnas.2402783121] [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: 02/09/2024] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
Ca2+/calmodulin (CaM)-dependent kinase II (CaMKII) plays a critical role in long-term potentiation (LTP), a well-established model for learning and memory through the enhancement of synaptic transmission. Biochemical studies indicate that CaMKII catalyzes a phosphotransferase (kinase) reaction of both itself (autophosphorylation) and of multiple downstream target proteins. However, whether either type of phosphorylation plays any role in the synaptic enhancing action of CaMKII remains hotly contested. We have designed a series of experiments to define the minimal requirements for the synaptic enhancement by CaMKII. We find that autophosphorylation of T286 and further binding of CaMKII to the GluN2B subunit are required both for initiating LTP and for its maintenance (synaptic memory). Once bound to the NMDA receptor, the synaptic action of CaMKII occurs in the absence of target protein phosphorylation. Thus, autophosphorylation and binding to the GluN2B subunit are the only two requirements for CaMKII in synaptic memory.
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Affiliation(s)
- Xiumin Chen
- Department of Neurology and Institute of Neuroscience of Soochow University, Second Affiliated Hospital of Soochow University, Suzhou215004, China
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA94158
| | - Qixu Cai
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Department of Laboratory Medicine, State Key Laboratory of Vaccines for Infectious Diseases,School of Public Heath, Xiamen University, Xiamen, Fujian361102, China
| | - Jing Zhou
- Department of Neurology, University of California, San Francisco, CA94158
| | - Samuel J. Pleasure
- Department of Neurology, University of California, San Francisco, CA94158
| | - Howard Schulman
- Department of Pharmacology, Stanford University School of Medicine, Stanford, CA
- Department of Pharmacology, Panorama Research Institute, Sunnyvale, CA
| | - Mingjie Zhang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Department of Laboratory Medicine, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong518055, China
| | - Roger A. Nicoll
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA94158
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6
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Zheng X, Wu B, Liu Y, Simmons SK, Kim K, Clarke GS, Ashiq A, Park J, Li J, Wang Z, Tong L, Wang Q, Rajamani KT, Muñoz-Castañeda R, Mu S, Qi T, Zhang Y, Ngiam ZC, Ohte N, Hanashima C, Wu Z, Xu X, Levin JZ, Jin X. Massively parallel in vivo Perturb-seq reveals cell-type-specific transcriptional networks in cortical development. Cell 2024; 187:3236-3248.e21. [PMID: 38772369 PMCID: PMC11193654 DOI: 10.1016/j.cell.2024.04.050] [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: 09/08/2023] [Revised: 11/30/2023] [Accepted: 04/30/2024] [Indexed: 05/23/2024]
Abstract
Leveraging AAVs' versatile tropism and labeling capacity, we expanded the scale of in vivo CRISPR screening with single-cell transcriptomic phenotyping across embryonic to adult brains and peripheral nervous systems. Through extensive tests of 86 vectors across AAV serotypes combined with a transposon system, we substantially amplified labeling efficacy and accelerated in vivo gene delivery from weeks to days. Our proof-of-principle in utero screen identified the pleiotropic effects of Foxg1, highlighting its tight regulation of distinct networks essential for cell fate specification of Layer 6 corticothalamic neurons. Notably, our platform can label >6% of cerebral cells, surpassing the current state-of-the-art efficacy at <0.1% by lentivirus, to achieve analysis of over 30,000 cells in one experiment and enable massively parallel in vivo Perturb-seq. Compatible with various phenotypic measurements (single-cell or spatial multi-omics), it presents a flexible approach to interrogate gene function across cell types in vivo, translating gene variants to their causal function.
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Affiliation(s)
- Xinhe Zheng
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Boli Wu
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Yuejia Liu
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Sean K Simmons
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kwanho Kim
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Grace S Clarke
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Abdullah Ashiq
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Joshua Park
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Jiwen Li
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Zhilin Wang
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Liqi Tong
- Center for Neural Circuit Mapping, Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, CA 92617, USA
| | - Qizhao Wang
- Center for Neural Circuit Mapping, Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, CA 92617, USA
| | - Keerthi T Rajamani
- Appel Alzheimer's Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Rodrigo Muñoz-Castañeda
- Appel Alzheimer's Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Shang Mu
- Appel Alzheimer's Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Tianbo Qi
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Yunxiao Zhang
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Zi Chao Ngiam
- Center for Advanced Biomedical Sciences, Waseda University, Tokyo 162-8480, Japan
| | - Naoto Ohte
- Center for Advanced Biomedical Sciences, Waseda University, Tokyo 162-8480, Japan
| | - Carina Hanashima
- Center for Advanced Biomedical Sciences, Waseda University, Tokyo 162-8480, Japan
| | - Zhuhao Wu
- Appel Alzheimer's Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Xiangmin Xu
- Center for Neural Circuit Mapping, Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, CA 92617, USA
| | - Joshua Z Levin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xin Jin
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA.
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7
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Bolondi A, Law BK, Kretzmer H, Gassaloglu SI, Buschow R, Riemenschneider C, Yang D, Walther M, Veenvliet JV, Meissner A, Smith ZD, Chan MM. Reconstructing axial progenitor field dynamics in mouse stem cell-derived embryoids. Dev Cell 2024; 59:1489-1505.e14. [PMID: 38579718 PMCID: PMC11187653 DOI: 10.1016/j.devcel.2024.03.024] [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: 08/15/2023] [Revised: 12/13/2023] [Accepted: 03/12/2024] [Indexed: 04/07/2024]
Abstract
Embryogenesis requires substantial coordination to translate genetic programs to the collective behavior of differentiating cells, but understanding how cellular decisions control tissue morphology remains conceptually and technically challenging. Here, we combine continuous Cas9-based molecular recording with a mouse embryonic stem cell-based model of the embryonic trunk to build single-cell phylogenies that describe the behavior of transient, multipotent neuro-mesodermal progenitors (NMPs) as they commit into neural and somitic cell types. We find that NMPs show subtle transcriptional signatures related to their recent differentiation and contribute to downstream lineages through a surprisingly broad distribution of individual fate outcomes. Although decision-making can be heavily influenced by environmental cues to induce morphological phenotypes, axial progenitors intrinsically mature over developmental time to favor the neural lineage. Using these data, we present an experimental and analytical framework for exploring the non-homeostatic dynamics of transient progenitor populations as they shape complex tissues during critical developmental windows.
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Affiliation(s)
- Adriano Bolondi
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Benjamin K Law
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Seher Ipek Gassaloglu
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - René Buschow
- Microscopy Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | | | - Dian Yang
- Department of Molecular Pharmacology and Therapeutics & Systems Biology, Columbia University, New York, NY 10032, USA
| | - Maria Walther
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Jesse V Veenvliet
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany; Cluster of Excellence Physics of Life, Technische Universität Dresden, 01307 Dresden, Germany; Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany.
| | - Zachary D Smith
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06519, USA.
| | - Michelle M Chan
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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8
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Baek S, Seo DS, Kang J, Ahmad Y, Park S, Joo S, Kim K, Jang Y. ChREBP plays a pivotal role in the nutrient-mediated regulation of metabolic gene expression in brown adipose tissue. Life Sci 2024; 351:122843. [PMID: 38880168 DOI: 10.1016/j.lfs.2024.122843] [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: 02/02/2024] [Revised: 05/27/2024] [Accepted: 06/12/2024] [Indexed: 06/18/2024]
Abstract
AIMS Carbohydrate-responsive element-binding protein (ChREBP) is a transcription factor that regulates several metabolic genes, including the lipogenic enzymes necessary for the metabolic conversion of carbohydrates into lipids. Although the crucial role of ChREBP in the liver, the primary site of de novo lipogenesis, has been studied, its functional role in adipose tissues, particularly brown adipose tissue (BAT), remains unclear. In this study, we investigated the role of ChREBP in BAT under conditions of a high-carbohydrate diet (HCD) and ketogenic diet (KD), represented by extremely low carbohydrate intake. MAIN METHODS Using an adeno-associated virus and Cas9 knock-in mice, we rapidly generated Chrebp brown adipocyte-specific knock-out (B-KO) mice, bypassing the necessity for prolonged breeding by using the Cre-Lox system. KEY FINDINGS We demonstrated that ChREBP is essential for glucose metabolism and lipogenic gene expression in BAT under HCD conditions in Chrebp B-KO mice. After nutrient intake, Chrebp B-KO attenuated the KD-induced expression of several inflammatory genes in BAT. SIGNIFICANCE Our results indicated that ChREBP, a nutrient-sensing regulator, is indispensable for expressing a diverse range of metabolic genes in BAT.
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Affiliation(s)
- Seungwoo Baek
- Department of Biology and Chemistry, Changwon National University, Changwon, Republic of Korea
| | - Dong Soo Seo
- Department of Biology and Chemistry, Changwon National University, Changwon, Republic of Korea
| | - Jaehyeon Kang
- Department of Biology and Chemistry, Changwon National University, Changwon, Republic of Korea
| | - Yusra Ahmad
- Department of Biology and Chemistry, Changwon National University, Changwon, Republic of Korea
| | - Sungjun Park
- Department of Biology and Chemistry, Changwon National University, Changwon, Republic of Korea
| | - Sungmin Joo
- Department of Biology and Chemistry, Changwon National University, Changwon, Republic of Korea
| | - KyeongJin Kim
- Department of Biomedical Sciences, College of Medicine, Inha University, Incheon, Republic of Korea
| | - Younghoon Jang
- Department of Biology and Chemistry, Changwon National University, Changwon, Republic of Korea.
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9
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Enk LUB, Hellmig M, Riecken K, Kilian C, Datlinger P, Jauch-Speer SL, Neben T, Sultana Z, Sivayoganathan V, Borchers A, Paust HJ, Zhao Y, Asada N, Liu S, Agalioti T, Pelczar P, Wiech T, Bock C, Huber TB, Huber S, Bonn S, Gagliani N, Fehse B, Panzer U, Krebs CF. Targeting T cell plasticity in kidney and gut inflammation by pooled single-cell CRISPR screening. Sci Immunol 2024; 9:eadd6774. [PMID: 38875317 DOI: 10.1126/sciimmunol.add6774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 05/23/2024] [Indexed: 06/16/2024]
Abstract
Pro-inflammatory CD4+ T cells are major drivers of autoimmune diseases, yet therapies modulating T cell phenotypes to promote an anti-inflammatory state are lacking. Here, we identify T helper 17 (TH17) cell plasticity in the kidneys of patients with antineutrophil cytoplasmic antibody-associated glomerulonephritis on the basis of single-cell (sc) T cell receptor analysis and scRNA velocity. To uncover molecules driving T cell polarization and plasticity, we established an in vivo pooled scCRISPR droplet sequencing (iCROP-seq) screen and applied it to mouse models of glomerulonephritis and colitis. CRISPR-based gene targeting in TH17 cells could be ranked according to the resulting transcriptional perturbations, and polarization biases into T helper 1 (TH1) and regulatory T cells could be quantified. Furthermore, we show that iCROP-seq can facilitate the identification of therapeutic targets by efficient functional stratification of genes and pathways in a disease- and tissue-specific manner. These findings uncover TH17 to TH1 cell plasticity in the human kidney in the context of renal autoimmunity.
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Affiliation(s)
- Leon U B Enk
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malte Hellmig
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kristoffer Riecken
- Department of Stem Cell Transplantation, Research Department Cell and Gene Therapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph Kilian
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Paul Datlinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Saskia L Jauch-Speer
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias Neben
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Zeba Sultana
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Varshi Sivayoganathan
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alina Borchers
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hans-Joachim Paust
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yu Zhao
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nariaki Asada
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Shuya Liu
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Theodora Agalioti
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Penelope Pelczar
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thorsten Wiech
- Institute of Pathology, Division of Nephropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Artificial Intelligence and Decision Support, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Samuel Huber
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Bonn
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nicola Gagliani
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department for General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Boris Fehse
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Stem Cell Transplantation, Research Department Cell and Gene Therapy, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulf Panzer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian F Krebs
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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10
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Martinez-Terroba E, Plasek-Hegde LM, Chiotakakos I, Li V, de Miguel FJ, Robles-Oteiza C, Tyagi A, Politi K, Zamudio JR, Dimitrova N. Overexpression of Malat1 drives metastasis through inflammatory reprogramming of the tumor microenvironment. Sci Immunol 2024; 9:eadh5462. [PMID: 38875320 DOI: 10.1126/sciimmunol.adh5462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/23/2024] [Indexed: 06/16/2024]
Abstract
Expression of the long noncoding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) correlates with tumor progression and metastasis in many tumor types. However, the impact and mechanism of action by which MALAT1 promotes metastatic disease remain elusive. Here, we used CRISPR activation (CRISPRa) to overexpress MALAT1/Malat1 in patient-derived lung adenocarcinoma (LUAD) cell lines and in the autochthonous K-ras/p53 LUAD mouse model. Malat1 overexpression was sufficient to promote the progression of LUAD to metastatic disease in mice. Overexpression of MALAT1/Malat1 enhanced cell mobility and promoted the recruitment of protumorigenic macrophages to the tumor microenvironment through paracrine secretion of CCL2/Ccl2. Ccl2 up-regulation was the result of increased global chromatin accessibility upon Malat1 overexpression. Macrophage depletion and Ccl2 blockade counteracted the effects of Malat1 overexpression. These data demonstrate that a single lncRNA can drive LUAD metastasis through reprogramming of the tumor microenvironment.
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Affiliation(s)
- Elena Martinez-Terroba
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Leah M Plasek-Hegde
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Ioannis Chiotakakos
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Vincent Li
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | | | - Camila Robles-Oteiza
- Departments of Pathology and Internal Medicine (Section of Medical Oncology), Yale School of Medicine, New Haven, CT 06511, USA
| | - Antariksh Tyagi
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06516, USA
| | - Katerina Politi
- Yale Cancer Center, Yale University, New Haven, CT 06511, USA
- Departments of Pathology and Internal Medicine (Section of Medical Oncology), Yale School of Medicine, New Haven, CT 06511, USA
| | - Jesse R Zamudio
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Nadya Dimitrova
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Yale Cancer Center, Yale University, New Haven, CT 06511, USA
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11
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Chung M, Imanaka K, Huang Z, Watarai A, Wang MY, Tao K, Ejima H, Aida T, Feng G, Okuyama T. Conditional knockout of Shank3 in the ventral CA1 by quantitative in vivo genome-editing impairs social memory in mice. Nat Commun 2024; 15:4531. [PMID: 38866749 PMCID: PMC11169449 DOI: 10.1038/s41467-024-48430-x] [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: 12/30/2022] [Accepted: 04/26/2024] [Indexed: 06/14/2024] Open
Abstract
Individuals with autism spectrum disorder (ASD) have a higher prevalence of social memory impairment. A series of our previous studies revealed that hippocampal ventral CA1 (vCA1) neurons possess social memory engram and that the neurophysiological representation of social memory in the vCA1 neurons is disrupted in ASD-associated Shank3 knockout mice. However, whether the dysfunction of Shank3 in vCA1 causes the social memory impairment observed in ASD remains unclear. In this study, we found that vCA1-specific Shank3 conditional knockout (cKO) by the adeno-associated virus (AAV)- or specialized extracellular vesicle (EV)- mediated in vivo gene editing was sufficient to recapitulate the social memory impairment in male mice. Furthermore, the utilization of EV-mediated Shank3-cKO allowed us to quantitatively examine the role of Shank3 in social memory. Our results suggested that there is a certain threshold for the proportion of Shank3-cKO neurons required for social memory disruption. Thus, our study provides insight into the population coding of social memory in vCA1, as well as the pathological mechanisms underlying social memory impairment in ASD.
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Affiliation(s)
- Myung Chung
- Laboratory of Behavioral Neuroscience, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Katsutoshi Imanaka
- Laboratory of Behavioral Neuroscience, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ziyan Huang
- Laboratory of Behavioral Neuroscience, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akiyuki Watarai
- Laboratory of Behavioral Neuroscience, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Mu-Yun Wang
- Laboratory of Behavioral Neuroscience, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Kentaro Tao
- Laboratory of Behavioral Neuroscience, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Hirotaka Ejima
- Department of Materials Engineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Tomomi Aida
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Guoping Feng
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Teruhiro Okuyama
- Laboratory of Behavioral Neuroscience, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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12
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Finlay JB, Ireland AS, Hawgood SB, Reyes T, Ko T, Olsen RR, Abi Hachem R, Jang DW, Bell D, Chan JM, Goldstein BJ, Oliver TG. Olfactory neuroblastoma mimics molecular heterogeneity and lineage trajectories of small-cell lung cancer. Cancer Cell 2024; 42:1086-1105.e13. [PMID: 38788720 PMCID: PMC11186085 DOI: 10.1016/j.ccell.2024.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/13/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024]
Abstract
The olfactory epithelium undergoes neuronal regeneration from basal stem cells and is susceptible to olfactory neuroblastoma (ONB), a rare tumor of unclear origins. Employing alterations in Rb1/Trp53/Myc (RPM), we establish a genetically engineered mouse model of high-grade metastatic ONB exhibiting a NEUROD1+ immature neuronal phenotype. We demonstrate that globose basal cells (GBCs) are a permissive cell of origin for ONB and that ONBs exhibit cell fate heterogeneity that mimics normal GBC developmental trajectories. ASCL1 loss in RPM ONB leads to emergence of non-neuronal histopathologies, including a POU2F3+ microvillar-like state. Similar to small-cell lung cancer (SCLC), mouse and human ONBs exhibit mutually exclusive NEUROD1 and POU2F3-like states, an immune-cold tumor microenvironment, intratumoral cell fate heterogeneity comprising neuronal and non-neuronal lineages, and cell fate plasticity-evidenced by barcode-based lineage tracing and single-cell transcriptomics. Collectively, our findings highlight conserved similarities between ONB and neuroendocrine tumors with significant implications for ONB classification and treatment.
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Affiliation(s)
- John B Finlay
- Department of Head and Neck Surgery & Communication Sciences, Duke University, Durham 27710, NC, USA
| | - Abbie S Ireland
- Department of Pharmacology and Cancer Biology, Duke University, Durham 27710, NC, USA
| | - Sarah B Hawgood
- Department of Pharmacology and Cancer Biology, Duke University, Durham 27710, NC, USA
| | - Tony Reyes
- Department of Pharmacology and Cancer Biology, Duke University, Durham 27710, NC, USA; Department of Oncological Sciences, University of Utah, Salt Lake City 84112, UT, USA
| | - Tiffany Ko
- Department of Head and Neck Surgery & Communication Sciences, Duke University, Durham 27710, NC, USA
| | - Rachelle R Olsen
- Department of Oncological Sciences, University of Utah, Salt Lake City 84112, UT, USA
| | - Ralph Abi Hachem
- Department of Head and Neck Surgery & Communication Sciences, Duke University, Durham 27710, NC, USA
| | - David W Jang
- Department of Head and Neck Surgery & Communication Sciences, Duke University, Durham 27710, NC, USA
| | - Diana Bell
- Division of Anatomic Pathology, City of Hope Comprehensive Cancer Center, Duarte 91010, CA, USA
| | - Joseph M Chan
- Human Oncology and Pathogenesis Program, Memorial-Sloan Kettering Cancer Center, New York City 10065, NY, USA
| | - Bradley J Goldstein
- Department of Head and Neck Surgery & Communication Sciences, Duke University, Durham 27710, NC, USA; Department of Neurobiology, Duke University, Durham 27710, NC, USA.
| | - Trudy G Oliver
- Department of Pharmacology and Cancer Biology, Duke University, Durham 27710, NC, USA; Department of Oncological Sciences, University of Utah, Salt Lake City 84112, UT, USA.
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13
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Mouro Pinto R, Murtha R, Azevedo A, Douglas C, Kovalenko M, Ulloa J, Crescenti S, Burch Z, Oliver E, Vitalo A, Mota-Silva E, Riggs MJ, Correia K, Elezi E, Demelo B, Carroll JB, Gillis T, Gusella JF, MacDonald ME, Wheeler VC. Identification of genetic modifiers of Huntington's disease somatic CAG repeat instability by in vivo CRISPR-Cas9 genome editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.08.597823. [PMID: 38895438 PMCID: PMC11185783 DOI: 10.1101/2024.06.08.597823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Huntington's disease (HD), one of >50 inherited repeat expansion disorders (Depienne and Mandel, 2021), is a dominantly-inherited neurodegenerative disease caused by a CAG expansion in HTT (The Huntington's Disease Collaborative Research Group, 1993). Inherited CAG repeat length is the primary determinant of age of onset, with human genetic studies underscoring that the property driving disease is the CAG length-dependent propensity of the repeat to further expand in brain (Swami et al ., 2009; GeM-HD, 2015; Hensman Moss et al ., 2017; Ciosi et al ., 2019; GeM-HD, 2019; Hong et al ., 2021). Routes to slowing somatic CAG expansion therefore hold great promise for disease-modifying therapies. Several DNA repair genes, notably in the mismatch repair (MMR) pathway, modify somatic expansion in HD mouse models (Wheeler and Dion, 2021). To identify novel modifiers of somatic expansion, we have used CRISPR-Cas9 editing in HD knock-in mice to enable in vivo screening of expansion-modifier candidates at scale. This has included testing of HD onset modifier genes emerging from human genome-wide association studies (GWAS), as well as interactions between modifier genes, thereby providing new insight into pathways underlying CAG expansion and potential therapeutic targets.
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14
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Banda A, Impomeni O, Singh A, Baloch AR, Hu W, Jaijyan DK. Precision in Action: The Role of Clustered Regularly Interspaced Short Palindromic Repeats/Cas in Gene Therapies. Vaccines (Basel) 2024; 12:636. [PMID: 38932365 PMCID: PMC11209408 DOI: 10.3390/vaccines12060636] [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: 04/14/2024] [Revised: 05/21/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated enzyme-CAS holds great promise for treating many uncured human diseases and illnesses by precisely correcting harmful point mutations and disrupting disease-causing genes. The recent Food and Drug Association (FDA) approval of the first CRISPR-based gene therapy for sickle cell anemia marks the beginning of a new era in gene editing. However, delivering CRISPR specifically into diseased cells in vivo is a significant challenge and an area of intense research. The identification of new CRISPR/Cas variants, particularly ultra-compact CAS systems with robust gene editing activities, paves the way for the low-capacity delivery vectors to be used in gene therapies. CRISPR/Cas technology has evolved beyond editing DNA to cover a wide spectrum of functionalities, including RNA targeting, disease diagnosis, transcriptional/epigenetic regulation, chromatin imaging, high-throughput screening, and new disease modeling. CRISPR/Cas can be used to engineer B-cells to produce potent antibodies for more effective vaccines and enhance CAR T-cells for the more precise and efficient targeting of tumor cells. However, CRISPR/Cas technology has challenges, including off-target effects, toxicity, immune responses, and inadequate tissue-specific delivery. Overcoming these challenges necessitates the development of a more effective and specific CRISPR/Cas delivery system. This entails strategically utilizing specific gRNAs in conjunction with robust CRISPR/Cas variants to mitigate off-target effects. This review seeks to delve into the intricacies of the CRISPR/Cas mechanism, explore progress in gene therapies, evaluate gene delivery systems, highlight limitations, outline necessary precautions, and scrutinize the ethical considerations associated with its application.
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Affiliation(s)
- Amrutha Banda
- Department of Biology, The College of New Jersey, Ewing Township, NJ 08618, USA
| | - Olivia Impomeni
- Department of Biology, The College of New Jersey, Ewing Township, NJ 08618, USA
| | - Aparana Singh
- Department of Chemistry, National Institute of Technology Agartala, Agartala 799046, India;
| | - Abdul Rasheed Baloch
- Department of Anatomy and Neurobiology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA;
| | - Wenhui Hu
- Department of Anatomy and Neurobiology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA;
| | - Dabbu Kumar Jaijyan
- Department of Anatomy and Neurobiology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA;
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15
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Singh D. Revolutionizing Lung Cancer Treatment: Innovative CRISPR-Cas9 Delivery Strategies. AAPS PharmSciTech 2024; 25:129. [PMID: 38844700 DOI: 10.1208/s12249-024-02834-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/08/2024] [Indexed: 06/11/2024] Open
Abstract
Lung carcinoma, including both non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC), remains a significant global health challenge due to its high morbidity and mortality rates. The objsective of this review is to meticulously examine the current advancements and strategies in the delivery of CRISPR-Cas9 gene-editing technology for the treatment of lung carcinoma. This technology heralds a new era in molecular biology, offering unprecedented precision in genomic modifications. However, its therapeutic potential is contingent upon the development of effective delivery mechanisms that ensure the efficient and specific transport of gene-editing tools to tumor cells. We explore a variety of delivery approaches, such as viral vectors, lipid-based nanoparticles, and physical methods, highlighting their respective advantages, limitations, and recent breakthroughs. This review also delves into the translational and clinical significance of these strategies, discussing preclinical and clinical studies that investigate the feasibility, efficacy, and safety of CRISPR-Cas9 delivery for lung carcinoma. By scrutinizing the landscape of ongoing clinical trials and offering translational perspectives, we aim to elucidate the current state and future directions of this rapidly evolving field. The review is structured to first introduce the problem and significance of lung carcinoma, followed by an overview of CRISPR-Cas9 technology, a detailed examination of delivery strategies, and an analysis of clinical applications and regulatory considerations. Our discussion concludes with future perspectives and challenges, such as optimizing delivery strategies, enhancing specificity, mitigating immunogenicity concerns, and addressing regulatory issues. This comprehensive overview seeks to provide insights into the potential of CRISPR-Cas9 as a revolutionary approach for targeted therapies and personalized medicine in lung carcinoma, emphasizing the importance of delivery strategy development in realizing the full potential of this groundbreaking technology.
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Affiliation(s)
- Dilpreet Singh
- University Institute of Pharma Sciences, Chandigarh University, Gharuan, Mohali, 140413, India.
- University Centre for Research and Development, Chandigarh University, Gharuan, Mohali, 140413, India.
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16
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Li J, Li R, Bai X, Zhang W, Nie Y, Hu S. Direct reprogramming of fibroblasts into functional hepatocytes via CRISPRa activation of endogenous Gata4 and Foxa3. Chin Med J (Engl) 2024; 137:1351-1359. [PMID: 38721807 PMCID: PMC11191006 DOI: 10.1097/cm9.0000000000003088] [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: 07/06/2023] [Indexed: 06/19/2024] Open
Abstract
BACKGROUND The ability to generate functional hepatocytes without relying on donor liver organs holds significant therapeutic promise in the fields of regenerative medicine and potential liver disease treatments. Clustered regularly interspaced short palindromic repeats (CRISPR) activator (CRISPRa) is a powerful tool that can conveniently and efficiently activate the expression of multiple endogenous genes simultaneously, providing a new strategy for cell fate determination. The main purpose of this study is to explore the feasibility of applying CRISPRa for hepatocyte reprogramming and its application in the treatment of mouse liver fibrosis. METHOD The differentiation of mouse embryonic fibroblasts (MEFs) into functional induced hepatocyte-like cells (iHeps) was achieved by utilizing the CRISPRa synergistic activation mediator (SAM) system, which drove the combined expression of three endogenous transcription factors- Gata4, Foxa3 , and Hnf1a -or alternatively, the expression of two transcription factors, Gata4 and Foxa3 . In vivo , we injected adeno-associated virus serotype 6 (AAV6) carrying the CRISPRa SAM system into liver fibrotic Col1a1-CreER ; Cas9fl/fl mice, effectively activating the expression of endogenous Gata4 and Foxa3 in fibroblasts. The endogenous transcriptional activation of genes was confirmed using real-time quantitative polymerase chain reaction (RT-qPCR) and RNA-seq, and the morphology and characteristics of the induced hepatocytes were observed through microscopy. The level of hepatocyte reprogramming in vivo is detected by immunofluorescence staining, while the improvement of liver fibrosis is evaluated through Sirius red staining, alpha-smooth muscle actin (α-SMA) immunofluorescence staining, and blood alanine aminotransferase (ALT) examination. RESULTS Activation of only two factors, Gata4 and Foxa3 , via CRISPRa was sufficient to successfully induce the transformation of MEFs into iHeps. These iHeps could be expanded in vitro and displayed functional characteristics similar to those of mature hepatocytes, such as drug metabolism and glycogen storage. Additionally, AAV6-based delivery of the CRISPRa SAM system effectively induced the hepatic reprogramming from fibroblasts in mice with live fibrosis. After 8 weeks of induction, the reprogrammed hepatocytes comprised 0.87% of the total hepatocyte population in the mice, significantly reducing liver fibrosis. CONCLUSION CRISPRa-induced hepatocyte reprogramming may be a promising strategy for generating functional hepatocytes and treating liver fibrosis caused by hepatic diseases.
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Affiliation(s)
- Jiacheng Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital and Cardiovascular Institute, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
- Department of Obstetrics and Gynecology, Beijing Advanced Innovation Center for Genomics, Third Hospital, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ruopu Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital and Cardiovascular Institute, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Xue Bai
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital and Cardiovascular Institute, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Wenlong Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital and Cardiovascular Institute, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Yu Nie
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital and Cardiovascular Institute, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Shengshou Hu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital and Cardiovascular Institute, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
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17
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Abbondanza A, Urushadze A, Alves-Barboza AR, Janickova H. Expression and function of nicotinic acetylcholine receptors in specific neuronal populations: Focus on striatal and prefrontal circuits. Pharmacol Res 2024; 204:107190. [PMID: 38704107 DOI: 10.1016/j.phrs.2024.107190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 05/06/2024]
Abstract
Nicotinic acetylcholine receptors (nAChRs) are widely expressed in the central nervous system and play an important role in the control of neural functions including neuronal activity, transmitter release and synaptic plasticity. Although the common subtypes of nAChRs are abundantly expressed throughout the brain, their expression in different brain regions and by individual neuronal types is not homogeneous or incidental. In recent years, several studies have emerged showing that particular subtypes of nAChRs are expressed by specific neuronal populations in which they have major influence on the activity of local circuits and behavior. It has been demonstrated that even nAChRs expressed by relatively rare neuronal types can induce significant changes in behavior and contribute to pathological processes. Depending on the identity and connectivity of the particular nAChRs-expressing neuronal populations, the activation of nAChRs can have distinct or even opposing effects on local neuronal signaling. In this review, we will summarize the available literature describing the expression of individual nicotinic subunits by different neuronal types in two crucial brain regions, the striatum and the prefrontal cortex. The review will also briefly discuss nicotinic expression in non-neuronal, glial cells, as they cannot be ignored as potential targets of nAChRs-modulating drugs. The final section will discuss options that could allow us to target nAChRs in a neuronal-type-specific manner, not only in the experimental field, but also eventually in clinical practice.
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Affiliation(s)
- Alice Abbondanza
- Laboratory of Neurochemistry, Institute of Physiology of the Czech Academy of Sciences, Prague 14200, Czech Republic
| | - Anna Urushadze
- Laboratory of Neurochemistry, Institute of Physiology of the Czech Academy of Sciences, Prague 14200, Czech Republic
| | - Amanda Rosanna Alves-Barboza
- Laboratory of Neurochemistry, Institute of Physiology of the Czech Academy of Sciences, Prague 14200, Czech Republic
| | - Helena Janickova
- Laboratory of Neurochemistry, Institute of Physiology of the Czech Academy of Sciences, Prague 14200, Czech Republic.
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18
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Yang L, Zhang Z, Jiang P, Kong D, Yu Z, Shi D, Han Y, Chen E, Zheng W, Sun J, Zhao Y, Luo Y, Shi J, Yao H, Huang H, Qian P. Phase separation-competent FBL promotes early pre-rRNA processing and translation in acute myeloid leukaemia. Nat Cell Biol 2024; 26:946-961. [PMID: 38745030 DOI: 10.1038/s41556-024-01420-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/04/2024] [Indexed: 05/16/2024]
Abstract
RNA-binding proteins (RBPs) are pivotal in acute myeloid leukaemia (AML), a lethal disease. Although specific phase separation-competent RBPs are recognized in AML, the effect of their condensate formation on AML leukaemogenesis, and the therapeutic potential of inhibition of phase separation are underexplored. In our in vivo CRISPR RBP screen, fibrillarin (FBL) emerges as a crucial nucleolar protein that regulates AML cell survival, primarily through its phase separation domains rather than methyltransferase or acetylation domains. These phase separation domains, with specific features, coordinately drive nucleoli formation and early processing of pre-rRNA (including efflux, cleavage and methylation), eventually enhancing the translation of oncogenes such as MYC. Targeting the phase separation capability of FBL with CGX-635 leads to elimination of AML cells, suggesting an additional mechanism of action for CGX-635 that complements its established therapeutic effects. We highlight the potential of PS modulation of critical proteins as a possible therapeutic strategy for AML.
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MESH Headings
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/metabolism
- RNA Precursors/metabolism
- RNA Precursors/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomal Proteins, Non-Histone/genetics
- RNA Processing, Post-Transcriptional
- Animals
- Cell Line, Tumor
- Protein Biosynthesis
- Cell Nucleolus/metabolism
- Cell Nucleolus/genetics
- Mice
- RNA-Binding Proteins/metabolism
- RNA-Binding Proteins/genetics
- Gene Expression Regulation, Leukemic
- Phase Separation
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Affiliation(s)
- Lin Yang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Zhaoru Zhang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Penglei Jiang
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Delin Kong
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Zebin Yu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Danrong Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yingli Han
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
| | - Ertuo Chen
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Weiyan Zheng
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Sun
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yanmin Zhao
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Luo
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jimin Shi
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hangping Yao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - He Huang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
- Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China.
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Pengxu Qian
- Bone Marrow Transplantation Center of the First Affiliated Hospital, and Center for Stem Cell and Regenerative Medicine, Zhejiang University School of Medicine, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
- State Key Laboratory of Experimental Hematology, Institute of Hematology, Zhejiang University & Zhejiang Provincial Engineering Research Center for Stem Cell and Immunity Therapy, Hangzhou, China.
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19
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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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20
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Ren G, Ku WL, Ge G, Hoffman JA, Kang JY, Tang Q, Cui K, He Y, Guan Y, Gao B, Liu C, Archer TK, Zhao K. Acute depletion of BRG1 reveals its primary function as an activator of transcription. Nat Commun 2024; 15:4561. [PMID: 38811575 PMCID: PMC11137027 DOI: 10.1038/s41467-024-48911-z] [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: 05/24/2023] [Accepted: 05/14/2024] [Indexed: 05/31/2024] Open
Abstract
The mammalian SWI/SNF-like BAF complexes play critical roles during animal development and pathological conditions. Previous gene deletion studies and characterization of human gene mutations implicate that the complexes both repress and activate a large number of genes. However, the direct function of the complexes in cells remains largely unclear due to the relatively long-term nature of gene deletion or natural mutation. Here we generate a mouse line by knocking in the auxin-inducible degron tag (AID) to the Smarca4 gene, which encodes BRG1, the essential ATPase subunit of the BAF complexes. We show that the tagged BRG1 can be efficiently depleted by osTIR1 expression and auxin treatment for 6 to 10 h in CD4 + T cells, hepatocytes, and fibroblasts isolated from the knock-in mice. The acute depletion of BRG1 leads to decreases in nascent RNAs and RNA polymerase II binding at a large number of genes, which are positively correlated with the loss of BRG1. Further, these changes are correlated with diminished accessibility at DNase I Hypersensitive Sites (DHSs) and p300 binding. The acute BRG1 depletion results in three major patterns of nucleosome shifts leading to narrower nucleosome spacing surrounding transcription factor motifs and at enhancers and transcription start sites (TSSs), which are correlated with loss of BRG1, decreased chromatin accessibility and decreased nascent RNAs. Acute depletion of BRG1 severely compromises the Trichostatin A (TSA) -induced histone acetylation, suggesting a substantial interplay between the chromatin remodeling activity of BRG1 and histone acetylation. Our data suggest BRG1 mainly plays a direct positive role in chromatin accessibility, RNAPII binding, and nascent RNA production by regulating nucleosome positioning and facilitating transcription factor binding to their target sites.
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Affiliation(s)
- Gang Ren
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
- College of Animal Science and Technology, Northwest Agriculture and Forest University, Yangling, Xianyang, Shaanxi, China
| | - Wai Lim Ku
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Guangzhe Ge
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Jackson A Hoffman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, North Carolina, USA
| | - Jee Youn Kang
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Qingsong Tang
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Kairong Cui
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Yong He
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Yukun Guan
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Bin Gao
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Chengyu Liu
- Transgenic Core Facility, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Trevor K Archer
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, Durham, North Carolina, USA
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA.
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21
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Bynigeri RR, Malireddi RKS, Mall R, Connelly JP, Pruett-Miller SM, Kanneganti TD. The protein phosphatase PP6 promotes RIPK1-dependent PANoptosis. BMC Biol 2024; 22:122. [PMID: 38807188 PMCID: PMC11134900 DOI: 10.1186/s12915-024-01901-5] [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: 11/15/2023] [Accepted: 04/23/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND The innate immune system serves as the first line of host defense. Transforming growth factor-β-activated kinase 1 (TAK1) is a key regulator of innate immunity, cell survival, and cellular homeostasis. Because of its importance in immunity, several pathogens have evolved to carry TAK1 inhibitors. In response, hosts have evolved to sense TAK1 inhibition and induce robust lytic cell death, PANoptosis, mediated by the RIPK1-PANoptosome. PANoptosis is a unique innate immune inflammatory lytic cell death pathway initiated by an innate immune sensor and driven by caspases and RIPKs. While PANoptosis can be beneficial to clear pathogens, excess activation is linked to pathology. Therefore, understanding the molecular mechanisms regulating TAK1 inhibitor (TAK1i)-induced PANoptosis is central to our understanding of RIPK1 in health and disease. RESULTS In this study, by analyzing results from a cell death-based CRISPR screen, we identified protein phosphatase 6 (PP6) holoenzyme components as regulators of TAK1i-induced PANoptosis. Loss of the PP6 enzymatic component, PPP6C, significantly reduced TAK1i-induced PANoptosis. Additionally, the PP6 regulatory subunits PPP6R1, PPP6R2, and PPP6R3 had redundant roles in regulating TAK1i-induced PANoptosis, and their combined depletion was required to block TAK1i-induced cell death. Mechanistically, PPP6C and its regulatory subunits promoted the pro-death S166 auto-phosphorylation of RIPK1 and led to a reduction in the pro-survival S321 phosphorylation. CONCLUSIONS Overall, our findings demonstrate a key requirement for the phosphatase PP6 complex in the activation of TAK1i-induced, RIPK1-dependent PANoptosis, suggesting this complex could be therapeutically targeted in inflammatory conditions.
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Affiliation(s)
- Ratnakar R Bynigeri
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - R K Subbarao Malireddi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Raghvendra Mall
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Current affiliation: Biotechnology Research Center, Technology Innovation Institute, Abu Dhabi, United Arab Emirates
| | - Jon P Connelly
- Center for Advanced Genome Engineering (CAGE), St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering (CAGE), St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
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22
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Liuzzi G, Artimagnella O, Frisari S, Mallamaci A. Foxg1 bimodally tunes L1-mRNA and -DNA dynamics in the developing murine neocortex. Development 2024; 151:dev202292. [PMID: 38655654 PMCID: PMC11190451 DOI: 10.1242/dev.202292] [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: 08/23/2023] [Accepted: 04/16/2024] [Indexed: 04/26/2024]
Abstract
Foxg1 masters telencephalic development via a pleiotropic control over its progression. Expressed within the central nervous system (CNS), L1 retrotransposons are implicated in progression of its histogenesis and tuning of its genomic plasticity. Foxg1 represses gene transcription, and L1 elements share putative Foxg1-binding motifs, suggesting the former might limit telencephalic expression (and activity) of the latter. We tested such a prediction, in vivo as well as in engineered primary neural cultures, using loss- and gain-of-function approaches. We found that Foxg1-dependent, transcriptional L1 repression specifically occurs in neopallial neuronogenic progenitors and post-mitotic neurons, where it is supported by specific changes in the L1 epigenetic landscape. Unexpectedly, we discovered that Foxg1 physically interacts with L1-mRNA and positively regulates neonatal neopallium L1-DNA content, antagonizing the retrotranscription-suppressing activity exerted by Mov10 and Ddx39a helicases. To the best of our knowledge, Foxg1 represents the first CNS patterning gene acting as a bimodal retrotransposon modulator, limiting transcription of L1 elements and promoting their amplification, within a specific domain of the developing mouse brain.
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Affiliation(s)
- Gabriele Liuzzi
- Laboratory of Cerebral Cortex Development, SISSA, Trieste 34136, Italy
| | | | - Simone Frisari
- Laboratory of Cerebral Cortex Development, SISSA, Trieste 34136, Italy
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23
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Ghorbani S, Li C, Lozinski BM, Moezzi D, D’Mello C, Dong Y, Visser F, Li H, Silva C, Khakpour M, Murray CJ, Tremblay MÈ, Xue M, Yong VW. Fibulin-2 is an extracellular matrix inhibitor of oligodendrocytes relevant to multiple sclerosis. J Clin Invest 2024; 134:e176910. [PMID: 38743490 PMCID: PMC11213512 DOI: 10.1172/jci176910] [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: 10/23/2023] [Accepted: 05/07/2024] [Indexed: 05/16/2024] Open
Abstract
Impairment of oligodendrocytes and myelin contributes to neurological disorders including multiple sclerosis (MS), stroke, and Alzheimer's disease. Regeneration of myelin (remyelination) decreases the vulnerability of demyelinated axons, but this repair process commonly fails with disease progression. A contributor to inefficient remyelination is the altered extracellular matrix (ECM) in lesions, which remains to be better defined. We have identified fibulin-2 (FBLN2) as a highly upregulated ECM component in lesions of MS and stroke and in proteome databases of Alzheimer's disease and traumatic brain injury. Focusing on MS, the inhibitory role of FBLN2 was suggested in the experimental autoimmune encephalomyelitis (EAE) model, in which genetic FBLN2 deficiency improved behavioral recovery by promoting the maturation of oligodendrocytes and enhancing remyelination. Mechanistically, when oligodendrocyte progenitors were cultured in differentiation medium, FBLN2 impeded their maturation into oligodendrocytes by engaging the Notch pathway, leading to cell death. Adeno-associated virus deletion of FBLN2 in astrocytes improved oligodendrocyte numbers and functional recovery in EAE and generated new myelin profiles after lysolecithin-induced demyelination. Collectively, our findings implicate FBLN2 as a hitherto unrecognized injury-elevated ECM, and a therapeutic target, that impairs oligodendrocyte maturation and myelin repair.
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Affiliation(s)
- Samira Ghorbani
- Hotchkiss Brain Institute and Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Cenxiao Li
- Hotchkiss Brain Institute and Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
| | - Brian M. Lozinski
- Hotchkiss Brain Institute and Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
| | - Dorsa Moezzi
- Hotchkiss Brain Institute and Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
| | - Charlotte D’Mello
- Hotchkiss Brain Institute and Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
| | - Yifei Dong
- Hotchkiss Brain Institute and Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry, Microbiology, and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Frank Visser
- Hotchkiss Brain Institute and Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
| | - Hongmin Li
- Hotchkiss Brain Institute and Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Claudia Silva
- Hotchkiss Brain Institute and Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
| | - Mohammadparsa Khakpour
- Division of Medical Sciences, University of Victoria, Victoria, British Columbia, Canada
| | - Colin J. Murray
- Division of Medical Sciences, University of Victoria, Victoria, British Columbia, Canada
| | - Marie-Ève Tremblay
- Division of Medical Sciences, University of Victoria, Victoria, British Columbia, Canada
| | - Mengzhou Xue
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - V. Wee Yong
- Hotchkiss Brain Institute and Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
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24
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Haddad R, Sadeh O, Ziv T, Erlich I, Haimovich-Caspi L, Shemesh A, van der Velden J, Kehat I. Localized translation and sarcomere maintenance requires ribosomal protein SA in mice. J Clin Invest 2024; 134:e174527. [PMID: 38743494 PMCID: PMC11213506 DOI: 10.1172/jci174527] [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: 08/11/2023] [Accepted: 05/07/2024] [Indexed: 05/16/2024] Open
Abstract
Cardiomyocyte sarcomeres contain localized ribosomes, but the factors responsible for their localization and the significance of localized translation are unknown. Using proximity labeling, we identified ribosomal protein SA (RPSA) as a Z-line protein. In cultured cardiomyocytes, the loss of RPSA led to impaired local protein translation and reduced sarcomere integrity. By employing CAS9-expressing mice, along with adeno-associated viruses expressing CRE recombinase and single-guide RNAs targeting Rpsa, we knocked out Rpsa in vivo and observed mislocalization of ribosomes and diminished local translation. These genetic mosaic mice with Rpsa knockout in a subset of cardiomyocytes developed dilated cardiomyopathy, featuring atrophy of RPSA-deficient cardiomyocytes, compensatory hypertrophy of unaffected cardiomyocytes, left ventricular dilation, and impaired contractile function. We demonstrated that RPSA C-terminal domain is sufficient for localization to the Z-lines and that if the microtubule network is disrupted RPSA loses its sarcomeric localization. These findings highlight RPSA as a ribosomal factor essential for ribosome localization to the Z-line, facilitating local translation and sarcomere maintenance.
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Affiliation(s)
- Rami Haddad
- Rappaport Family Institute for Research in the Medical Sciences and The Ruth and Bruce Rappaport Faculty of Medicine
| | - Omer Sadeh
- Rappaport Family Institute for Research in the Medical Sciences and The Ruth and Bruce Rappaport Faculty of Medicine
| | - Tamar Ziv
- Smoler Proteomics Center, Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, and
| | - Itai Erlich
- Rappaport Family Institute for Research in the Medical Sciences and The Ruth and Bruce Rappaport Faculty of Medicine
| | - Lilac Haimovich-Caspi
- Rappaport Family Institute for Research in the Medical Sciences and The Ruth and Bruce Rappaport Faculty of Medicine
| | - Ariel Shemesh
- Biomedical Core Facility at the Faculty of Medicine, Technion – Israel Institute of Technology, Haifa, Israel
| | - Jolanda van der Velden
- Department of Physiology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands
| | - Izhak Kehat
- Rappaport Family Institute for Research in the Medical Sciences and The Ruth and Bruce Rappaport Faculty of Medicine
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25
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Zhang W, Li J, Yamamoto K, Goyama S. Modeling and therapeutic targeting of t(8;21) AML with/without TP53 deficiency. Int J Hematol 2024:10.1007/s12185-024-03783-3. [PMID: 38702444 DOI: 10.1007/s12185-024-03783-3] [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: 01/09/2024] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 05/06/2024]
Abstract
Acute myeloid leukemia (AML) with t(8;21)(q22;q22.1);RUNX1-ETO is one of the most common subtypes of AML. Although t(8;21) AML has been classified as favorable-risk, only about half of patients are cured with current therapies. Several genetic abnormalities, including TP53 mutations and deletions, negatively impact survival in t(8;21) AML. In this study, we established Cas9+ mouse models of t(8;21) AML with intact or deficient Tpr53 (a mouse homolog of TP53) using a retrovirus-mediated gene transfer and transplantation system. Trp53 deficiency accelerates the in vivo development of AML driven by RUNX1-ETO9a, a short isoform of RUNX1-ETO with strong leukemogenic potential. Trp53 deficiency also confers resistance to genetic depletion of RUNX1 and a TP53-activating drug in t(8;21) AML. However, Trp53-deficient t(8;21) AML cells were still sensitive to several drugs such as dexamethasone. Cas9+ RUNX1-ETO9a cells with/without Trp53 deficiency can produce AML in vivo, can be cultured in vitro for several weeks, and allow efficient gene depletion using the CRISPR/Cas9 system, providing useful tools to advance our understanding of t(8;21) AML.
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Affiliation(s)
- Wenyu Zhang
- Division of Molecular Oncology, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Jingmei Li
- Division of Molecular Oncology, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Keita Yamamoto
- Division of Molecular Oncology, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Susumu Goyama
- Division of Molecular Oncology, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan.
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26
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Sánchez Rivera FJ, Dow LE. How CRISPR Is Revolutionizing the Generation of New Models for Cancer Research. Cold Spring Harb Perspect Med 2024; 14:a041384. [PMID: 37487630 PMCID: PMC11065179 DOI: 10.1101/cshperspect.a041384] [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] [Indexed: 07/26/2023]
Abstract
Cancers arise through acquisition of mutations in genes that regulate core biological processes like cell proliferation and cell death. Decades of cancer research have led to the identification of genes and mutations causally involved in disease development and evolution, yet defining their precise function across different cancer types and how they influence therapy responses has been challenging. Mouse models have helped define the in vivo function of cancer-associated alterations, and genome-editing approaches using CRISPR have dramatically accelerated the pace at which these models are developed and studied. Here, we highlight how CRISPR technologies have impacted the development and use of mouse models for cancer research and discuss the many ways in which these rapidly evolving platforms will continue to transform our understanding of this disease.
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Affiliation(s)
- Francisco J Sánchez Rivera
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, New York 10065, USA
- Department of Medicine, Weill Cornell Medicine, New York, New York 10065, USA
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Dvoretskova E, Ho MC, Kittke V, Neuhaus F, Vitali I, Lam DD, Delgado I, Feng C, Torres M, Winkelmann J, Mayer C. Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development. Nat Neurosci 2024; 27:862-872. [PMID: 38528203 PMCID: PMC11088997 DOI: 10.1038/s41593-024-01611-9] [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: 02/23/2024] [Indexed: 03/27/2024]
Abstract
The mammalian telencephalon contains distinct GABAergic projection neuron and interneuron types, originating in the germinal zone of the embryonic basal ganglia. How genetic information in the germinal zone determines cell types is unclear. Here we use a combination of in vivo CRISPR perturbation, lineage tracing and ChIP-sequencing analyses and show that the transcription factor MEIS2 favors the development of projection neurons by binding enhancer regions in projection-neuron-specific genes during mouse embryonic development. MEIS2 requires the presence of the homeodomain transcription factor DLX5 to direct its functional activity toward the appropriate binding sites. In interneuron precursors, the transcription factor LHX6 represses the MEIS2-DLX5-dependent activation of projection-neuron-specific enhancers. Mutations of Meis2 result in decreased activation of regulatory enhancers, affecting GABAergic differentiation. We propose a differential binding model where the binding of transcription factors at cis-regulatory elements determines differential gene expression programs regulating cell fate specification in the mouse ganglionic eminence.
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Affiliation(s)
- Elena Dvoretskova
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
- Max Planck Institute of Neurobiology, Martinsried, Germany
| | - May C Ho
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
- Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Volker Kittke
- Institute of Neurogenomics, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Neuhererg, Germany
- TUM School of Medicine and Health, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- DZPG (German Center for Mental Health), Munich, Germany
| | - Florian Neuhaus
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
- Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Ilaria Vitali
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
- Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Daniel D Lam
- Institute of Neurogenomics, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Neuhererg, Germany
- TUM School of Medicine and Health, Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Irene Delgado
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, Madrid, Spain
| | - Chao Feng
- Max Planck Institute for Biological Intelligence, Martinsried, Germany
- Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Miguel Torres
- Cardiovascular Development Program, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Neuhererg, Germany
- TUM School of Medicine and Health, Institute of Human Genetics, Technical University of Munich, Munich, Germany
- DZPG (German Center for Mental Health), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Christian Mayer
- Max Planck Institute for Biological Intelligence, Martinsried, Germany.
- Max Planck Institute of Neurobiology, Martinsried, Germany.
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Kang SK, Hawkins NA, Thompson CH, Baker EM, Echevarria-Cooper DM, Barse L, Thenstedt T, Dixon CJ, Speakes N, George AL, Kearney JA. Altered neurological and neurobehavioral phenotypes in a mouse model of the recurrent KCNB1-p.R306C voltage-sensor variant. Neurobiol Dis 2024; 194:106470. [PMID: 38485094 PMCID: PMC11024897 DOI: 10.1016/j.nbd.2024.106470] [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: 03/29/2023] [Revised: 02/23/2024] [Accepted: 03/06/2024] [Indexed: 03/21/2024] Open
Abstract
Pathogenic variants in KCNB1 are associated with a neurodevelopmental disorder spectrum that includes global developmental delays, cognitive impairment, abnormal electroencephalogram (EEG) patterns, and epilepsy with variable age of onset and severity. Additionally, there are prominent behavioral disturbances, including hyperactivity, aggression, and features of autism spectrum disorder. The most frequently identified recurrent variant is KCNB1-p.R306C, a missense variant located within the S4 voltage-sensing transmembrane domain. Individuals with the R306C variant exhibit mild to severe developmental delays, behavioral disorders, and a diverse spectrum of seizures. Previous in vitro characterization of R306C described altered sensitivity and cooperativity of the voltage sensor and impaired capacity for repetitive firing of neurons. Existing Kcnb1 mouse models include dominant negative missense variants, as well as knockout and frameshifts alleles. While all models recapitulate key features of KCNB1 encephalopathy, mice with dominant negative alleles were more severely affected. In contrast to existing loss-of-function and dominant-negative variants, KCNB1-p.R306C does not affect channel expression, but rather affects voltage-sensing. Thus, modeling R306C in mice provides a novel opportunity to explore impacts of a voltage-sensing mutation in Kcnb1. Using CRISPR/Cas9 genome editing, we generated the Kcnb1R306C mouse model and characterized the molecular and phenotypic effects. Consistent with the in vitro studies, neurons from Kcnb1R306C mice showed altered excitability. Heterozygous and homozygous R306C mice exhibited hyperactivity, altered susceptibility to chemoconvulsant-induced seizures, and frequent, long runs of slow spike wave discharges on EEG, reminiscent of the slow spike and wave activity characteristic of Lennox Gastaut syndrome. This novel model of channel dysfunction in Kcnb1 provides an additional, valuable tool to study KCNB1 encephalopathies. Furthermore, this allelic series of Kcnb1 mouse models will provide a unique platform to evaluate targeted therapies.
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Affiliation(s)
- Seok Kyu Kang
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Northwestern University Interdepartmental Neuroscience Program, Northwestern University, Chicago, IL 60611, USA
| | - Nicole A Hawkins
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Christopher H Thompson
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Erin M Baker
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Dennis M Echevarria-Cooper
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Northwestern University Interdepartmental Neuroscience Program, Northwestern University, Chicago, IL 60611, USA
| | - Levi Barse
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Tyler Thenstedt
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Conor J Dixon
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Nathan Speakes
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Alfred L George
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Northwestern University Interdepartmental Neuroscience Program, Northwestern University, Chicago, IL 60611, USA
| | - Jennifer A Kearney
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Northwestern University Interdepartmental Neuroscience Program, Northwestern University, Chicago, IL 60611, USA.
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Wang X, Han S, Liang J, Xu C, Cao R, Liu S, Luan Y, Gu Y, Han P. Essential role of Alix in regulating cardiomyocyte exosome biogenesis under physiological and stress conditions. J Mol Cell Cardiol 2024; 190:35-47. [PMID: 38593639 DOI: 10.1016/j.yjmcc.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/04/2024] [Accepted: 04/02/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND Exosomes released by cardiomyocytes are essential mediators of intercellular communications within the heart, and various exosomal proteins and miRNAs are associated with cardiovascular diseases. However, whether the endosomal sorting complex required for transport (ESCRT) and its key component Alix is required for exosome biogenesis within cardiomyocyte remains poorly understood. METHODS Super-resolution imaging was performed to investigate the subcellular location of Alix and multivesicular body (MVB) in primary cardiomyocytes. Cardiomyocyte-specific Alix-knockout mice were generated using AAV9/CRISPR/Cas9-mediated in vivo gene editing. A stable Alix-knockdown H9c2 cardiomyocyte line was constructed through lentiviral-mediated delivery of short hairpin RNA. In order to determine the role of Alix in controlling exosome biogenesis, exosomes from cardiomyocyte-specific Alix-knockout mice plasma and Alix-knockdown H9c2 culture medium were isolated and examined by western blot, NTA analysis and transmission electron microscopy. Biochemical and immunofluorescence analysis were performed to determine the role of ESCRT machinery in regulating MVB formation. Lastly, transverse aortic constriction (TAC)-induced cardiac pressure overload model was established to further explore the role of Alix-mediated exosome biogenesis under stress conditions. RESULTS A significant proportion of Alix localized to the MVB membrane within cardiomyocytes. Genetic deletion of Alix in murine heart resulted in a reduction of plasma exosome content without affecting cardiac structure or contractile function. Consistently, the downregulation of Alix in H9c2 cardiomyocyte line also suppressed the biogenesis of exosomes. We found the defective ESCRT machinery and suppressed MVB formation upon Alix depletion caused compromised exosome biogenesis. Remarkably, TAC-induced cardiac pressure overload led to increased Alix, MVB levels, and elevated plasma exosome content, which could be totally abolished by Alix deletion. CONCLUSION These results establish Alix as an essential and stress-sensitive regulator of cardiac exosome biogenesis and the findings may yield valuable therapeutic implications.
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Affiliation(s)
- Xinjian Wang
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang, China; Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China; Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, Zhejiang, China
| | - Shuxian Han
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang, China; Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China; Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, Zhejiang, China
| | - Jinxiu Liang
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang, China; Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China; Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, Zhejiang, China
| | - Chen Xu
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang, China; Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China; Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, Zhejiang, China
| | - Ranran Cao
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang, China; Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China; Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, Zhejiang, China
| | - Shuoyang Liu
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang, China; Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China; Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, Zhejiang, China
| | - Yi Luan
- Department of Cardiology, Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Ying Gu
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang, China; Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China; Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, Zhejiang, China
| | - Peidong Han
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang, China; Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang, China; Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, Zhejiang, China.
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Katerndahl CDS, Rogers ORS, Day RB, Xu Z, Helton NM, Ramakrishnan SM, Miller CA, Ley TJ. PML::RARA and GATA2 proteins interact via DNA templates to induce aberrant self-renewal in mouse and human hematopoietic cells. Proc Natl Acad Sci U S A 2024; 121:e2317690121. [PMID: 38648485 PMCID: PMC11067031 DOI: 10.1073/pnas.2317690121] [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: 10/17/2023] [Accepted: 03/15/2024] [Indexed: 04/25/2024] Open
Abstract
The underlying mechanism(s) by which the PML::RARA fusion protein initiates acute promyelocytic leukemia is not yet clear. We defined the genomic binding sites of PML::RARA in primary mouse and human hematopoietic progenitor cells with V5-tagged PML::RARA, using anti-V5-PML::RARA chromatin immunoprecipitation sequencing and CUT&RUN approaches. Most genomic PML::RARA binding sites were found in regions that were already chromatin-accessible (defined by ATAC-seq) in unmanipulated, wild-type promyelocytes, suggesting that these regions are "open" prior to PML::RARA expression. We found that GATA binding motifs, and the direct binding of the chromatin "pioneering factor" GATA2, were significantly enriched near PML::RARA binding sites. Proximity labeling studies revealed that PML::RARA interacts with ~250 proteins in primary mouse hematopoietic cells; GATA2 and 33 others require PML::RARA binding to DNA for the interaction to occur, suggesting that binding to their cognate DNA target motifs may stabilize their interactions. In the absence of PML::RARA, Gata2 overexpression induces many of the same epigenetic and transcriptional changes as PML::RARA. These findings suggested that PML::RARA may indirectly initiate its transcriptional program by activating Gata2 expression: Indeed, we demonstrated that inactivation of Gata2 prior to PML::RARA expression prevented its ability to induce self-renewal. These data suggested that GATA2 binding creates accessible chromatin regions enriched for both GATA and Retinoic Acid Receptor Element motifs, where GATA2 and PML::RARA can potentially bind and interact with each other. In turn, PML::RARA binding to DNA promotes a feed-forward transcriptional program by positively regulating Gata2 expression. Gata2 may therefore be required for PML::RARA to establish its transcriptional program.
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Affiliation(s)
- Casey D. S. Katerndahl
- Division of Oncology, Department of Internal Medicine, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO63110
| | - Olivia R. S. Rogers
- Division of Oncology, Department of Internal Medicine, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO63110
| | - Ryan B. Day
- Division of Oncology, Department of Internal Medicine, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO63110
| | - Ziheng Xu
- Division of Oncology, Department of Internal Medicine, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO63110
| | - Nichole M. Helton
- Division of Oncology, Department of Internal Medicine, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO63110
| | - Sai Mukund Ramakrishnan
- Division of Oncology, Department of Internal Medicine, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO63110
| | - Christopher A. Miller
- Division of Oncology, Department of Internal Medicine, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO63110
| | - Timothy J. Ley
- Division of Oncology, Department of Internal Medicine, Section of Stem Cell Biology, Washington University School of Medicine, St. Louis, MO63110
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Xu C, Zhang G, Wang X, Huang X, Zhang J, Han S, Wang J, Hall DD, Xu R, He F, Chang X, Wang F, Xie W, Wu Z, Song LS, Han P. Ptpn23 Controls Cardiac T-Tubule Patterning by Promoting the Assembly of Dystrophin-Glycoprotein Complex. Circulation 2024; 149:1375-1390. [PMID: 38214189 PMCID: PMC11039371 DOI: 10.1161/circulationaha.123.065767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 12/14/2023] [Indexed: 01/13/2024]
Abstract
BACKGROUND Cardiac transverse tubules (T-tubules) are anchored to sarcomeric Z-discs by costameres to establish a regular spaced pattern. One of the major components of costameres is the dystrophin-glycoprotein complex (DGC). Nevertheless, how the assembly of the DGC coordinates with the formation and maintenance of T-tubules under physiological and pathological conditions remains unclear. METHODS Given the known role of Ptpn23 (protein tyrosine phosphatase, nonreceptor type 23) in regulating membrane deformation, its expression in patients with dilated cardiomyopathy was determined. Taking advantage of Cre/Loxp, CRISPR/Cas9, and adeno-associated virus 9 (AAV9)-mediated in vivo gene editing, we generated cardiomyocyte-specific Ptpn23 and Actn2 (α-actinin-2, a major component of Z-discs) knockout mice. We also perturbed the DGC by using dystrophin global knockout mice (DmdE4*). MM 4-64 and Di-8-ANEPPS staining, Cav3 immunofluorescence, and transmission electron microscopy were performed to determine T-tubule structure in isolated cells and intact hearts. In addition, the assembly of the DGC with Ptpn23 and dystrophin loss of function was determined by glycerol-gradient fractionation and SDS-PAGE analysis. RESULTS The expression level of Ptpn23 was reduced in failing hearts from dilated cardiomyopathy patients and mice. Genetic deletion of Ptpn23 resulted in disorganized T-tubules with enlarged diameters and progressive dilated cardiomyopathy without affecting sarcomere organization. AAV9-mediated mosaic somatic mutagenesis further indicated a cell-autonomous role of Ptpn23 in regulating T-tubule formation. Genetic and biochemical analyses showed that Ptpn23 was essential for the integrity of costameres, which anchor the T-tubule membrane to Z-discs, through interactions with α-actinin and dystrophin. Deletion of α-actinin altered the subcellular localization of Ptpn23 and DGCs. In addition, genetic inactivation of dystrophin caused similar T-tubule defects to Ptpn23 loss-of-function without affecting Ptpn23 localization at Z-discs. Last, inducible Ptpn23 knockout at 1 month of age showed Ptpn23 is also required for the maintenance of T-tubules in adult cardiomyocytes. CONCLUSIONS Ptpn23 is essential for cardiac T-tubule formation and maintenance along Z-discs. During postnatal heart development, Ptpn23 interacts with sarcomeric α-actinin and coordinates the assembly of the DGC at costameres to sculpt T-tubule spatial patterning and morphology.
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Affiliation(s)
- Chen Xu
- Center for Genetic Medicine, The Fourth Affiliated Hospital (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.), Zhejiang University School of Medicine, Hangzhou, China
- Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, China (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.)
- Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, China (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.)
| | - Ge Zhang
- Center for Genetic Medicine, The Fourth Affiliated Hospital (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.), Zhejiang University School of Medicine, Hangzhou, China
- Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, China (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.)
- Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, China (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.)
| | - Xinjian Wang
- Center for Genetic Medicine, The Fourth Affiliated Hospital (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.), Zhejiang University School of Medicine, Hangzhou, China
- Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, China (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.)
- Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, China (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.)
| | - Xiaozhi Huang
- Center for Genetic Medicine, The Fourth Affiliated Hospital (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.), Zhejiang University School of Medicine, Hangzhou, China
- Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, China (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.)
- Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, China (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.)
| | - Jiayin Zhang
- Center for Genetic Medicine, The Fourth Affiliated Hospital (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.), Zhejiang University School of Medicine, Hangzhou, China
- Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, China (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.)
- Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, China (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.)
| | - Shuxian Han
- Center for Genetic Medicine, The Fourth Affiliated Hospital (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.), Zhejiang University School of Medicine, Hangzhou, China
- Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, China (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.)
- Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, China (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.)
| | - Jinxi Wang
- Department of Internal Medicine, Abboud Cardiovascular Research Center, Carver College of Medicine, University of Iowa, Iowa City (J.W., D.D.H., L.-S.S.)
| | - Duane D Hall
- Department of Internal Medicine, Abboud Cardiovascular Research Center, Carver College of Medicine, University of Iowa, Iowa City (J.W., D.D.H., L.-S.S.)
| | - Ruoqing Xu
- Center for Genetic Medicine, The Fourth Affiliated Hospital (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.), Zhejiang University School of Medicine, Hangzhou, China
- Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, China (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.)
- Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, China (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.)
| | - Feng He
- Center for Genetic Medicine, The Fourth Affiliated Hospital (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.), Zhejiang University School of Medicine, Hangzhou, China
- Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, China (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.)
- Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, China (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.)
| | - Xing Chang
- Research Center for Industries of the Future, Westlake University, Hangzhou, China (X.C.)
| | - Fudi Wang
- School of Public Health, State Key Laboratory of Experimental Hematology (F.W.), Zhejiang University School of Medicine, Hangzhou, China
| | - Wenjun Xie
- Department of Cardiology, First Affiliated Hospital of Xi'an Jiaotong University, China (W.X.)
| | - Zhichao Wu
- Department of Thoracic Surgery, People's Hospital of Xinjiang Uyghur Autonomous Region, Urumqi, China (Z.W.)
- Department of Cardiovascular Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China (Z.W.)
| | - Long-Sheng Song
- Department of Internal Medicine, Abboud Cardiovascular Research Center, Carver College of Medicine, University of Iowa, Iowa City (J.W., D.D.H., L.-S.S.)
| | - Peidong Han
- Center for Genetic Medicine, The Fourth Affiliated Hospital (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.), Zhejiang University School of Medicine, Hangzhou, China
- Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, China (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.)
- Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Hangzhou, China (C.X., G.Z., X.W., X.H., J.Z., S.H., R.X., F.H., P.H.)
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Zhang ML, Li HB, Jin Y. Application and perspective of CRISPR/Cas9 genome editing technology in human diseases modeling and gene therapy. Front Genet 2024; 15:1364742. [PMID: 38666293 PMCID: PMC11043577 DOI: 10.3389/fgene.2024.1364742] [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: 01/03/2024] [Accepted: 03/11/2024] [Indexed: 04/28/2024] Open
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) mediated Cas9 nuclease system has been extensively used for genome editing and gene modification in eukaryotic cells. CRISPR/Cas9 technology holds great potential for various applications, including the correction of genetic defects or mutations within the human genome. The application of CRISPR/Cas9 genome editing system in human disease research is anticipated to solve a multitude of intricate molecular biology challenges encountered in life science research. Here, we review the fundamental principles underlying CRISPR/Cas9 technology and its recent application in neurodegenerative diseases, cardiovascular diseases, autoimmune related diseases, and cancer, focusing on the disease modeling and gene therapy potential of CRISPR/Cas9 in these diseases. Finally, we provide an overview of the limitations and future prospects associated with employing CRISPR/Cas9 technology for diseases study and treatment.
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Affiliation(s)
- Man-Ling Zhang
- Department of Rheumatology and Immunology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
- Inner Mongolia Key Laboratory for Pathogenesis and Diagnosis of Rheumatic and Autoimmune Diseases, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Hong-Bin Li
- Department of Rheumatology and Immunology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
- Inner Mongolia Key Laboratory for Pathogenesis and Diagnosis of Rheumatic and Autoimmune Diseases, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Yong Jin
- Department of Rheumatology and Immunology, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
- Inner Mongolia Key Laboratory for Pathogenesis and Diagnosis of Rheumatic and Autoimmune Diseases, The Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
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Lin CP, Levy PL, Alflen A, Apriamashvili G, Ligtenberg MA, Vredevoogd DW, Bleijerveld OB, Alkan F, Malka Y, Hoekman L, Markovits E, George A, Traets JJH, Krijgsman O, van Vliet A, Poźniak J, Pulido-Vicuña CA, de Bruijn B, van Hal-van Veen SE, Boshuizen J, van der Helm PW, Díaz-Gómez J, Warda H, Behrens LM, Mardesic P, Dehni B, Visser NL, Marine JC, Markel G, Faller WJ, Altelaar M, Agami R, Besser MJ, Peeper DS. Multimodal stimulation screens reveal unique and shared genes limiting T cell fitness. Cancer Cell 2024; 42:623-645.e10. [PMID: 38490212 PMCID: PMC11003465 DOI: 10.1016/j.ccell.2024.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 01/03/2024] [Accepted: 02/22/2024] [Indexed: 03/17/2024]
Abstract
Genes limiting T cell antitumor activity may serve as therapeutic targets. It has not been systematically studied whether there are regulators that uniquely or broadly contribute to T cell fitness. We perform genome-scale CRISPR-Cas9 knockout screens in primary CD8 T cells to uncover genes negatively impacting fitness upon three modes of stimulation: (1) intense, triggering activation-induced cell death (AICD); (2) acute, triggering expansion; (3) chronic, causing dysfunction. Besides established regulators, we uncover genes controlling T cell fitness either specifically or commonly upon differential stimulation. Dap5 ablation, ranking highly in all three screens, increases translation while enhancing tumor killing. Loss of Icam1-mediated homotypic T cell clustering amplifies cell expansion and effector functions after both acute and intense stimulation. Lastly, Ctbp1 inactivation induces functional T cell persistence exclusively upon chronic stimulation. Our results functionally annotate fitness regulators based on their unique or shared contribution to traits limiting T cell antitumor activity.
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Affiliation(s)
- Chun-Pu Lin
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Pierre L Levy
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Tumor Immunology and Immunotherapy Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Astrid Alflen
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Hematology and Medical Oncology, University Medical Center, Johannes Gutenberg-University, 55131 Mainz, Germany; Research Center for Immunotherapy (FZI), University Medical Center, Johannes Gutenberg-University, 55131 Mainz, Germany
| | - Georgi Apriamashvili
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Maarten A Ligtenberg
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - David W Vredevoogd
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Onno B Bleijerveld
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Ferhat Alkan
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Yuval Malka
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Liesbeth Hoekman
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Ettai Markovits
- Ella Lemelbaum Institute for Immuno-oncology and Melanoma, Sheba Medical Center, Ramat Gan 52612, Israel; Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel
| | - Austin George
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Joleen J H Traets
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Oscar Krijgsman
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Alex van Vliet
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Joanna Poźniak
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Carlos Ariel Pulido-Vicuña
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Beaunelle de Bruijn
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Susan E van Hal-van Veen
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Julia Boshuizen
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Pim W van der Helm
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Judit Díaz-Gómez
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Hamdy Warda
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Leonie M Behrens
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Paula Mardesic
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Bilal Dehni
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Nils L Visser
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, 3000 Leuven, Belgium; Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Gal Markel
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel; Davidoff Cancer Center and Samueli Integrative Cancer Pioneering Institute, Rabin Medical Center, Petach Tikva 4941492, Israel
| | - William J Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Maarten Altelaar
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Biomolecular Mass Spectrometry and Proteomics, Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Reuven Agami
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Michal J Besser
- Ella Lemelbaum Institute for Immuno-oncology and Melanoma, Sheba Medical Center, Ramat Gan 52612, Israel; Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel-Aviv 6997801, Israel; Davidoff Cancer Center and Samueli Integrative Cancer Pioneering Institute, Rabin Medical Center, Petach Tikva 4941492, Israel; Felsenstein Medical Research Center, Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Daniel S Peeper
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Pathology, VU University Amsterdam, 1081 HV Amsterdam, the Netherlands.
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Dwivedi D, Dumontier D, Sherer M, Lin S, Mirow AM, Qiu Y, Xu Q, Liebman SA, Joseph D, Datta SR, Fishell G, Pouchelon G. Metabotropic signaling within somatostatin interneurons controls transient thalamocortical inputs during development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.21.558862. [PMID: 37790336 PMCID: PMC10542166 DOI: 10.1101/2023.09.21.558862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
During brain development, neural circuits undergo major activity-dependent restructuring. Circuit wiring mainly occurs through synaptic strengthening following the Hebbian "fire together, wire together" precept. However, select connections, essential for circuit development, are transient. They are effectively connected early in development, but strongly diminish during maturation. The mechanisms by which transient connectivity recedes are unknown. To investigate this process, we characterize transient thalamocortical inputs, which depress onto somatostatin inhibitory interneurons during development, by employing optogenetics, chemogenetics, transcriptomics and CRISPR-based strategies. We demonstrate that in contrast to typical activity-dependent mechanisms, transient thalamocortical connectivity onto somatostatin interneurons is non-canonical and involves metabotropic signaling. Specifically, metabotropic-mediated transcription, of guidance molecules in particular, supports the elimination of this connectivity. Remarkably, we found that this developmental process impacts the development of normal exploratory behaviors of adult mice.
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35
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Lanza DG, Mao J, Lorenzo I, Liao L, Seavitt JR, Ljungberg MC, Simpson EM, DeMayo FJ, Heaney JD. An oocyte-specific Cas9-expressing mouse for germline CRISPR/Cas9-mediated genome editing. Genesis 2024; 62:e23589. [PMID: 38523431 PMCID: PMC10987075 DOI: 10.1002/dvg.23589] [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: 12/22/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/26/2024]
Abstract
Cas9 transgenes can be employed for genome editing in mouse zygotes. However, using transgenic instead of exogenous Cas9 to produce gene-edited animals creates unique issues including ill-defined transgene integration sites, the potential for prolonged Cas9 expression in transgenic embryos, and increased genotyping burden. To overcome these issues, we generated mice harboring an oocyte-specific, Gdf9 promoter driven, Cas9 transgene (Gdf9-Cas9) targeted as a single copy into the Hprt1 locus. The X-linked Hprt1 locus was selected because it is a defined integration site that does not influence transgene expression, and breeding of transgenic males generates obligate transgenic females to serve as embryo donors. Using microinjections and electroporation to introduce sgRNAs into zygotes derived from transgenic dams, we demonstrate that Gdf9-Cas9 mediates genome editing as efficiently as exogenous Cas9 at several loci. We show that genome editing efficiency is independent of transgene inheritance, verifying that maternally derived Cas9 facilitates genome editing. We also show that paternal inheritance of Gdf9-Cas9 does not mediate genome editing, confirming that Gdf9-Cas9 is not expressed in embryos. Finally, we demonstrate that off-target mutagenesis is equally rare when using transgenic or exogenous Cas9. Together, these results show that the Gdf9-Cas9 transgene is a viable alternative to exogenous Cas9.
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Affiliation(s)
- Denise G. Lanza
- Department of Molecular and Human Genetics, Baylor College of Medicine Houston, TX, USA 77030
| | - Jianqiang Mao
- Department of Molecular & Cellular Biology, Baylor College of Medicine Houston, TX, USA 77030
| | - Isabel Lorenzo
- Department of Molecular and Human Genetics, Baylor College of Medicine Houston, TX, USA 77030
| | - Lan Liao
- Department of Molecular & Cellular Biology, Baylor College of Medicine Houston, TX, USA 77030
| | - John R. Seavitt
- Department of Molecular and Human Genetics, Baylor College of Medicine Houston, TX, USA 77030
- Present address: The Jackson Laboratory 600 Main St., Bar Harbor, Maine, ME, USA 04609
| | - M. Cecilia Ljungberg
- Department of Pediatrics – Neurology, Baylor College of Medicine Houston, TX, USA 77030
- Duncan Neurological Research Institute, Texas Children’s Hospital Houston, TX, USA 77030
| | - Elizabeth M. Simpson
- Centre for Molecular Medicine and Therapeutics at BC Children’s Hospital Department of Medical Genetics, The University of British Columbia Vancouver, British Columbia V5Z 4H4, Canada
| | - Francesco J. DeMayo
- Reproductive and Developmental Biology Laboratory National Institute of Environmental Health Sciences Research Triangle Park, NC, USA 27709
| | - Jason D. Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine Houston, TX, USA 77030
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine Houston, TX, USA 77030
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36
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Murphy KC, Ruscetti M. Advances in Making Cancer Mouse Models More Accessible and Informative through Non-Germline Genetic Engineering. Cold Spring Harb Perspect Med 2024; 14:a041348. [PMID: 37277206 PMCID: PMC10982712 DOI: 10.1101/cshperspect.a041348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Genetically engineered mouse models (GEMMs) allow for modeling of spontaneous tumorigenesis within its native microenvironment in mice and have provided invaluable insights into mechanisms of tumorigenesis and therapeutic strategies to treat human disease. However, as their generation requires germline manipulation and extensive animal breeding that is time-, labor-, and cost-intensive, traditional GEMMs are not accessible to most researchers, and fail to model the full breadth of cancer-associated genetic alterations and therapeutic targets. Recent advances in genome-editing technologies and their implementation in somatic tissues of mice have ushered in a new class of mouse models: non-germline GEMMs (nGEMMs). nGEMM approaches can be leveraged to generate somatic tumors de novo harboring virtually any individual or group of genetic alterations found in human cancer in a mouse through simple procedures that do not require breeding, greatly increasing the accessibility and speed and scale on which GEMMs can be produced. Here we describe the technologies and delivery systems used to create nGEMMs and highlight new biological insights derived from these models that have rapidly informed functional cancer genomics, precision medicine, and immune oncology.
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Affiliation(s)
- Katherine C Murphy
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Marcus Ruscetti
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA;
- Immunology and Microbiology Program, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
- Cancer Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
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37
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Cubillos P, Ditzer N, Kolodziejczyk A, Schwenk G, Hoffmann J, Schütze TM, Derihaci RP, Birdir C, Köllner JE, Petzold A, Sarov M, Martin U, Long KR, Wimberger P, Albert M. The growth factor EPIREGULIN promotes basal progenitor cell proliferation in the developing neocortex. EMBO J 2024; 43:1388-1419. [PMID: 38514807 PMCID: PMC11021537 DOI: 10.1038/s44318-024-00068-7] [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: 09/13/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/23/2024] Open
Abstract
Neocortex expansion during evolution is linked to higher numbers of neurons, which are thought to result from increased proliferative capacity and neurogenic potential of basal progenitor cells during development. Here, we show that EREG, encoding the growth factor EPIREGULIN, is expressed in the human developing neocortex and in gorilla cerebral organoids, but not in the mouse neocortex. Addition of EPIREGULIN to the mouse neocortex increases proliferation of basal progenitor cells, whereas EREG ablation in human cortical organoids reduces proliferation in the subventricular zone. Treatment of cortical organoids with EPIREGULIN promotes a further increase in proliferation of gorilla but not of human basal progenitor cells. EPIREGULIN competes with the epidermal growth factor (EGF) to promote proliferation, and inhibition of the EGF receptor abrogates the EPIREGULIN-mediated increase in basal progenitor cells. Finally, we identify putative cis-regulatory elements that may contribute to the observed inter-species differences in EREG expression. Our findings suggest that species-specific regulation of EPIREGULIN expression may contribute to the increased neocortex size of primates by providing a tunable pro-proliferative signal to basal progenitor cells in the subventricular zone.
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Affiliation(s)
- Paula Cubillos
- Center for Regenerative Therapies TU Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany
| | - Nora Ditzer
- Center for Regenerative Therapies TU Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany
| | - Annika Kolodziejczyk
- Center for Regenerative Therapies TU Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany
| | - Gustav Schwenk
- Center for Regenerative Therapies TU Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany
| | - Janine Hoffmann
- Center for Regenerative Therapies TU Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany
| | - Theresa M Schütze
- Center for Regenerative Therapies TU Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany
| | - Razvan P Derihaci
- Department of Gynecology and Obstetrics, TU Dresden, 01307, Dresden, Germany
- National Center for Tumor Diseases, 01307, Dresden, Germany
| | - Cahit Birdir
- Department of Gynecology and Obstetrics, TU Dresden, 01307, Dresden, Germany
- Center for feto/neonatal Health, TU Dresden, 01307, Dresden, Germany
| | - Johannes Em Köllner
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Andreas Petzold
- DRESDEN-concept Genome Center, Center for Molecular and Cellular Bioengineering, TUD Dresden University of Technology, 01307, Dresden, Germany
| | - Mihail Sarov
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307, Dresden, Germany
| | - Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs, Department of Cardiothoracic, Transplantation and Vascular Surgery, Hannover Medical School, 30625, Hannover, Germany
- REBIRTH-Cluster of Excellence, Hannover, Germany
| | - Katherine R Long
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE1 1UL, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, SE1 1UL, United Kingdom
| | - Pauline Wimberger
- Department of Gynecology and Obstetrics, TU Dresden, 01307, Dresden, Germany
- National Center for Tumor Diseases, 01307, Dresden, Germany
| | - Mareike Albert
- Center for Regenerative Therapies TU Dresden, TUD Dresden University of Technology, 01307, Dresden, Germany.
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Wakasa K, Tamura R, Osaka S, Takei H, Asai A, Nittono H, Kusuhara H, Hayashi H. Rapid in vivo evaluation system for cholestasis-related genes in mice with humanized bile acid profiles. Hepatol Commun 2024; 8:e0382. [PMID: 38517206 PMCID: PMC10962888 DOI: 10.1097/hc9.0000000000000382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/05/2023] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Pediatric cholestatic liver diseases (Ped-CLD) comprise many ultrarare disorders with a genetic basis. Pharmacologic therapy for severe cases of Ped-CLD has not been established. Species differences in bile acid (BA) metabolism between humans and rodents contribute to the lack of phenocopy of patients with Ped-CLD in rodents and hinder the development of therapeutic strategies. We aimed to establish an efficient in vivo system to understand BA-related pathogenesis, such as Ped-CLD. METHODS We generated mice that express spCas9 specifically in the liver (L-Cas9Tg/Tg [liver-specific Cas9Tg/Tg] mice) and designed recombinant adeno-associated virus serotype 8 encoding small-guide RNA (AAV8 sgRNA) targeting Abcc2, Abcb11, and Cyp2c70. In humans, ABCC2 and ABCB11 deficiencies cause constitutional hyperbilirubinemia and most severe Ped-CLD, respectively. Cyp2c70 encodes an enzyme responsible for the rodent-specific BA profile. Six-week-old L-Cas9Tg/Tg mice were injected with this AAV8 sgRNA and subjected to biochemical and histological analysis. RESULTS Fourteen days after the injection with AAV8 sgRNA targeting Abcc2, L-Cas9Tg/Tg mice exhibited jaundice and phenocopied patients with ABCC2 deficiency. L-Cas9Tg/Tg mice injected with AAV8 sgRNA targeting Abcb11 showed hepatomegaly and cholestasis without histological evidence of liver injury. Compared to Abcb11 alone, simultaneous injection of AAV8 sgRNA for Abcb11 and Cyp2c70 humanized the BA profile and caused higher transaminase levels and parenchymal necrosis, resembling phenotypes with ABCB11 deficiency. CONCLUSIONS This study provides proof of concept for efficient in vivo assessment of cholestasis-related genes in humanized bile acid profiles. Our platform offers a more time- and cost-effective alternative to conventional genetically engineered mice, increasing our understanding of BA-related pathogenesis such as Ped-CLD and expanding the potential for translational research.
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Affiliation(s)
- Kihiro Wakasa
- Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Science, The University of Tokyo, Tokyo, Japan
| | - Ryutaro Tamura
- Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Science, The University of Tokyo, Tokyo, Japan
| | - Shuhei Osaka
- Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Science, The University of Tokyo, Tokyo, Japan
| | - Hajime Takei
- Junshin Clinic Bile Acid Institute, Tokyo, Japan
| | - Akihiro Asai
- Department of Gastroenterology, and Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | | | - Hiroyuki Kusuhara
- Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Science, The University of Tokyo, Tokyo, Japan
| | - Hisamitsu Hayashi
- Laboratory of Molecular Pharmacokinetics, Graduate School of Pharmaceutical Science, The University of Tokyo, Tokyo, Japan
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39
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Milling LE, Markson SC, Tjokrosurjo Q, Derosia NM, Streeter IS, Hickok GH, Lemmen AM, Nguyen TH, Prathima P, Fithian W, Schwartz MA, Hacohen N, Doench JG, LaFleur MW, Sharpe AH. Framework for in vivo T cell screens. J Exp Med 2024; 221:e20230699. [PMID: 38411617 PMCID: PMC10899089 DOI: 10.1084/jem.20230699] [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: 04/24/2023] [Revised: 12/14/2023] [Accepted: 01/19/2024] [Indexed: 02/28/2024] Open
Abstract
In vivo T cell screens are a powerful tool for elucidating complex mechanisms of immunity, yet there is a lack of consensus on the screen design parameters required for robust in vivo screens: gene library size, cell transfer quantity, and number of mice. Here, we describe the Framework for In vivo T cell Screens (FITS) to provide experimental and analytical guidelines to determine optimal parameters for diverse in vivo contexts. As a proof-of-concept, we used FITS to optimize the parameters for a CD8+ T cell screen in the B16-OVA tumor model. We also included unique molecular identifiers (UMIs) in our screens to (1) improve statistical power and (2) track T cell clonal dynamics for distinct gene knockouts (KOs) across multiple tissues. These findings provide an experimental and analytical framework for performing in vivo screens in immune cells and illustrate a case study for in vivo T cell screens with UMIs.
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Affiliation(s)
- Lauren E. Milling
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women’s Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Samuel C. Markson
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women’s Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Qin Tjokrosurjo
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women’s Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Nicole M. Derosia
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women’s Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ivy S.L. Streeter
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women’s Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Grant H. Hickok
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women’s Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ashlyn M. Lemmen
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women’s Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Thao H. Nguyen
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women’s Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Priyamvada Prathima
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women’s Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - William Fithian
- Department of Statistics, University of California, Berkeley, Berkeley, CA, USA
| | - Marc A. Schwartz
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Medicine, Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Nir Hacohen
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Medicine, Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - John G. Doench
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Martin W. LaFleur
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women’s Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Arlene H. Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women’s Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
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40
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Wang S, Gong X, Xiao F, Yang Y. Recent advances in host-focused molecular tools for investigating host-gut microbiome interactions. Front Microbiol 2024; 15:1335036. [PMID: 38605718 PMCID: PMC11007152 DOI: 10.3389/fmicb.2024.1335036] [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: 11/08/2023] [Accepted: 03/18/2024] [Indexed: 04/13/2024] Open
Abstract
Microbial communities in the human gut play a significant role in regulating host gene expression, influencing a variety of biological processes. To understand the molecular mechanisms underlying host-microbe interactions, tools that can dissect signaling networks are required. In this review, we discuss recent advances in molecular tools used to study this interplay, with a focus on those that explore how the microbiome regulates host gene expression. These tools include CRISPR-based whole-body genetic tools for deciphering host-specific genes involved in the interaction process, Cre-loxP based tissue/cell-specific gene editing approaches, and in vitro models of host-derived organoids. Overall, the application of these molecular tools is revolutionizing our understanding of how host-microbiome interactions contribute to health and disease, paving the way for improved therapies and interventions that target microbial influences on the host.
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Affiliation(s)
- Siyao Wang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Ministry of Industry and Information Technology, Beihang University, Beijing, China
| | - Xu Gong
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Ministry of Industry and Information Technology, Beihang University, Beijing, China
| | - Fei Xiao
- Department of Thoracic Surgery, China-Japan Friendship Hospital, Beijing, China
| | - Yun Yang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, China
- Key Laboratory of Big Data-Based Precision Medicine, Ministry of Industry and Information Technology, Beihang University, Beijing, China
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41
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Sekiya T, Hidano S, Takaki S. Tonic TCR and IL-1β signaling mediate phenotypic alterations of naive CD4 + T cells. Cell Rep 2024; 43:113954. [PMID: 38492221 DOI: 10.1016/j.celrep.2024.113954] [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: 05/30/2023] [Revised: 11/06/2023] [Accepted: 02/28/2024] [Indexed: 03/18/2024] Open
Abstract
Inert naive CD4+ T (TN) cells differentiate into functional T helper (Th) or regulatory T (Treg) cell subsets upon encountering antigens, mediating properly directed immune responses. Although all TN cells can differentiate into any of the Th and Treg cell subsets, heterogeneity exists among TN cells. By constructing reporter mice to detect ongoing T cell receptor (TCR) signaling, we identify that interleukin (IL)-1β signaling affects TN cell characteristics, independent of tonic TCR signaling, which also alters TN cell phenotypes. IL-1β reversibly attenuates the differentiation potential of TN cells toward Treg cells. IL-1β signaling is elevated in the splenic TN cells, consequently attenuating their differentiation potential toward Treg cells. Aberrant elevation of IL-1β signaling augments colitogenic activities of TN cells. TN cells in patients with colitis exhibited elevated IL-1β signaling. We demonstrate that phenotypic alteration in TN cells by IL-1β is an important mechanism in the regulation of immune responses.
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Affiliation(s)
- Takashi Sekiya
- Section of Immune Response Modification, The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan; Department of Immune Regulation, The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan.
| | - Shinya Hidano
- Department of Immune Regulation, The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan
| | - Satoshi Takaki
- Department of Immune Regulation, The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan
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42
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Wang S, Zhu Y, Du S, Zheng Y. Preclinical Advances in LNP-CRISPR Therapeutics for Solid Tumor Treatment. Cells 2024; 13:568. [PMID: 38607007 PMCID: PMC11011435 DOI: 10.3390/cells13070568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 03/10/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024] Open
Abstract
Solid tumors, with their intricate cellular architecture and genetic heterogeneity, have long posed therapeutic challenges. The advent of the CRISPR genome editing system offers a promising, precise genetic intervention. However, the journey from bench to bedside is fraught with hurdles, chief among them being the efficient delivery of CRISPR components to tumor cells. Lipid nanoparticles (LNPs) have emerged as a potential solution. This biocompatible nanomaterial can encapsulate the CRISPR/Cas9 system, ensuring targeted delivery while mitigating off-target effects. Pre-clinical investigations underscore the efficacy of LNP-mediated CRISPR delivery, with marked disruption of oncogenic pathways and subsequent tumor regression. Overall, CRISPR/Cas9 technology, when combined with LNPs, presents a groundbreaking approach to cancer therapy, offering precision, efficacy, and potential solutions to current limitations. While further research and clinical testing are required, the future of personalized cancer treatment based on CRISPR/Cas9 holds immense promise.
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Affiliation(s)
- Shuting Wang
- School of Pharmacy, Hainan Medical University, Haikou 571199, China;
| | - Yuxi Zhu
- Department of Pediatrics, University Hospitals Rainbow Babies & Children’s Hospital, Cleveland, OH 44106, USA;
| | - Shi Du
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Yunsi Zheng
- School of Pharmacy, Hainan Medical University, Haikou 571199, China;
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43
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Yu S, Lei X, Qu C. MicroRNA Sensors Based on CRISPR/Cas12a Technologies: Evolution From Indirect to Direct Detection. Crit Rev Anal Chem 2024:1-17. [PMID: 38489095 DOI: 10.1080/10408347.2024.2329229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
MicroRNA (miRNA) has emerged as a promising biomarker for disease diagnosis and a potential therapeutic targets for drug development. The detection of miRNA can serve as a noninvasive tool in diseases diagnosis and predicting diseases prognosis. CRISPR/Cas12a system has great potential in nucleic acid detection due to its high sensitivity and specificity, which has been developed to be a versatile tool for nucleic acid-based detection of targets in various fields. However, conversion from RNA to DNA with or without amplification operation is necessary for miRNA detection based on CRISPR/Cas12a system, because dsDNA containing PAM sequence or ssDNA is traditionally considered as the activator of Cas12a. Until recently, direct detection of miRNA by CRISPR/Cas12a system has been reported. In this review, we provide an overview of the evolution of biosensors based on CRISPR/Cas12a for miRNA detection from indirect to direct, which would be beneficial to the development of CRISPR/Cas12a-based sensors with better performance for direct detection of miRNA.
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Affiliation(s)
- Songcheng Yu
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xueying Lei
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Chenling Qu
- School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou, China
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44
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Gao M, He Y, Zhu X, Peng W, Zhou Y, Deng Y, Liao G, Ni W, Li Y, Gao J, Bu H, Yang J, Yang G, Yang Y, Bao J. One-step in vivo gene knock-out in porcine embryos using recombinant adeno-associated viruses. Front Cell Dev Biol 2024; 12:1376936. [PMID: 38559814 PMCID: PMC10978582 DOI: 10.3389/fcell.2024.1376936] [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: 01/26/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction: Gene-edited pigs have become prominent models for studying human disease mechanisms, gene therapy, and xenotransplantation. CRISPR (clustered regularly interspaced short palindromic repeats)/CRISPR-associated 9 (CRISPR/Cas9) technology is a widely employed tool for generating gene-edited pigs. Nevertheless, delivering CRISPR/Cas9 to pre-implantation embryos has traditionally posed challenges due to its reliance on intricate micromanipulation equipment and specialized techniques, resulting in high costs and time-consuming procedures. This study aims to introduce a novel one-step approach for generating genetically modified pigs by transducing CRISPR/Cas9 components into pre-implantation porcine embryos through oviductal injection of recombinant adeno-associated viruses (rAAV). Methods: We first used rAAV-1, rAAV-6, rAAV-8, rAAV-9 expressing EGFP to screen for rAAV serotypes that efficiently target porcine embryos, and then, to achieve efficient expression of CRISPR/Cas9 in vivo for a short period, we packaged sgRNAs targeting the GHR genes to self-complementary adeno-associated virus (scAAV), and Cas9 proteins to single-stranded adeno-associated virus (ssAAV). The efficiency of porcine embryos -based editing was then validated in vitro. The feasibility of this one-step method to produce gene-edited pigs using rAAV-CRISPR/Cas9 oviductal injection into sows within 24 h of conception was then validated. Results: Our research firstly establishes the efficient delivery of CRISPR/Cas9 to pig zygotes, both in vivo and in vitro, using rAAV6. Successful gene editing in pigs was achieved through oviductal injection of rAAV-CRISPR/Cas9. Conclusion: This method circumvents the intricate procedures involved in in vitro embryo manipulation and embryo transfers, providing a straightforward and cost-effective approach for the production of gene-edited pigs.
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Affiliation(s)
- Mengyu Gao
- Department of Pathology, Institute of Clinical Pathology, Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - YuTing He
- Department of Pathology, Institute of Clinical Pathology, Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - XingLong Zhu
- Department of Pathology, Institute of Clinical Pathology, Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - WanLiu Peng
- Department of Pathology, Institute of Clinical Pathology, Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - YanYan Zhou
- Department of Pathology, Institute of Clinical Pathology, Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Deng
- Department of Pathology, Institute of Clinical Pathology, Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Guangneng Liao
- Experimental Animal Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Ni
- Security Department, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Li
- Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu, China
| | - Jun Gao
- Department of Toxicological Inspection, Sichuan Center for Disease Prevention and Control, Chengdu, China
| | - Hong Bu
- Department of Pathology, Institute of Clinical Pathology, Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiayin Yang
- Laboratory of Liver Transplantation, Frontiers Science Center for Disease-related Molecular, Network, West China Hospital, Sichuan University, Chengdu, China
| | - Guang Yang
- Experimental Animal Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ji Bao
- Department of Pathology, Institute of Clinical Pathology, Key Laboratory of Transplant Engineering and Immunology, West China Hospital, Sichuan University, Chengdu, China
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45
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Noguchi Y, Onodera Y, Miyamoto T, Maruoka M, Kosako H, Suzuki J. In vivo CRISPR screening directly targeting testicular cells. CELL GENOMICS 2024; 4:100510. [PMID: 38447574 PMCID: PMC10943590 DOI: 10.1016/j.xgen.2024.100510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 12/10/2023] [Accepted: 02/06/2024] [Indexed: 03/08/2024]
Abstract
CRISPR-Cas9 short guide RNA (sgRNA) library screening is a powerful approach to understand the molecular mechanisms of biological phenomena. However, its in vivo application is currently limited. Here, we developed our previously established in vitro revival screening method into an in vivo one to identify factors involved in spermatogenesis integrity by utilizing sperm capacitation as an indicator. By introducing an sgRNA library into testicular cells, we successfully pinpointed the retinal degeneration 3 (Rd3) gene as a significant factor in spermatogenesis. Single-cell RNA sequencing (scRNA-seq) analysis highlighted the high expression of Rd3 in round spermatids, and proteomics analysis indicated that Rd3 interacts with mitochondria. To search for cell-type-specific signaling pathways based on scRNA-seq and proteomics analyses, we developed a computational tool, Hub-Explorer. Through this, we discovered that Rd3 modulates oxidative stress by regulating mitochondrial distribution upon ciliogenesis induction. Collectively, our screening system provides a valuable in vivo approach to decipher molecular mechanisms in biological processes.
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Affiliation(s)
- Yuki Noguchi
- Graduate School of Biostudies, Kyoto University, Konoe-cho, Yoshida, Sakyoku, Kyoto 606-8501, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyoku, Kyoto 606-8501, Japan
| | - Yasuhito Onodera
- Global Center for Biomedical Science and Engineering, Faculty of Medicine, Hokkaido University, N15W7 Kita-ku, Sapporo, Hokkaido 060-8638, Japan
| | - Tatsuo Miyamoto
- Department of Molecular and Cellular Physiology, Yamaguchi University, Graduate School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505, Japan
| | - Masahiro Maruoka
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyoku, Kyoto 606-8501, Japan; Center for Integrated Biosystems, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan
| | - Jun Suzuki
- Graduate School of Biostudies, Kyoto University, Konoe-cho, Yoshida, Sakyoku, Kyoto 606-8501, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyoku, Kyoto 606-8501, Japan; Center for Integrated Biosystems, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan; CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan.
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46
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Hebert JD, Tang YJ, Andrejka L, Lopez SS, Petrov DA, Boross G, Winslow MM. Combinatorial in vivo genome editing identifies widespread epistasis during lung tumorigenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583981. [PMID: 38496564 PMCID: PMC10942407 DOI: 10.1101/2024.03.07.583981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Lung adenocarcinoma, the most common subtype of lung cancer, is genomically complex, with tumors containing tens to hundreds of non-synonymous mutations. However, little is understood about how genes interact with each other to enable tumorigenesis in vivo , largely due to a lack of methods for investigating genetic interactions in a high-throughput and multiplexed manner. Here, we employed a novel platform to generate tumors with all pairwise inactivation of ten tumor suppressor genes within an autochthonous mouse model of oncogenic KRAS-driven lung cancer. By quantifying the fitness of tumors with every single and double mutant genotype, we show that most tumor suppressor genetic interactions exhibited negative epistasis, with diminishing returns on tumor fitness. In contrast, Apc inactivation showed positive epistasis with the inactivation of several other genes, including dramatically synergistic effects on tumor fitness in combination with Lkb1 or Nf1 inactivation. This approach has the potential to expand the scope of genetic interactions that may be functionally characterized in vivo , which could lead to a better understanding of how complex tumor genotypes impact each step of carcinogenesis.
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47
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Ashraf H, Heydarnejad M, Kosari F. The Confounding Role of Graft-Versus-Host Disease in Animal Models of Cancer Immunotherapy: A Systematic Review. ARCHIVES OF IRANIAN MEDICINE 2024; 27:159-167. [PMID: 38685841 PMCID: PMC11097315 DOI: 10.34172/aim.2024.24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 02/14/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND Cancer immunotherapy has emerged as a transformative approach for treating various malignancies, including melanoma, lung cancer, breast cancer, and leukemia. Animal models have been instrumental in elucidating the mechanisms and potential of these therapies. However, graft-versus-host disease (GVHD) is an inherent challenge in these studies, primarily because the introduction of foreign immune cells or tissues often triggers immune responses. METHODS A detailed systematic search was conducted across various scientific databases, including PubMed, Scopus, Embase, and Web of Science. The search aimed to identify peer-reviewed articles published in English from January 2000 to September 2023. Keywords and phrases used in the search included "Graft-versus-Host Disease", "GVHD", "animal models", "cancer immunotherapy", and combinations thereof. Boolean operators (AND/OR) were employed to refine the search. Finally, 6 articles were included in this systematic review, which is registered on PROSPERO (ID number CRD42024488544). RESULTS Our systematic review identified several mechanisms employed in animal studies to mitigate the confounding effects of GVHD. These included genetically modified mouse models, immunosuppressive drugs, and humanized mice. Furthermore, the review highlights innovative approaches such as selective T-cell depletion and the use of specific cytokine inhibitors. CONCLUSION By systematically identifying and mitigating the confounding effects of GVHD, we can significantly improve the predictive validity of preclinical trials, obtain broadly applicable findings, improve the efficiency of drugs, enhance safety profiling, and develop better therapeutic strategies. This approach is crucial in ensuring that the immunotherapeutic strategies developed in the laboratory are reflective of the human physiological response, thereby bridging a critical translational gap in oncological research.
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Affiliation(s)
- Hami Ashraf
- Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Heydarnejad
- Department of Pathology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farid Kosari
- Department of Pathology, Shariati Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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48
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Barwe SP, Kolb EA, Gopalakrishnapillai A. Down syndrome and leukemia: An insight into the disease biology and current treatment options. Blood Rev 2024; 64:101154. [PMID: 38016838 DOI: 10.1016/j.blre.2023.101154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/31/2023] [Accepted: 11/19/2023] [Indexed: 11/30/2023]
Abstract
Children with Down syndrome (DS) have a 10- to 20-fold greater predisposition to develop acute leukemia compared to the general population, with a skew towards myeloid leukemia (ML-DS). While ML-DS is known to be a subtype with good outcome, patients who relapse face a dismal prognosis. Acute lymphocytic leukemia in DS (DS-ALL) is considered to have poor prognosis. The relapse rate is high in DS-ALL compared to their non-DS counterparts. We have a better understanding about the mutational spectrum of DS leukemia. Studies using animal, embryonic stem cell- and induced pluripotent stem cell-based models have shed light on the mechanism by which these mutations contribute to disease initiation and progression. In this review, we list the currently available treatment strategies for DS-leukemias along with their outcome with emphasis on challenges with chemotherapy-related toxicities in children with DS. We focus on the mechanisms of initiation and progression of leukemia in children with DS and highlight the novel molecular targets with greater success in preclinical trials that have the potential to progress to the clinic.
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Affiliation(s)
- Sonali P Barwe
- Lisa Dean Moseley Institute for Cancer and Blood Disorders, Nemours Children's Health, Wilmington, Delaware, 19803, USA
| | - E Anders Kolb
- Lisa Dean Moseley Institute for Cancer and Blood Disorders, Nemours Children's Health, Wilmington, Delaware, 19803, USA
| | - Anilkumar Gopalakrishnapillai
- Lisa Dean Moseley Institute for Cancer and Blood Disorders, Nemours Children's Health, Wilmington, Delaware, 19803, USA.
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49
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Bu W, Li Y. Advances in Immunocompetent Mouse and Rat Models. Cold Spring Harb Perspect Med 2024; 14:a041328. [PMID: 37217281 PMCID: PMC10810718 DOI: 10.1101/cshperspect.a041328] [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] [Indexed: 05/24/2023]
Abstract
Rodent models of breast cancer have played critical roles in our understanding of breast cancer development and progression as well as preclinical testing of cancer prevention and therapeutics. In this article, we first review the values and challenges of conventional genetically engineered mouse (GEM) models and newer iterations of these models, especially those with inducible or conditional regulation of oncogenes and tumor suppressors. Then, we discuss nongermline (somatic) GEM models of breast cancer with temporospatial control, made possible by intraductal injection of viral vectors to deliver oncogenes or to manipulate the genome of mammary epithelial cells. Next, we introduce the latest development in precision editing of endogenous genes using in vivo CRISPR-Cas9 technology. We conclude with the recent development in generating somatic rat models for modeling estrogen receptor-positive breast cancer, something that has been difficult to accomplish in mice.
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Affiliation(s)
- Wen Bu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yi Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA
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50
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Istadi A, Porazinski S, Pajic M. Cancer variant modeling in vivo. Nat Biotechnol 2024; 42:383-385. [PMID: 38123743 DOI: 10.1038/s41587-023-02080-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Affiliation(s)
- Aji Istadi
- Personalised Cancer Therapeutics Laboratory, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Sean Porazinski
- Personalised Cancer Therapeutics Laboratory, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Marina Pajic
- Personalised Cancer Therapeutics Laboratory, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia.
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