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Schloßhauer JL, Tholen L, Körner A, Kubick S, Chatzopoulou S, Hönow A, Zemella A. Promoting the production of challenging proteins via induced expression in CHO cells and modified cell-free lysates harboring T7 RNA polymerase and mutant eIF2α. Synth Syst Biotechnol 2024; 9:416-424. [PMID: 38601208 PMCID: PMC11004649 DOI: 10.1016/j.synbio.2024.03.011] [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: 12/08/2023] [Revised: 02/12/2024] [Accepted: 03/16/2024] [Indexed: 04/12/2024] Open
Abstract
Chinese hamster ovary (CHO) cells are crucial in biopharmaceutical production due to their scalability and capacity for human-like post-translational modifications. However, toxic proteins and membrane proteins are often difficult-to-express in living cells. Alternatively, cell-free protein synthesis can be employed. This study explores innovative strategies for enhancing the production of challenging proteins through the modification of CHO cells by investigating both, cell-based and cell-free approaches. A major result in our study involves the integration of a mutant eIF2 translation initiation factor and T7 RNA polymerase into CHO cell lysates for cell-free protein synthesis. This resulted in elevated yields, while eliminating the necessity for exogenous additions during cell-free production, thereby substantially enhancing efficiency. Additionally, we explore the potential of the Rosa26 genomic site for the integration of T7 RNA polymerase and cell-based tetracycline-controlled protein expression. These findings provide promising advancements in bioproduction technologies, offering flexibility to switch between cell-free and cell-based protein production as needed.
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Affiliation(s)
- Jeffrey L. Schloßhauer
- Fraunhofer Project Group PZ-Syn of the Fraunhofer Institute for Cell Therapy and Immunology-IZI, Branch Bioanalytics and Bioprocesses-IZI-BB, Am Mühlenberg, Potsdam, Germany
- Fraunhofer Institute for Cell Therapy and Immunology-IZI, Branch Bioanalytics and Bioprocesses-IZI-BB, Am Mühlenberg, Potsdam, Germany
- Institute for Chemistry and Biochemistry, Laboratory of Protein Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Lena Tholen
- Fraunhofer Institute for Cell Therapy and Immunology-IZI, Branch Bioanalytics and Bioprocesses-IZI-BB, Am Mühlenberg, Potsdam, Germany
| | - Alexander Körner
- Fraunhofer Institute for Cell Therapy and Immunology-IZI, Branch Bioanalytics and Bioprocesses-IZI-BB, Am Mühlenberg, Potsdam, Germany
- Institute of Biotechnology, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology-IZI, Branch Bioanalytics and Bioprocesses-IZI-BB, Am Mühlenberg, Potsdam, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus –Senftenberg, The Brandenburg Medical School Theodor Fontane, University of Potsdam, Potsdam, Germany
- Institute for Chemistry and Biochemistry, Laboratory of Protein Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Sofia Chatzopoulou
- Fraunhofer Institute for Cell Therapy and Immunology-IZI, Branch Bioanalytics and Bioprocesses-IZI-BB, Am Mühlenberg, Potsdam, Germany
| | - Anja Hönow
- New/era/mabs GmbH, August-Bebel-Str. 89, 14482, Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology-IZI, Branch Bioanalytics and Bioprocesses-IZI-BB, Am Mühlenberg, Potsdam, Germany
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2
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Mseis-Jackson N, Sharma M, Li H. Controlling the Expression Level of the Neuronal Reprogramming Factors for a Successful Reprogramming Outcome. Cells 2024; 13:1223. [PMID: 39056804 PMCID: PMC11274869 DOI: 10.3390/cells13141223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/16/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Neuronal reprogramming is a promising approach for making major advancement in regenerative medicine. Distinct from the approach of induced pluripotent stem cells, neuronal reprogramming converts non-neuronal cells to neurons without going through a primitive stem cell stage. In vivo neuronal reprogramming brings this approach to a higher level by changing the cell fate of glial cells to neurons in neural tissue through overexpressing reprogramming factors. Despite the ongoing debate over the validation and interpretation of newly generated neurons, in vivo neuronal reprogramming is still a feasible approach and has the potential to become clinical treatment with further optimization and refinement. Here, we discuss the major neuronal reprogramming factors (mostly pro-neurogenic transcription factors during development), especially the significance of their expression levels during neurogenesis and the reprogramming process focusing on NeuroD1. In the developing central nervous system, these pro-neurogenic transcription factors usually elicit distinct spatiotemporal expression patterns that are critical to their function in generating mature neurons. We argue that these dynamic expression patterns may be similarly needed in the process of reprogramming adult cells into neurons and further into mature neurons with subtype identities. We also summarize the existing approaches and propose new ones that control gene expression levels for a successful reprogramming outcome.
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Affiliation(s)
- Natalie Mseis-Jackson
- Department of Neuroscience & Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA;
| | - Mehek Sharma
- Department of Biological Sciences, College of Science & Mathematics, Augusta University, Augusta, GA 30912, USA;
| | - Hedong Li
- Department of Neuroscience & Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA;
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3
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Gillespie W, Zhang Y, Ruiz OE, Cerda J, Ortiz-Guzman J, Turner WD, Largoza G, Sherman M, Mosser LE, Fujimoto E, Chien CB, Kwan KM, Arenkiel BR, Devine WP, Wythe JD. Multisite Assembly of Gateway Induced Clones (MAGIC): a flexible cloning toolbox with diverse applications in vertebrate model systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.13.603267. [PMID: 39026881 PMCID: PMC11257631 DOI: 10.1101/2024.07.13.603267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Here we present the Multisite Assembly of Gateway Induced Clones (MAGIC) system, which harnesses site-specific recombination-based cloning via Gateway technology for rapid, modular assembly of between 1 and 3 "Entry" vector components, all into a fourth, standard high copy "Destination" plasmid backbone. The MAGIC toolkit spans a range of in vitro and in vivo uses, from directing tunable gene expression, to driving simultaneous expression of microRNAs and fluorescent reporters, to enabling site-specific recombinase-dependent gene expression. All MAGIC system components are directly compatible with existing multisite gateway Tol2 systems currently used in zebrafish, as well as existing eukaryotic cell culture expression Destination plasmids, and available mammalian lentiviral and adenoviral Destination vectors, allowing rapid cross-species experimentation. Moreover, herein we describe novel vectors with flanking piggyBac transposon elements for stable genomic integration in vitro or in vivo when used with piggyBac transposase. Collectively, the MAGIC system facilitates transgenesis in cultured mammalian cells, electroporated mouse and chick embryos, as well as in injected zebrafish embryos, enabling the rapid generation of innovative DNA constructs for biological research due to a shared, common plasmid platform.
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4
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Kojima L, Seiriki K, Rokujo H, Nakazawa T, Kasai A, Hashimoto H. Optimization of AAV vectors for transactivator-regulated enhanced gene expression within targeted neuronal populations. iScience 2024; 27:109878. [PMID: 38799556 PMCID: PMC11126825 DOI: 10.1016/j.isci.2024.109878] [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: 09/13/2023] [Revised: 03/03/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024] Open
Abstract
Adeno-associated virus (AAV) vectors are potential tools for cell-type-selective gene delivery to the central nervous system. Although cell-type-specific enhancers and promoters have been identified for AAV systems, there is limited information regarding the effects of AAV genomic components on the selectivity and efficiency of gene expression. Here, we offer an alternative strategy to provide specific and efficient gene delivery to a targeted neuronal population by optimizing recombinant AAV genomic components, named TAREGET (TransActivator-Regulated Enhanced Gene Expression within Targeted neuronal populations). We established this strategy in oxytocinergic neurons and showed that the TAREGET enabled sufficient gene expression to label long-projecting axons in wild-type mice. Its application to other cell types, including serotonergic and dopaminergic neurons, was also demonstrated. These results demonstrate that optimization of AAV expression cassettes can improve the specificity and efficiency of cell-type-specific gene expression and that TAREGET can renew previously established cell-type-specific promoters with improved performance.
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Affiliation(s)
- Leo Kojima
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kaoru Seiriki
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hiroki Rokujo
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Takanobu Nakazawa
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan
| | - Atsushi Kasai
- Systems Neuropharmacology, Research Institute of Environmental Medicine, Nagoya University, Nagoya 464-8601, Japan
| | - Hitoshi Hashimoto
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565-0871, Japan
- Molecular Research Center for Children’s Mental Development, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Suita, Osaka 565-0871, Japan
- Institute for Datability Science, Osaka University, Suita, Osaka 565-0871, Japan
- Department of Molecular Pharmaceutical Sciences, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
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5
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Caulier B, Joaquina S, Gelebart P, Dowling TH, Kaveh F, Thomas M, Tandaric L, Wernhoff P, Katyayini NU, Wogsland C, Gjerstad ME, Fløisand Y, Kvalheim G, Marr C, Kobold S, Enserink JM, Gjertsen BT, McCormack E, Inderberg EM, Wälchli S. CD37 is a safe chimeric antigen receptor target to treat acute myeloid leukemia. Cell Rep Med 2024; 5:101572. [PMID: 38754420 PMCID: PMC11228397 DOI: 10.1016/j.xcrm.2024.101572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/05/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024]
Abstract
Acute myeloid leukemia (AML) is characterized by the accumulation of immature myeloid cells in the bone marrow and the peripheral blood. Nearly half of the AML patients relapse after standard induction therapy, and new forms of therapy are urgently needed. Chimeric antigen receptor (CAR) T therapy has so far not been successful in AML due to lack of efficacy and safety. Indeed, the most attractive antigen targets are stem cell markers such as CD33 or CD123. We demonstrate that CD37, a mature B cell marker, is expressed in AML samples, and its presence correlates with the European LeukemiaNet (ELN) 2017 risk stratification. We repurpose the anti-lymphoma CD37CAR for the treatment of AML and show that CD37CAR T cells specifically kill AML cells, secrete proinflammatory cytokines, and control cancer progression in vivo. Importantly, CD37CAR T cells display no toxicity toward hematopoietic stem cells. Thus, CD37 is a promising and safe CAR T cell AML target.
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MESH Headings
- Humans
- Leukemia, Myeloid, Acute/therapy
- Leukemia, Myeloid, Acute/immunology
- Leukemia, Myeloid, Acute/pathology
- Receptors, Chimeric Antigen/immunology
- Receptors, Chimeric Antigen/metabolism
- Animals
- Immunotherapy, Adoptive/methods
- Mice
- Tetraspanins/immunology
- Cell Line, Tumor
- T-Lymphocytes/immunology
- Antigens, Differentiation, Myelomonocytic/metabolism
- Antigens, Differentiation, Myelomonocytic/immunology
- Female
- Male
- Antigens, Neoplasm
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Affiliation(s)
- Benjamin Caulier
- Translational Research Unit, Section for Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway; Institute for Cancer Research, Department of Molecular Cell Biology, Oslo University Hospital, Oslo, Norway; Center for Cancer Cell Reprogramming (CanCell), Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Sandy Joaquina
- Translational Research Unit, Section for Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Pascal Gelebart
- Department of Clinical Science, Precision Oncology Research Group, University of Bergen, 5021 Bergen, Norway; Centre for Cancer Biomarkers (CCBIO), University of Bergen, Bergen, Norway
| | - Tara Helén Dowling
- Department of Clinical Science, Precision Oncology Research Group, University of Bergen, 5021 Bergen, Norway; Centre for Pharmacy, Department of Clinical Science, University of Bergen, Bergen, Norway; Centre for Cancer Biomarkers (CCBIO), University of Bergen, Bergen, Norway
| | - Fatemeh Kaveh
- Translational Research Unit, Section for Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Moritz Thomas
- Institue of AI for Health, Helmholtz Munich, 85764 Neuherberg, Germany; School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Luka Tandaric
- Centre for Cancer Biomarkers (CCBIO), University of Bergen, Bergen, Norway; Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Patrik Wernhoff
- Translational Research Unit, Section for Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Niveditha Umesh Katyayini
- Institute for Cancer Research, Department of Molecular Cell Biology, Oslo University Hospital, Oslo, Norway; Center for Cancer Cell Reprogramming (CanCell), Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Cara Wogsland
- Department of Clinical Science, Precision Oncology Research Group, University of Bergen, 5021 Bergen, Norway; Centre for Cancer Biomarkers (CCBIO), University of Bergen, Bergen, Norway
| | - May Eriksen Gjerstad
- Department of Clinical Science, Precision Oncology Research Group, University of Bergen, 5021 Bergen, Norway; Centre for Cancer Biomarkers (CCBIO), University of Bergen, Bergen, Norway
| | - Yngvar Fløisand
- Institute for Cancer Research, Department of Molecular Cell Biology, Oslo University Hospital, Oslo, Norway
| | - Gunnar Kvalheim
- Translational Research Unit, Section for Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Carsten Marr
- Institue of AI for Health, Helmholtz Munich, 85764 Neuherberg, Germany
| | - Sebastian Kobold
- Division of Clinical Pharmacology, Department of Medicine IV, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany; German Center for Translational Cancer Research (DKTK), Partner Site Munich, Munich, Germany; Einheit für Klinische Pharmakologie (EKLiP), Helmholtz Zentrum München, Research Center for Environmental Health (HMGU), Neuherberg, Germany
| | - Jorrit M Enserink
- Institute for Cancer Research, Department of Molecular Cell Biology, Oslo University Hospital, Oslo, Norway; Center for Cancer Cell Reprogramming (CanCell), Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Section for Biochemistry and Molecular Biology, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Bjørn Tore Gjertsen
- Centre for Cancer Biomarkers (CCBIO), University of Bergen, Bergen, Norway; Department of Medicine, Hematology Section, Haukeland University Hospital, Bergen, Norway
| | - Emmet McCormack
- Department of Clinical Science, Precision Oncology Research Group, University of Bergen, 5021 Bergen, Norway; Centre for Pharmacy, Department of Clinical Science, University of Bergen, Bergen, Norway; Centre for Cancer Biomarkers (CCBIO), University of Bergen, Bergen, Norway
| | - Else Marit Inderberg
- Translational Research Unit, Section for Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Sébastien Wälchli
- Translational Research Unit, Section for Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway.
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6
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Li C, Yi Y, Ouyang Y, Chen F, Lu C, Peng S, Wang Y, Chen X, Yan X, Xu H, Li S, Feng L, Xie X. TORSEL, a 4EBP1-based mTORC1 live-cell sensor, reveals nutrient-sensing targeting by histone deacetylase inhibitors. Cell Biosci 2024; 14:68. [PMID: 38824577 PMCID: PMC11143692 DOI: 10.1186/s13578-024-01250-4] [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: 01/22/2024] [Accepted: 05/21/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Mammalian or mechanistic target of rapamycin complex 1 (mTORC1) is an effective therapeutic target for diseases such as cancer, diabetes, aging, and neurodegeneration. However, an efficient tool for monitoring mTORC1 inhibition in living cells or tissues is lacking. RESULTS We developed a genetically encoded mTORC1 sensor called TORSEL. This sensor changes its fluorescence pattern from diffuse to punctate when 4EBP1 dephosphorylation occurs and interacts with eIF4E. TORSEL can specifically sense the physiological, pharmacological, and genetic inhibition of mTORC1 signaling in living cells and tissues. Importantly, TORSEL is a valuable tool for imaging-based visual screening of mTORC1 inhibitors. Using TORSEL, we identified histone deacetylase inhibitors that selectively block nutrient-sensing signaling to inhibit mTORC1. CONCLUSIONS TORSEL is a unique living cell sensor that efficiently detects the inhibition of mTORC1 activity, and histone deacetylase inhibitors such as panobinostat target mTORC1 signaling through amino acid sensing.
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Affiliation(s)
- Canrong Li
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Yuguo Yi
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Yingyi Ouyang
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Fengzhi Chen
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Chuxin Lu
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Shujun Peng
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Yifan Wang
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Xinyu Chen
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Xiao Yan
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Haolun Xu
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Shuiming Li
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, China
| | - Lin Feng
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiaoduo Xie
- School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
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7
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Chen D, Fan X, Wang K, Gong L, Melero-Martin JM, Pu WT. Pioneer factor ETV2 safeguards endothelial cell specification by recruiting the repressor REST to restrict alternative lineage commitment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.595971. [PMID: 38853821 PMCID: PMC11160620 DOI: 10.1101/2024.05.28.595971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Mechanisms of cell fate specification remain a central question for developmental biology and regenerative medicine. The pioneer factor ETV2 is a master regulator for the endothelial cell (EC) lineage specification. Here, we studied mechanisms of ETV2-driven fate specification using a highly efficient system in which ETV2 directs human induced pluripotent stem cell-derived mesodermal progenitors to form ECs over two days. By applying CUT&RUN, single-cell RNA-sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) analyses, we characterized the transcriptomic profiles, chromatin landscapes, dynamic cis-regulatory elements (CREs), and molecular features of EC cell differentiation mediated by ETV2. This defined the scope of ETV2 pioneering activity and identified its direct downstream target genes. Induced ETV2 expression both directed specification of endothelial progenitors and suppressed acquisition of alternative fates. Functional screening and candidate validation revealed cofactors essential for efficient EC specification, including the transcriptional activator GABPA. Surprisingly, the transcriptional repressor REST was also necessary for efficient EC specification. ETV2 recruited REST to occupy and repress non-EC lineage genes. Collectively, our study provides an unparalleled molecular analysis of EC specification at single-cell resolution and identifies the important role of pioneer factors to recruit repressors that suppress commitment to alternative lineages.
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8
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Saldana-Guerrero IM, Montano-Gutierrez LF, Boswell K, Hafemeister C, Poon E, Shaw LE, Stavish D, Lea RA, Wernig-Zorc S, Bozsaky E, Fetahu IS, Zoescher P, Pötschger U, Bernkopf M, Wenninger-Weinzierl A, Sturtzel C, Souilhol C, Tarelli S, Shoeb MR, Bozatzi P, Rados M, Guarini M, Buri MC, Weninger W, Putz EM, Huang M, Ladenstein R, Andrews PW, Barbaric I, Cresswell GD, Bryant HE, Distel M, Chesler L, Taschner-Mandl S, Farlik M, Tsakiridis A, Halbritter F. A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations. Nat Commun 2024; 15:3745. [PMID: 38702304 PMCID: PMC11068915 DOI: 10.1038/s41467-024-47945-7] [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: 01/06/2023] [Accepted: 04/15/2024] [Indexed: 05/06/2024] Open
Abstract
Early childhood tumours arise from transformed embryonic cells, which often carry large copy number alterations (CNA). However, it remains unclear how CNAs contribute to embryonic tumourigenesis due to a lack of suitable models. Here we employ female human embryonic stem cell (hESC) differentiation and single-cell transcriptome and epigenome analysis to assess the effects of chromosome 17q/1q gains, which are prevalent in the embryonal tumour neuroblastoma (NB). We show that CNAs impair the specification of trunk neural crest (NC) cells and their sympathoadrenal derivatives, the putative cells-of-origin of NB. This effect is exacerbated upon overexpression of MYCN, whose amplification co-occurs with CNAs in NB. Moreover, CNAs potentiate the pro-tumourigenic effects of MYCN and mutant NC cells resemble NB cells in tumours. These changes correlate with a stepwise aberration of developmental transcription factor networks. Together, our results sketch a mechanistic framework for the CNA-driven initiation of embryonal tumours.
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Affiliation(s)
- Ingrid M Saldana-Guerrero
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
- Sheffield Institute for Nucleic Acids (SInFoNiA), School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | | | - Katy Boswell
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | | | - Evon Poon
- Division of Clinical Studies, The Institute of Cancer Research (ICR) & Royal Marsden NHS Trust, London, UK
| | - Lisa E Shaw
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Dylan Stavish
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Rebecca A Lea
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Sara Wernig-Zorc
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Eva Bozsaky
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Irfete S Fetahu
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Medical University of Vienna, Department of Neurology, Division of Neuropathology and Neurochemistry, Vienna, Austria
| | - Peter Zoescher
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Ulrike Pötschger
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Marie Bernkopf
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia Labordiagnostik GmbH, Vienna, Austria
| | | | - Caterina Sturtzel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Celine Souilhol
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
- Biomolecular Sciences Research Centre, Department of Biosciences and Chemistry, Sheffield Hallam University, Sheffield, UK
| | - Sophia Tarelli
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Mohamed R Shoeb
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Polyxeni Bozatzi
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Magdalena Rados
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Maria Guarini
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Michelle C Buri
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Wolfgang Weninger
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Eva M Putz
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Miller Huang
- Children's Hospital Los Angeles, Cancer and Blood Disease Institutes, and The Saban Research Institute, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ruth Ladenstein
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Peter W Andrews
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
| | - Ivana Barbaric
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | | | - Helen E Bryant
- Sheffield Institute for Nucleic Acids (SInFoNiA), School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Martin Distel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Louis Chesler
- Division of Clinical Studies, The Institute of Cancer Research (ICR) & Royal Marsden NHS Trust, London, UK
| | | | - Matthias Farlik
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Anestis Tsakiridis
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK.
- Neuroscience Institute, The University of Sheffield, Sheffield, UK.
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9
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De Carluccio G, Fusco V, di Bernardo D. Engineering a synthetic gene circuit for high-performance inducible expression in mammalian systems. Nat Commun 2024; 15:3311. [PMID: 38632224 PMCID: PMC11024104 DOI: 10.1038/s41467-024-47592-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
Inducible gene expression systems can be used to control the expression of a gene of interest by means of a small-molecule. One of the most common designs involves engineering a small-molecule responsive transcription factor (TF) and its cognate promoter, which often results in a compromise between minimal uninduced background expression (leakiness) and maximal induced expression. Here, we focus on an alternative strategy using quantitative synthetic biology to mitigate leakiness while maintaining high expression, without modifying neither the TF nor the promoter. Through mathematical modelling and experimental validations, we design the CASwitch, a mammalian synthetic gene circuit based on combining two well-known network motifs: the Coherent Feed-Forward Loop (CFFL) and the Mutual Inhibition (MI). The CASwitch combines the CRISPR-Cas endoribonuclease CasRx with the state-of-the-art Tet-On3G inducible gene system to achieve high performances. To demonstrate the potentialities of the CASwitch, we apply it to three different scenarios: enhancing a whole-cell biosensor, controlling expression of a toxic gene and inducible production of Adeno-Associated Virus (AAV) vectors.
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Affiliation(s)
- Giuliano De Carluccio
- Telethon Institute of Genetics and Medicine, Naples, Italy
- University of Naples Federico II, Department of Chemical Materials and Industrial Engineering, Naples, Italy
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
| | - Virginia Fusco
- Telethon Institute of Genetics and Medicine, Naples, Italy
- University of Naples Federico II, Department of Chemical Materials and Industrial Engineering, Naples, Italy
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine, Naples, Italy.
- University of Naples Federico II, Department of Chemical Materials and Industrial Engineering, Naples, Italy.
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10
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Casey NP, Kleinmanns K, Forcados C, Gelebart PF, Joaquina S, Lode M, Benard E, Kaveh F, Caulier B, Helgestad Gjerde C, García de Jalón E, Warren DJ, Lindemann K, Rokkones E, Davidson B, Myhre MR, Kvalheim G, Bjørge L, McCormack E, Inderberg EM, Wälchli S. Efficient CAR T cell targeting of the CA125 extracellular repeat domain of MUC16. J Immunother Cancer 2024; 12:e008179. [PMID: 38604812 PMCID: PMC11015285 DOI: 10.1136/jitc-2023-008179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2024] [Indexed: 04/13/2024] Open
Abstract
BACKGROUND Ovarian cancer (OC) is the leading cause of death from gynecologic malignancies in the Western world. Contributing factors include a high frequency of late-stage diagnosis, the development of chemoresistance, and the evasion of host immune responses. Currently, debulking surgery and platinum-based chemotherapy are the treatment cornerstones, although recurrence is common. As the clinical efficacy of immune checkpoint blockade is low, new immunotherapeutic strategies are needed. Chimeric antigen receptor (CAR) T cell therapy empowers patients' own T cells to fight and eradicate cancer, and has been tested against various targets in OC. A promising candidate is the MUC16 ectodomain. This ectodomain remains on the cell surface after cleavage of cancer antigen 125 (CA125), the domain distal from the membrane, which is currently used as a serum biomarker for OC. CA125 itself has not been tested as a possible CAR target. In this study, we examined the suitability of the CA125 as a target for CAR T cell therapy. METHODS We tested a series of antibodies raised against the CA125 extracellular repeat domain of MUC16 and adapted them to the CAR format. Comparisons between these candidates, and against an existing CAR targeting the MUC16 ectodomain, identified K101 as having high potency and specificity. The K101CAR was subjected to further biochemical and functional tests, including examination of the effect of soluble CA125 on its activity. Finally, we used cell lines and advanced orthotopic patient-derived xenograft (PDX) models to validate, in vivo, the efficiency of our K101CAR construct. RESULTS We observed a high efficacy of K101CAR T cells against cell lines and patient-derived tumors, in vitro and in vivo. We also demonstrated that K101CAR functionality was not impaired by the soluble antigen. Finally, in direct comparisons, K101CAR, which targets the CA125 extracellular repeat domains, was shown to have similar efficacy to the previously validated 4H11CAR, which targets the MUC16 ectodomain. CONCLUSIONS Our in vitro and in vivo results, including PDX studies, demonstrate that the CA125 domain of MUC16 represents an excellent target for treating MUC16-positive malignancies.
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Affiliation(s)
- Nicholas P Casey
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Katrin Kleinmanns
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Christopher Forcados
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Pascal F Gelebart
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Sandy Joaquina
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Martine Lode
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Emmanuelle Benard
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Fatemeh Kaveh
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Benjamin Caulier
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Center for Cancer Cell Reprogramming (CanCell), Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Christiane Helgestad Gjerde
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Elvira García de Jalón
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - David J Warren
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Kristina Lindemann
- Department of Gynecologic Oncology, Oslo University Hospital, Oslo, Norway
- Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Erik Rokkones
- Department of Gynecologic Oncology, Oslo University Hospital, Oslo, Norway
| | - Ben Davidson
- Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Pathology, Division of Laboratory Medicine, Oslo University Hospital, Oslo, Norway
| | - Marit Renee Myhre
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Gunnar Kvalheim
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Line Bjørge
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Emmet McCormack
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
- Centre for Pharmacy, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Bergen, Norway
| | - Else Marit Inderberg
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Sébastien Wälchli
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
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Shepherdson JL, Granas DM, Li J, Shariff Z, Plassmeyer SP, Holehouse AS, White MA, Cohen BA. Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.585809. [PMID: 38585983 PMCID: PMC10996540 DOI: 10.1101/2024.03.21.585809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Cone-Rod Homeobox, encoded by CRX, is a transcription factor (TF) essential for the terminal differentiation and maintenance of mammalian photoreceptors. Structurally, CRX comprises an ordered DNA-binding homeodomain and an intrinsically disordered transcriptional effector domain. Although a handful of human variants in CRX have been shown to cause several different degenerative retinopathies with varying cone and rod predominance, as with most human disease genes the vast majority of observed CRX genetic variants are uncharacterized variants of uncertain significance (VUS). We performed a deep mutational scan (DMS) of nearly all possible single amino acid substitution variants in CRX, using an engineered cell-based transcriptional reporter assay. We measured the ability of each CRX missense variant to transactivate a synthetic fluorescent reporter construct in a pooled fluorescence-activated cell sorting assay and compared the activation strength of each variant to that of wild-type CRX to compute an activity score, identifying thousands of variants with altered transcriptional activity. We calculated a statistical confidence for each activity score derived from multiple independent measurements of each variant marked by unique sequence barcodes, curating a high-confidence list of nearly 2,000 variants with significantly altered transcriptional activity compared to wild-type CRX. We evaluated the performance of the DMS assay as a clinical variant classification tool using gold-standard classified human variants from ClinVar, and determined that activity scores could be used to identify pathogenic variants with high specificity. That this performance could be achieved using a synthetic reporter assay in a foreign cell type, even for a highly cell type-specific TF like CRX, suggests that this approach shows promise for DMS of other TFs that function in cell types that are not easily accessible. Per-position average activity scores closely aligned to a predicted structure of the ordered homeodomain and demonstrated position-specific residue requirements. The intrinsically disordered transcriptional effector domain, by contrast, displayed a qualitatively different pattern of substitution effects, following compositional constraints without specific residue position requirements in the peptide chain. The observed compositional constraints of the effector domain were consistent with the acidic exposure model of transcriptional activation. Together, the results of the CRX DMS identify molecular features of the CRX effector domain and demonstrate clinical utility for variant classification.
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Affiliation(s)
- James L. Shepherdson
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - David M. Granas
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Jie Li
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Zara Shariff
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Stephen P. Plassmeyer
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Center for Biomolecular Condensates, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Center for Biomolecular Condensates, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Michael A. White
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Barak A. Cohen
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
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12
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Zhang A, Jin L, Yao S, Matsuyama M, van Velthoven CTJ, Sullivan HA, Sun N, Kellis M, Tasic B, Wickersham I, Chen X. Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing. eLife 2024; 12:RP87866. [PMID: 38319699 PMCID: PMC10942611 DOI: 10.7554/elife.87866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Abstract
Mapping the connectivity of diverse neuronal types provides the foundation for understanding the structure and function of neural circuits. High-throughput and low-cost neuroanatomical techniques based on RNA barcode sequencing have the potential to map circuits at cellular resolution and a brain-wide scale, but existing Sindbis virus-based techniques can only map long-range projections using anterograde tracing approaches. Rabies virus can complement anterograde tracing approaches by enabling either retrograde labeling of projection neurons or monosynaptic tracing of direct inputs to genetically targeted postsynaptic neurons. However, barcoded rabies virus has so far been only used to map non-neuronal cellular interactions in vivo and synaptic connectivity of cultured neurons. Here we combine barcoded rabies virus with single-cell and in situ sequencing to perform retrograde labeling and transsynaptic labeling in the mouse brain. We sequenced 96 retrogradely labeled cells and 295 transsynaptically labeled cells using single-cell RNA-seq, and 4130 retrogradely labeled cells and 2914 transsynaptically labeled cells in situ. We found that the transcriptomic identities of rabies virus-infected cells can be robustly identified using both single-cell RNA-seq and in situ sequencing. By associating gene expression with connectivity inferred from barcode sequencing, we distinguished long-range projecting cortical cell types from multiple cortical areas and identified cell types with converging or diverging synaptic connectivity. Combining in situ sequencing with barcoded rabies virus complements existing sequencing-based neuroanatomical techniques and provides a potential path for mapping synaptic connectivity of neuronal types at scale.
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Affiliation(s)
- Aixin Zhang
- Allen Institute for Brain ScienceSeattleUnited States
| | - Lei Jin
- McGovern Institute for Brain Research, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Shenqin Yao
- Allen Institute for Brain ScienceSeattleUnited States
| | - Makoto Matsuyama
- McGovern Institute for Brain Research, Massachusetts Institute of TechnologyCambridgeUnited States
| | | | - Heather Anne Sullivan
- McGovern Institute for Brain Research, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Na Sun
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Broad Institute of MIT and HarvardCambridgeUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Manolis Kellis
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Broad Institute of MIT and HarvardCambridgeUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
| | | | - Ian Wickersham
- McGovern Institute for Brain Research, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Xiaoyin Chen
- Allen Institute for Brain ScienceSeattleUnited States
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13
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Noviello G, Gjaltema RAF. Fine-Tuning the Epigenetic Landscape: Chemical Modulation of Epigenome Editors. Methods Mol Biol 2024; 2842:57-77. [PMID: 39012590 DOI: 10.1007/978-1-0716-4051-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Epigenome editing has emerged as a powerful technique for targeted manipulation of the chromatin and transcriptional landscape, employing designer DNA binding domains fused with effector domains, known as epi-editors. However, the constitutive expression of dCas9-based epi-editors presents challenges, including off-target activity and lack of temporal resolution. Recent advancements of dCas9-based epi-editors have addressed these limitations by introducing innovative switch systems that enable temporal control of their activity. These systems allow precise modulation of gene expression over time and offer a means to deactivate epi-editors, thereby reducing off-target effects associated with prolonged expression. The development of novel dCas9 effectors regulated by exogenous chemical signals has revolutionized temporal control in epigenome editing, significantly expanding the researcher's toolbox. Here, we provide a comprehensive review of the current state of these cutting-edge systems and specifically discuss their advantages and limitations, offering context to better understand their capabilities.
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Affiliation(s)
- Gemma Noviello
- Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory (EMBL), Rome, Italy
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Rutger A F Gjaltema
- Molecular & Cellular Epigenetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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14
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Zboray K, Toth AV, Miskolczi TD, Pesti K, Casanova E, Kreidl E, Mike A, Szenes Á, Sági L, Lukacs P. High-throughput ligand profile characterization in novel cell lines expressing seven heterologous insect olfactory receptors for the detection of volatile plant biomarkers. Sci Rep 2023; 13:21757. [PMID: 38066004 PMCID: PMC10709440 DOI: 10.1038/s41598-023-47455-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 11/14/2023] [Indexed: 12/18/2023] Open
Abstract
Agriculturally important crop plants emit a multitude of volatile organic compounds (VOCs), which are excellent indicators of their health status and their interactions with pathogens and pests. In this study, we have developed a novel cellular olfactory panel for detecting fungal pathogen-related VOCs we had identified in the field, as well as during controlled inoculations of several crop plants. The olfactory panel consists of seven stable HEK293 cell lines each expressing a functional Drosophila olfactory receptor as a biosensing element along with GCaMP6, a fluorescent calcium indicator protein. An automated 384-well microplate reader was used to characterize the olfactory receptor cell lines for their sensitivity to reference VOCs. Subsequently, we profiled a set of 66 VOCs on all cell lines, covering a concentration range from 1 to 100 μM. Results showed that 49 VOCs (74.2%) elicited a response in at least one olfactory receptor cell line. Some VOCs activated the cell lines even at nanomolar (ppb) concentrations. The interaction profiles obtained here will support the development of biosensors for agricultural applications. Additionally, the olfactory receptor proteins can be purified from these cell lines with sufficient yields for further processing, such as structure determination or integration with sensor devices.
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Affiliation(s)
- Katalin Zboray
- Plant Protection Institute, Centre for Agricultural Research, Martonvásár, Hungary
- TetraLab Ltd., Budapest, Hungary
| | - Adam V Toth
- Plant Protection Institute, Centre for Agricultural Research, Martonvásár, Hungary
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Tímea D Miskolczi
- Plant Protection Institute, Centre for Agricultural Research, Martonvásár, Hungary
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Krisztina Pesti
- TetraLab Ltd., Budapest, Hungary
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Emilio Casanova
- Department of Pharmacology, Center of Physiology and Pharmacology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Emanuel Kreidl
- Department of Pharmacology, Center of Physiology and Pharmacology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Novartis AG, 6336, Langkampfen, Austria
| | - Arpad Mike
- Plant Protection Institute, Centre for Agricultural Research, Martonvásár, Hungary
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Áron Szenes
- Department of Pathology, University of Veterinary Medicine, Budapest, Hungary
| | - László Sági
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Peter Lukacs
- Plant Protection Institute, Centre for Agricultural Research, Martonvásár, Hungary.
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary.
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15
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Mukai Y, Okubo TS, Lazarus M, Ono D, Tanaka KF, Yamanaka A. Prostaglandin E 2 Induces Long-Lasting Inhibition of Noradrenergic Neurons in the Locus Coeruleus and Moderates the Behavioral Response to Stressors. J Neurosci 2023; 43:7982-7999. [PMID: 37734949 PMCID: PMC10669809 DOI: 10.1523/jneurosci.0353-23.2023] [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: 02/26/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 09/23/2023] Open
Abstract
Neuronal activity is modulated not only by inputs from other neurons but also by various factors, such as bioactive substances. Noradrenergic (NA) neurons in the locus coeruleus (LC-NA neurons) are involved in diverse physiological functions, including sleep/wakefulness and stress responses. Previous studies have identified various substances and receptors that modulate LC-NA neuronal activity through techniques including electrophysiology, calcium imaging, and single-cell RNA sequencing. However, many substances with unknown physiological significance have been overlooked. Here, we established an efficient screening method for identifying substances that modulate LC-NA neuronal activity through intracellular calcium ([Ca2+]i) imaging using brain slices. Using both sexes of mice, we screened 53 bioactive substances, and identified five novel substances: gastrin-releasing peptide, neuromedin U, and angiotensin II, which increase [Ca2+]i, and pancreatic polypeptide and prostaglandin D2, which decrease [Ca2+]i Among them, neuromedin U induced the greatest response in female mice. In terms of the duration of [Ca2+]i change, we focused on prostaglandin E2 (PGE2), since it induces a long-lasting decrease in [Ca2+]i via the EP3 receptor. Conditional knock-out of the receptor in LC-NA neurons resulted in increased depression-like behavior, prolonged wakefulness in the dark period, and increased [Ca2+]i after stress exposure. Our results demonstrate the effectiveness of our screening method for identifying substances that modulate a specific neuronal population in an unbiased manner and suggest that stress-induced prostaglandin E2 can suppress LC-NA neuronal activity to moderate the behavioral response to stressors. Our screening method will contribute to uncovering previously unknown physiological functions of uncharacterized bioactive substances in specific neuronal populations.SIGNIFICANCE STATEMENT Bioactive substances modulate the activity of specific neuronal populations. However, since only a limited number of substances with predicted effects have been investigated, many substances that may modulate neuronal activity have gone unrecognized. Here, we established an unbiased method for identifying modulatory substances by measuring the intracellular calcium signal, which reflects neuronal activity. We examined noradrenergic (NA) neurons in the locus coeruleus (LC-NA neurons), which are involved in diverse physiological functions. We identified five novel substances that modulate LC-NA neuronal activity. We also found that stress-induced prostaglandin E2 (PGE2) may suppress LC-NA neuronal activity and influence behavioral outcomes. Our screening method will help uncover previously overlooked functions of bioactive substances and provide insight into unrecognized roles of specific neuronal populations.
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Affiliation(s)
- Yasutaka Mukai
- Department of Neuroscience II, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Aichi 464-8601, Japan
- Department of Neural Regulation, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Tatsuo S Okubo
- Chinese Institute for Brain Research, Beijing 102206, China
| | - Michael Lazarus
- International Institute for Integrative Sleep Medicine (WPI-IIIS) and Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Daisuke Ono
- Department of Neuroscience II, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Aichi 464-8601, Japan
- Department of Neural Regulation, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Kenji F Tanaka
- Division of Brain Sciences, Institute for Advanced Medical Research, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Akihiro Yamanaka
- Department of Neuroscience II, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Aichi 464-8601, Japan
- Department of Neural Regulation, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
- Chinese Institute for Brain Research, Beijing 102206, China
- Division of Brain Sciences, Institute for Advanced Medical Research, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan
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16
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Jin Z, Lakshmanan A, Zhang R, Tran TA, Rabut C, Dutka P, Duan M, Hurt RC, Malounda D, Yao Y, Shapiro MG. Ultrasonic reporters of calcium for deep tissue imaging of cellular signals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566364. [PMID: 37986929 PMCID: PMC10659314 DOI: 10.1101/2023.11.09.566364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Calcium imaging has enabled major biological discoveries. However, the scattering of light by tissue limits the use of standard fluorescent calcium indicators in living animals. To address this limitation, we introduce the first genetically encoded ultrasonic reporter of calcium (URoC). Based on a unique class of air-filled protein nanostructures called gas vesicles, we engineered URoC to produce elevated nonlinear ultrasound signal upon binding to calcium ions. With URoC expressed in mammalian cells, we demonstrate noninvasive ultrasound imaging of calcium signaling in vivo during drug-induced receptor activation. URoC brings the depth and resolution advantages of ultrasound to the in vivo imaging of dynamic cellular function and paves the way for acoustic biosensing of a broader variety of biological signals.
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17
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Zhang A, Jin L, Yao S, Matsuyama M, van Velthoven C, Sullivan H, Sun N, Kellis M, Tasic B, Wickersham IR, Chen X. Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.532873. [PMID: 36993334 PMCID: PMC10055146 DOI: 10.1101/2023.03.16.532873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Mapping the connectivity of diverse neuronal types provides the foundation for understanding the structure and function of neural circuits. High-throughput and low-cost neuroanatomical techniques based on RNA barcode sequencing have the potential to map circuits at cellular resolution and a brain-wide scale, but existing Sindbis virus-based techniques can only map long-range projections using anterograde tracing approaches. Rabies virus can complement anterograde tracing approaches by enabling either retrograde labeling of projection neurons or monosynaptic tracing of direct inputs to genetically targeted postsynaptic neurons. However, barcoded rabies virus has so far been only used to map non-neuronal cellular interactions in vivo and synaptic connectivity of cultured neurons. Here we combine barcoded rabies virus with single-cell and in situ sequencing to perform retrograde labeling and transsynaptic labeling in the mouse brain. We sequenced 96 retrogradely labeled cells and 295 transsynaptically labeled cells using single-cell RNA-seq, and 4,130 retrogradely labeled cells and 2,914 transsynaptically labeled cells in situ. We found that the transcriptomic identities of rabies virus-infected cells can be robustly identified using both single-cell RNA-seq and in situ sequencing. By associating gene expression with connectivity inferred from barcode sequencing, we distinguished long-range projecting cortical cell types from multiple cortical areas and identified cell types with converging or diverging synaptic connectivity. Combining in situ sequencing with barcoded rabies virus complements existing sequencing-based neuroanatomical techniques and provides a potential path for mapping synaptic connectivity of neuronal types at scale.
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Affiliation(s)
- Aixin Zhang
- Allen Institute for Brain Science, Seattle, WA
| | - Lei Jin
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA
- Current address: Lingang Laboratory, Shanghai, China
| | - Shenqin Yao
- Allen Institute for Brain Science, Seattle, WA
| | - Makoto Matsuyama
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA
- Current address: Metcela Inc., Kawasaki, Kanagawa, Japan
| | | | - Heather Sullivan
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA
| | - Na Sun
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Manolis Kellis
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Ian R. Wickersham
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA
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18
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Matsuyama M, Ortega JT, Fedorov Y, Scott-McKean J, Muller-Greven J, Buck M, Adams D, Jastrzebska B, Greenlee W, Matsuyama S. Development of novel cytoprotective small compounds inhibiting mitochondria-dependent cell death. iScience 2023; 26:107916. [PMID: 37841588 PMCID: PMC10568349 DOI: 10.1016/j.isci.2023.107916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/27/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
We identified cytoprotective small molecules (CSMs) by a cell-based high-throughput screening of Bax inhibitors. Through a medicinal chemistry program, M109S was developed, which is orally bioactive and penetrates the blood-brain/retina barriers. M109S protected retinal cells in ocular disease mouse models. M109S directly interacted with Bax and inhibited the conformational change and mitochondrial translocation of Bax. M109S inhibited ABT-737-induced apoptosis both in Bax-only and Bak-only mouse embryonic fibroblasts. M109S also inhibited apoptosis induced by staurosporine, etoposide, and obatoclax. M109S decreased maximal mitochondrial oxygen consumption rate and reactive oxygen species production, whereas it increased glycolysis. These effects on cellular metabolism may contribute to the cytoprotective activity of M109S. M109S is a novel small molecule protecting cells from mitochondria-dependent apoptosis both in vitro and in vivo. M109S has the potential to become a research tool for studying cell death mechanisms and to develop therapeutics targeting mitochondria-dependent cell death pathway.
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Affiliation(s)
- Mieko Matsuyama
- Department of Ophthalmology and Visual Science, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Joseph T. Ortega
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Yuri Fedorov
- Department of Genetics and Genome Science, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jonah Scott-McKean
- Department of Ophthalmology and Visual Science, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Macromolecular Science and Engineering, School of Engineering, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jeannie Muller-Greven
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Matthias Buck
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Drew Adams
- Department of Genetics and Genome Science, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Beata Jastrzebska
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | - Shigemi Matsuyama
- Department of Ophthalmology and Visual Science, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
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19
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Legnini I, Emmenegger L, Zappulo A, Rybak-Wolf A, Wurmus R, Martinez AO, Jara CC, Boltengagen A, Hessler T, Mastrobuoni G, Kempa S, Zinzen R, Woehler A, Rajewsky N. Spatiotemporal, optogenetic control of gene expression in organoids. Nat Methods 2023; 20:1544-1552. [PMID: 37735569 PMCID: PMC10555836 DOI: 10.1038/s41592-023-01986-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/25/2023] [Indexed: 09/23/2023]
Abstract
Organoids derived from stem cells have become an increasingly important tool for studying human development and modeling disease. However, methods are still needed to control and study spatiotemporal patterns of gene expression in organoids. Here we combined optogenetics and gene perturbation technologies to activate or knock-down RNA of target genes in programmable spatiotemporal patterns. To illustrate the usefulness of our approach, we locally activated Sonic Hedgehog (SHH) signaling in an organoid model for human neurodevelopment. Spatial and single-cell transcriptomic analyses showed that this local induction was sufficient to generate stereotypically patterned organoids and revealed new insights into SHH's contribution to gene regulation in neurodevelopment. With this study, we propose optogenetic perturbations in combination with spatial transcriptomics as a powerful technology to reprogram and study cell fates and tissue patterning in organoids.
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Affiliation(s)
- Ivano Legnini
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.
- Human Technopole, Milan, Italy.
| | - Lisa Emmenegger
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Alessandra Zappulo
- Systems Biology of Neural Tissue Differentiation, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
- Human Technopole, Milan, Italy
| | - Agnieszka Rybak-Wolf
- Organoid Platform, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Ricardo Wurmus
- Bioinformatics and Omics Data Science, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Anna Oliveras Martinez
- Systems Biology Imaging Platform, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Cledi Cerda Jara
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Anastasiya Boltengagen
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Talé Hessler
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Guido Mastrobuoni
- Proteomic and Metabolomics Platform, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Stefan Kempa
- Proteomic and Metabolomics Platform, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Robert Zinzen
- Systems Biology of Neural Tissue Differentiation, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
- Systems Biology Imaging Platform, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Andrew Woehler
- Systems Biology Imaging Platform, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA
| | - Nikolaus Rajewsky
- Laboratory for Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.
- Charité-Universitätsmedizin, Berlin, Germany.
- German Center for Cardiovascular Research (DZHK), Berlin, Germany.
- NeuroCure Cluster of Excellence, Berlin, Germany.
- National Center for Tumor Diseases (NCT), German Cancer Consortium (DKTK), Berlin, Germany.
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20
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Burke CT, Vitko I, Straub J, Nylund EO, Gawda A, Blair K, Sullivan KA, Ergun L, Ottolini M, Patel MK, Perez-Reyes E. EpiPro, a Novel, Synthetic, Activity-Regulated Promoter That Targets Hyperactive Neurons in Epilepsy for Gene Therapy Applications. Int J Mol Sci 2023; 24:14467. [PMID: 37833914 PMCID: PMC10572392 DOI: 10.3390/ijms241914467] [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: 08/17/2023] [Revised: 09/16/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Epileptogenesis is characterized by intrinsic changes in neuronal firing, resulting in hyperactive neurons and the subsequent generation of seizure activity. These alterations are accompanied by changes in gene transcription networks, first with the activation of early-immediate genes and later with the long-term activation of genes involved in memory. Our objective was to engineer a promoter containing binding sites for activity-dependent transcription factors upregulated in chronic epilepsy (EpiPro) and validate it in multiple rodent models of epilepsy. First, we assessed the activity dependence of EpiPro: initial electrophysiology studies found that EpiPro-driven GFP expression was associated with increased firing rates when compared with unlabeled neurons, and the assessment of EpiPro-driven GFP expression revealed that GFP expression was increased ~150× after status epilepticus. Following this, we compared EpiPro-driven GFP expression in two rodent models of epilepsy, rat lithium/pilocarpine and mouse electrical kindling. In rodents with chronic epilepsy, GFP expression was increased in most neurons, but particularly in dentate granule cells, providing in vivo evidence to support the "breakdown of the dentate gate" hypothesis of limbic epileptogenesis. Finally, we assessed the time course of EpiPro activation and found that it was rapidly induced after seizures, with inactivation following over weeks, confirming EpiPro's potential utility as a gene therapy driver for epilepsy.
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Affiliation(s)
- Cassidy T. Burke
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA
| | - Iuliia Vitko
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA
| | - Justyna Straub
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA
| | - Elsa O. Nylund
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA
| | - Agnieszka Gawda
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA
| | - Kathryn Blair
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA
| | - Kyle A. Sullivan
- Computational and Predictive Biology, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Lara Ergun
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA
| | - Matteo Ottolini
- Department of Anesthesiology, University of Virginia, Charlottesville, VA 22908, USA (M.K.P.)
| | - Manoj K. Patel
- Department of Anesthesiology, University of Virginia, Charlottesville, VA 22908, USA (M.K.P.)
- UVA Brain Institute, University of Virginia, Charlottesville, VA 22908, USA
| | - Edward Perez-Reyes
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22908, USA
- UVA Brain Institute, University of Virginia, Charlottesville, VA 22908, USA
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21
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Klee CH, Villatoro A, Casey NP, Inderberg EM, Wälchli S. In vitro re-challenge of CAR T cells. Methods Cell Biol 2023; 183:335-353. [PMID: 38548418 DOI: 10.1016/bs.mcb.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Chimeric antigen receptor (CAR) T cells (CAR T) have emerged as a potential therapy for cancer patients. CAR T cells are capable of recognizing membrane proteins on cancer cells which initiates a downstream signaling in T cells that ends in cancer cell death. Continuous antigen exposure over time, activation of inhibitory signaling pathways and/or chronic inflammation can lead to CAR T cell exhaustion. In this context, the design of CARs can have a great impact on the functionality of CAR T cells, on their potency and exhaustion. Here, using CD19CAR as model, we provide a re-challenge protocol where CAR T cells are cultured weekly with malignant lymphoid cell lines BL-41 and Nalm-6 to simulate them with continuous antigen pressure over a four-week period. This protocol can be value for assessing CAR T cell functionality and for the comparison of different CAR constructs.
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Affiliation(s)
- Clara Helena Klee
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Alicia Villatoro
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Nicholas Paul Casey
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Else Marit Inderberg
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Sébastien Wälchli
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway.
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22
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Shimizu N, Shiraishi H, Hanada T. Zebrafish as a Useful Model System for Human Liver Disease. Cells 2023; 12:2246. [PMID: 37759472 PMCID: PMC10526867 DOI: 10.3390/cells12182246] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/31/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Liver diseases represent a significant global health challenge, thereby necessitating extensive research to understand their intricate complexities and to develop effective treatments. In this context, zebrafish (Danio rerio) have emerged as a valuable model organism for studying various aspects of liver disease. The zebrafish liver has striking similarities to the human liver in terms of structure, function, and regenerative capacity. Researchers have successfully induced liver damage in zebrafish using chemical toxins, genetic manipulation, and other methods, thereby allowing the study of disease mechanisms and the progression of liver disease. Zebrafish embryos or larvae, with their transparency and rapid development, provide a unique opportunity for high-throughput drug screening and the identification of potential therapeutics. This review highlights how research on zebrafish has provided valuable insights into the pathological mechanisms of human liver disease.
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Affiliation(s)
- Nobuyuki Shimizu
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu 879-5593, Oita, Japan;
| | | | - Toshikatsu Hanada
- Department of Cell Biology, Oita University Faculty of Medicine, Yufu 879-5593, Oita, Japan;
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23
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Sullivan KA, Vitko I, Blair K, Gaykema RP, Failor MJ, San Pietro JM, Dey D, Williamson JM, Stornetta RL, Kapur J, Perez-Reyes E. Drug-Inducible Gene Therapy Effectively Reduces Spontaneous Seizures in Kindled Rats but Creates Off-Target Side Effects in Inhibitory Neurons. Int J Mol Sci 2023; 24:11347. [PMID: 37511107 PMCID: PMC10379297 DOI: 10.3390/ijms241411347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/05/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Over a third of patients with temporal lobe epilepsy (TLE) are not effectively treated with current anti-seizure drugs, spurring the development of gene therapies. The injection of adeno-associated viral vectors (AAV) into the brain has been shown to be a safe and viable approach. However, to date, AAV expression of therapeutic genes has not been regulated. Moreover, a common property of antiepileptic drugs is a narrow therapeutic window between seizure control and side effects. Therefore, a long-term goal is to develop drug-inducible gene therapies that can be regulated by clinically relevant drugs. In this study, a first-generation doxycycline-regulated gene therapy that delivered an engineered version of the leak potassium channel Kcnk2 (TREK-M) was injected into the hippocampus of male rats. Rats were electrically stimulated until kindled. EEG was monitored 24/7. Electrical kindling revealed an important side effect, as even low expression of TREK M in the absence of doxycycline was sufficient to cause rats to develop spontaneous recurring seizures. Treating the epileptic rats with doxycycline successfully reduced spontaneous seizures. Localization studies of infected neurons suggest seizures were caused by expression in GABAergic inhibitory neurons. In contrast, doxycycline increased the expression of TREK-M in excitatory neurons, thereby reducing seizures through net inhibition of firing. These studies demonstrate that drug-inducible gene therapies are effective in reducing spontaneous seizures and highlight the importance of testing for side effects with pro-epileptic stressors such as electrical kindling. These studies also show the importance of evaluating the location and spread of AAV-based gene therapies in preclinical studies.
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Affiliation(s)
- Kyle A Sullivan
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22980, USA
- Computational and Predictive Biology, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Iuliia Vitko
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22980, USA
| | - Kathryn Blair
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22980, USA
| | - Ronald P Gaykema
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22980, USA
| | - Madison J Failor
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22980, USA
| | | | - Deblina Dey
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22980, USA
| | - John M Williamson
- Department of Neurology, University of Virginia, Charlottesville, VA 22980, USA
| | - Ruth L Stornetta
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22980, USA
| | - Jaideep Kapur
- Department of Neurology, University of Virginia, Charlottesville, VA 22980, USA
- UVA Brain Institute, University of Virginia, Charlottesville, VA 22980, USA
| | - Edward Perez-Reyes
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22980, USA
- UVA Brain Institute, University of Virginia, Charlottesville, VA 22980, USA
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24
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Di Blasi R, Pisani M, Tedeschi F, Marbiah MM, Polizzi K, Furini S, Siciliano V, Ceroni F. Resource-aware construct design in mammalian cells. Nat Commun 2023; 14:3576. [PMID: 37328476 PMCID: PMC10275982 DOI: 10.1038/s41467-023-39252-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 06/06/2023] [Indexed: 06/18/2023] Open
Abstract
Resource competition can be the cause of unintended coupling between co-expressed genetic constructs. Here we report the quantification of the resource load imposed by different mammalian genetic components and identify construct designs with increased performance and reduced resource footprint. We use these to generate improved synthetic circuits and optimise the co-expression of transfected cassettes, shedding light on how this can be useful for bioproduction and biotherapeutic applications. This work provides the scientific community with a framework to consider resource demand when designing mammalian constructs to achieve robust and optimised gene expression.
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Affiliation(s)
- Roberto Di Blasi
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK
- Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Mara Pisani
- Synthetic and Systems Biology lab for Biomedicine, Instituto Italiano di Tecnologia-IIT, Largo Barsanti e Matteucci, Naples, Italy
- Open University affiliated centre, Milton Keynes, UK
| | - Fabiana Tedeschi
- Synthetic and Systems Biology lab for Biomedicine, Instituto Italiano di Tecnologia-IIT, Largo Barsanti e Matteucci, Naples, Italy
- University of Naples Federico II, Naples, Italy
| | - Masue M Marbiah
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK
- Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Karen Polizzi
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK
- Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Simone Furini
- Department of Electrical, Electronic and Information Engineering ″Guglielmo Marconi", University of Bologna, Cesena, Italy
| | - Velia Siciliano
- Synthetic and Systems Biology lab for Biomedicine, Instituto Italiano di Tecnologia-IIT, Largo Barsanti e Matteucci, Naples, Italy
| | - Francesca Ceroni
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK.
- Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK.
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25
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Noviello G, Gjaltema RAF, Schulz EG. CasTuner is a degron and CRISPR/Cas-based toolkit for analog tuning of endogenous gene expression. Nat Commun 2023; 14:3225. [PMID: 37270532 DOI: 10.1038/s41467-023-38909-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 05/22/2023] [Indexed: 06/05/2023] Open
Abstract
Certain cellular processes are dose-dependent, requiring specific quantities or stoichiometries of gene products, as exemplified by haploinsufficiency and sex-chromosome dosage compensation. Understanding dosage-sensitive processes requires tools to quantitatively modulate protein abundance. Here we present CasTuner, a CRISPR-based toolkit for analog tuning of endogenous gene expression. The system exploits Cas-derived repressors that are quantitatively tuned by ligand titration through a FKBP12F36V degron domain. CasTuner can be applied at the transcriptional or post-transcriptional level using a histone deacetylase (hHDAC4) fused to dCas9, or the RNA-targeting CasRx, respectively. We demonstrate analog tuning of gene expression homogeneously across cells in mouse and human cells, as opposed to KRAB-dependent CRISPR-interference systems, which exhibit digital repression. Finally, we quantify the system's dynamics and use it to measure dose-response relationships of NANOG and OCT4 with their target genes and with the cellular phenotype. CasTuner thus provides an easy-to-implement tool to study dose-responsive processes in their physiological context.
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Affiliation(s)
- Gemma Noviello
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Rutger A F Gjaltema
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Edda G Schulz
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany.
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26
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Casey NP, Klee CH, Fåne A, Caulier B, Graczyk-Jarzynka A, Krawczyk M, Fidyt K, Josefsson SE, Köksal H, Dillard P, Patkowska E, Firczuk M, Smeland EB, Winiarska M, Myklebust JH, Inderberg EM, Wälchli S. Efficient chimeric antigen receptor (CAR) targeting of a central epitope of CD22. J Biol Chem 2023:104883. [PMID: 37269947 PMCID: PMC10331463 DOI: 10.1016/j.jbc.2023.104883] [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: 11/17/2022] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/05/2023] Open
Abstract
Chimeric antigen receptor (CAR) T cell therapy has had considerable success in the treatment of B cell malignancies. Targeting the B-lineage markerCD19 has brought great advances to treatment of acute lymphoblastic leukemia (ALL) and B cell lymphomas. However, relapse remains an issue in many cases. Such relapse can result from downregulation or loss of CD19 from the malignant cell population, or expression of alternate isoforms. Consequently, there remains a need to target alternative B-cell antigens and diversify the spectrum of epitopes targeted within the same antigen. CD22 has been identified as a substitute target in cases of CD19-negative relapse. One anti-CD22 antibody - clone m971 - targets a membrane-proximal epitope of CD22 and has been widely validated and used in the clinic. Here we have compared m971-CAR with a novel CAR derived from IS7, an antibody that targets a central epitope on CD22. The IS7-CAR has superior avidity, and is active and specific against CD22 positive targets, including B-ALL patient-derived xenograft (PDX) samples. Side-by-side comparisons indicated that while IS7-CAR killed less rapidly than m971-CAR in vitro, it remains efficient in controlling lymphoma xenograft models in vivo. Thus, IS7-CAR presents a potential alternative candidate for treatment of refractory B-cell malignancies.
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Affiliation(s)
- Nicholas Paul Casey
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Clara Helena Klee
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Anne Fåne
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Benjamin Caulier
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway; Center for Cancer Cell Reprogramming (CanCell), Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Agnieszka Graczyk-Jarzynka
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland; Laboratory of Immunology, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Marta Krawczyk
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland; Laboratory of Immunology, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Klaudyna Fidyt
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland
| | - Sarah E Josefsson
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Hakan Köksal
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Pierre Dillard
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway
| | | | - Malgorzata Firczuk
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland; Laboratory of Immunology, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Erlend B Smeland
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Magdalena Winiarska
- Department of Immunology, Medical University of Warsaw, Warsaw, Poland; Laboratory of Immunology, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - June H Myklebust
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Else Marit Inderberg
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway.
| | - Sébastien Wälchli
- Translational Research Unit, Section of Cellular Therapy, Department of Oncology, Oslo University Hospital, Oslo, Norway.
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27
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Vudatha V, Herremans KM, Freudenberger DC, Liu C, Trevino JG. In vivo models of pancreatic ductal adenocarcinoma. Adv Cancer Res 2023; 159:75-112. [PMID: 37268402 DOI: 10.1016/bs.acr.2023.02.002] [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: 06/04/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy with high mortality rate. Within the next decade, PDAC is projected to become the second leading cause of cancer-associated death in the United States. Understanding the pathophysiology of PDAC tumorigenesis and metastases is crucial toward developing new therapeutics. One of the challenges in cancer research is generating in vivo models that closely recapitulate the genomic, histological, and clinical characteristics of human tumors. An ideal model for PDAC not only captures the tumor and stromal environment of human disease, but also allows for mutational control and is easy to reproduce in terms of time and cost. In this review, we highlight evolution of in vivo models for PDAC including spontaneous tumors models (i.e., chemical induction, genetic modification, viral delivery), implantation models including patient derived xenografts (PDX), and humanized PDX. We discuss the implementation of each system and evaluate the benefits and shortcomings of these models. Overall, this review provides a broad overview of prior and current techniques of in vivo PDAC modeling and their associated challenges.
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Affiliation(s)
- Vignesh Vudatha
- Department of Surgery, Virginia Commonwealth University School of Medicine, Richmond, VA, United States
| | - Kelly M Herremans
- Department of Surgery, University of Florida College of Medicine, Gainesville, FL, United States
| | - Devon C Freudenberger
- Department of Surgery, Virginia Commonwealth University School of Medicine, Richmond, VA, United States
| | - Christopher Liu
- Department of Surgery, Virginia Commonwealth University School of Medicine, Richmond, VA, United States
| | - Jose G Trevino
- Department of Surgery, Virginia Commonwealth University School of Medicine, Richmond, VA, United States; Division of Surgical Oncology, VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA, United States.
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28
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Influence of Canonical and Non-Canonical IFNLR1 Isoform Expression on Interferon Lambda Signaling. Viruses 2023; 15:v15030632. [PMID: 36992341 PMCID: PMC10052089 DOI: 10.3390/v15030632] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/10/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Interferon lambdas (IFNLs) are innate immune cytokines that induce antiviral cellular responses by signaling through a heterodimer composed of IL10RB and the interferon lambda receptor 1 (IFNLR1). Multiple IFNLR1 transcriptional variants are expressed in vivo and are predicted to encode distinct protein isoforms whose function is not fully established. IFNLR1 isoform 1 has the highest relative transcriptional expression and encodes the full-length functional form that supports canonical IFNL signaling. IFNLR1 isoforms 2 and 3 have lower relative expression and are predicted to encode signaling-defective proteins. To gain insight into IFNLR1 function and regulation, we explored how altering relative expression of IFNLR1 isoforms influenced the cellular response to IFNLs. To achieve this, we generated and functionally characterized stable HEK293T clones expressing doxycycline-inducible FLAG-tagged IFNLR1 isoforms. Minimal FLAG-IFNLR1 isoform 1 overexpression markedly increased IFNL3-dependent expression of antiviral and pro-inflammatory genes, a phenotype that could not be further augmented by expressing higher levels of FLAG-IFNLR1 isoform 1. Expression of low levels of FLAG-IFNLR1 isoform 2 led to partial induction of antiviral genes, but not pro-inflammatory genes, after IFNL3 treatment, a phenotype that was largely abrogated at higher FLAG-IFNLR1 isoform 2 expression levels. Expression of FLAG-IFNLR1 isoform 3 partially augmented antiviral gene expression after IFNL3 treatment. In addition, FLAG-IFNLR1 isoform 1 significantly reduced cellular sensitivity to the type-I IFN IFNA2 when overexpressed. These results identify a unique influence of canonical and non-canonical IFNLR1 isoforms on mediating the cellular response to interferons and provide insight into possible pathway regulation in vivo.
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Lee C, Lee BH, Jung H, Lee C, Sung Y, Kim H, Kim J, Shim JY, Kim JI, Choi DI, Park HY, Kaang BK. Hippocampal engram networks for fear memory recruit new synapses and modify pre-existing synapses in vivo. Curr Biol 2023; 33:507-516.e3. [PMID: 36638799 DOI: 10.1016/j.cub.2022.12.038] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/07/2022] [Accepted: 12/14/2022] [Indexed: 01/14/2023]
Abstract
As basic units of neural networks, ensembles of synapses underlie cognitive functions such as learning and memory. These synaptic engrams show elevated synaptic density among engram cells following contextual fear memory formation. Subsequent analysis of the CA3-CA1 engram synapse revealed larger spine sizes, as the synaptic connectivity correlated with the memory strength. Here, we elucidate the synapse dynamics between CA3 and CA1 by tracking identical synapses at multiple time points by adapting two-photon microscopy and dual-eGRASP technique in vivo. After memory formation, synaptic connections between engram populations are enhanced in conjunction with synaptogenesis within the hippocampal network. However, extinction learning specifically correlated with the disappearance of CA3 engram to CA1 engram (E-E) synapses. We observed "newly formed" synapses near pre-existing synapses, which clustered CA3-CA1 engram synapses after fear memory formation. Overall, we conclude that dynamics at CA3 to CA1 E-E synapses are key sites for modification during fear memory states.
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Affiliation(s)
- Chaery Lee
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, South Korea
| | - Byung Hun Lee
- Department of Physics and Astronomy, College of Natural Sciences, Seoul National University, Seoul 08826, South Korea
| | - Hyunsu Jung
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, South Korea; Interdisciplinary Program in Neuroscience, Seoul National University, Seoul 08826, South Korea
| | - Chiwoo Lee
- Interdisciplinary Program in Neuroscience, Seoul National University, Seoul 08826, South Korea
| | - Yongmin Sung
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, South Korea
| | - Hyopil Kim
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, South Korea
| | - Jooyoung Kim
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, South Korea
| | - Jae Youn Shim
- Department of Physics and Astronomy, College of Natural Sciences, Seoul National University, Seoul 08826, South Korea
| | - Ji-Il Kim
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, South Korea
| | - Dong Il Choi
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, South Korea
| | - Hye Yoon Park
- Department of Physics and Astronomy, College of Natural Sciences, Seoul National University, Seoul 08826, South Korea; Department of Electrical and Computer Engineering, College of Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Bong-Kiun Kaang
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, South Korea; Interdisciplinary Program in Neuroscience, Seoul National University, Seoul 08826, South Korea.
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30
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Genomically mined acoustic reporter genes for real-time in vivo monitoring of tumors and tumor-homing bacteria. Nat Biotechnol 2023:10.1038/s41587-022-01581-y. [PMID: 36593411 DOI: 10.1038/s41587-022-01581-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 10/20/2022] [Indexed: 01/03/2023]
Abstract
Ultrasound allows imaging at a much greater depth than optical methods, but existing genetically encoded acoustic reporters for in vivo cellular imaging have been limited by poor sensitivity, specificity and in vivo expression. Here we describe two acoustic reporter genes (ARGs)-one for use in bacteria and one for use in mammalian cells-identified through a phylogenetic screen of candidate gas vesicle gene clusters from diverse bacteria and archaea that provide stronger ultrasound contrast, produce non-linear signals distinguishable from background tissue and have stable long-term expression. Compared to their first-generation counterparts, these improved bacterial and mammalian ARGs produce 9-fold and 38-fold stronger non-linear contrast, respectively. Using these new ARGs, we non-invasively imaged in situ tumor colonization and gene expression in tumor-homing therapeutic bacteria, tracked the progression of tumor gene expression and growth in a mouse model of breast cancer, and performed gene-expression-guided needle biopsies of a genetically mosaic tumor, demonstrating non-invasive access to dynamic biological processes at centimeter depth.
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31
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Kuzmin AA, Tomilin AN. Building Blocks of Artificial CRISPR-Based Systems beyond Nucleases. Int J Mol Sci 2022; 24:ijms24010397. [PMID: 36613839 PMCID: PMC9820447 DOI: 10.3390/ijms24010397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022] Open
Abstract
Tools developed in the fields of genome engineering, precise gene regulation, and synthetic gene networks have an increasing number of applications. When shared with the scientific community, these tools can be used to further unlock the potential of precision medicine and tissue engineering. A large number of different genetic elements, as well as modifications, have been used to create many different systems and to validate some technical concepts. New studies have tended to optimize or improve existing elements or approaches to create complex synthetic systems, especially those based on the relatively new CRISPR technology. In order to maximize the output of newly developed approaches and to move from proof-of-principle experiments to applications in regenerative medicine, it is important to navigate efficiently through the vast number of genetic elements to choose those most suitable for specific needs. In this review, we have collected information regarding the main genetic elements and their modifications, which can be useful in different synthetic systems with an emphasis of those based on CRISPR technology. We have indicated the most suitable elements and approaches to choose or combine in planning experiments, while providing their deeper understanding, and have also stated some pitfalls that should be avoided.
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32
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Carr S, Buan NR. Insights into the biotechnology potential of Methanosarcina. Front Microbiol 2022; 13:1034674. [PMID: 36590411 PMCID: PMC9797515 DOI: 10.3389/fmicb.2022.1034674] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/28/2022] [Indexed: 12/23/2022] Open
Abstract
Methanogens are anaerobic archaea which conserve energy by producing methane. Found in nearly every anaerobic environment on earth, methanogens serve important roles in ecology as key organisms of the global carbon cycle, and in industry as a source of renewable biofuels. Environmentally, methanogenic archaea play an essential role in the reintroducing unavailable carbon to the carbon cycle by anaerobically converting low-energy, terminal metabolic degradation products such as one and two-carbon molecules into methane which then returns to the aerobic portion of the carbon cycle. In industry, methanogens are commonly used as an inexpensive source of renewable biofuels as well as serving as a vital component in the treatment of wastewater though this is only the tip of the iceberg with respect to their metabolic potential. In this review we will discuss how the efficient central metabolism of methanoarchaea could be harnessed for future biotechnology applications.
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33
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Sapozhnikov DM, Szyf M. Enzyme-free targeted DNA demethylation using CRISPR-dCas9-based steric hindrance to identify DNA methylation marks causal to altered gene expression. Nat Protoc 2022; 17:2840-2881. [PMID: 36207463 DOI: 10.1038/s41596-022-00741-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/22/2022] [Indexed: 11/09/2022]
Abstract
DNA methylation involves the enzymatic addition of a methyl group primarily to cytosine residues in DNA. This protocol describes how to produce complete and minimally confounded DNA demethylation of specific sites in the genome of cultured cells by clustered regularly interspaced short palindromic repeats (CRISPR)-dCas9 and without the involvement of an epigenetic-modifying enzyme, the purpose of which is the evaluation of the functional (i.e., gene expression or phenotypic) consequences of DNA demethylation of specific sites that have been previously implicated in particular pathological or physiological contexts. This protocol maximizes the ability of the easily reprogrammable CRISPR-dCas9 system to assess the impact of DNA methylation from a causal rather than correlational perspective: alternative protocols for CRISPR-dCas9-based site-specific DNA methylation or demethylation rely on the recruitment of epigenetic enzymes that exhibit additional nonspecific activities at both the targeted site and throughout the genome, confounding conclusions of causality of DNA methylation. Inhibition or loss of DNA methylation is accomplished by three consecutive lentiviral transductions. The first two lentiviruses establish stable expression of dCas9 and a guide RNA, which will physically obstruct either maintenance or de novo DNA methyltransferase activity at the guide RNA target site. A third lentivirus introduces Cre recombinase to delete the dCas9 transgene, which leads to loss of dCas9 from the target site, allowing transcription factors and/or the transcription machinery to interact with the demethylated target site. This protocol requires 3-8 months to complete owing to prolonged cell passaging times, but there is little hands-on time, and no specific skills beyond basic molecular biology techniques are necessary.
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Affiliation(s)
- Daniel M Sapozhnikov
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.
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34
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Choi JE, Choi DI, Lee J, Kim J, Kim MJ, Hong I, Jung H, Sung Y, Kim JI, Kim T, Yu NK, Lee SH, Choe HK, Koo JW, Kim JH, Kaang BK. Synaptic ensembles between raphe and D 1R-containing accumbens shell neurons underlie postisolation sociability in males. SCIENCE ADVANCES 2022; 8:eabo7527. [PMID: 36223467 PMCID: PMC9555785 DOI: 10.1126/sciadv.abo7527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Social animals expend considerable energy to maintain social bonds throughout their life. Male and female mice show sexually dimorphic behaviors, yet the underlying neural mechanisms of sociability and their dysregulation during social disconnection remain unknown. Dopaminergic neurons in dorsal raphe nucleus (DRNTH) is known to contribute to a loneliness-like state and modulate sociability. We identified that activated subpopulations in DRNTH and nucleus accumbens shell (NAcsh) during 24 hours of social isolation underlie the increase in isolation-induced sociability in male but not in female mice. This effect was reversed by chemogenetically and optogenetically inhibiting the DRNTH-NAcsh circuit. Moreover, synaptic connectivity among the activated neuronal ensembles in this circuit was increased, primarily in D1 receptor-expressing neurons in NAcsh. The increase in synaptic density functionally correlated with elevated dopamine release into NAcsh. Overall, specific synaptic ensembles in DRNTH-NAcsh mediate sex differences in isolation-induced sociability, indicating that sex-dependent circuit dynamics underlie the expression of sexually dimorphic behaviors.
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Affiliation(s)
- Ja Eun Choi
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Dong Il Choi
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Jisu Lee
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Jooyoung Kim
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Min Jung Kim
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Ilgang Hong
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Hyunsu Jung
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Yongmin Sung
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Ji-il Kim
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - TaeHyun Kim
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Nam-Kyung Yu
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Seung-Hee Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, South Korea
| | - Han Kyoung Choe
- Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), 333 Technojoongang-daero, Dalseong-gun, Daegu 42988, South Korea
| | - Ja Wook Koo
- Emotion, Cognition & Behavior Research Group, Korea Brain Research Institute, 61, Cheomdan-ro, Dong-gu, Daegu 41062, South Korea
| | - Joung-Hun Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), 77, Cheongam-ro, Nam-Gu, Pohang 37673, South Korea
| | - Bong-Kiun Kaang
- School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
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35
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Huang J, Huang X, Huang J. CAR-T cell therapy for hematological malignancies: Limitations and optimization strategies. Front Immunol 2022; 13:1019115. [PMID: 36248810 PMCID: PMC9557333 DOI: 10.3389/fimmu.2022.1019115] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 09/13/2022] [Indexed: 02/04/2023] Open
Abstract
In the past decade, the emergence of chimeric antigen receptor (CAR) T-cell therapy has led to a cellular immunotherapy revolution against various cancers. Although CAR-T cell therapies have demonstrated remarkable efficacy for patients with certain B cell driven hematological malignancies, further studies are required to broaden the use of CAR-T cell therapy against other hematological malignancies. Moreover, treatment failure still occurs for a significant proportion of patients. CAR antigen loss on cancer cells is one of the most common reasons for cancer relapse. Additionally, immune evasion can arise due to the hostile immunosuppressive tumor microenvironment and the impaired CAR-T cells in vivo persistence. Other than direct antitumor activity, the adverse effects associated with CAR-T cell therapy are another major concern during treatment. As a newly emerged treatment approach, numerous novel preclinical studies have proposed different strategies to enhance the efficacy and attenuate CAR-T cell associated toxicity in recent years. The major obstacles that impede promising outcomes for patients with hematological malignancies during CAR-T cell therapy have been reviewed herein, along with recent advancements being made to surmount them.
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36
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Saunderson SC, Hosseini-Rad SMA, McLellan AD. Noise-Reduction and Sensitivity-Enhancement of a Sleeping Beauty-Based Tet-On System. Genes (Basel) 2022; 13:genes13101679. [PMID: 36292564 PMCID: PMC9602432 DOI: 10.3390/genes13101679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Tetracycline-inducible systems are widely used control elements for mammalian gene expression. Despite multiple iterations to improve inducibility, their use is still compromised by basal promoter activity in the absence of tetracyclines. In a mammalian system, we previously showed that the introduction of the G72V mutation in the rtTA-M2 tetracycline activator lowers the basal level expression and increases the fold-induction of multiple genetic elements in a long chimeric antigen receptor construct. In this study, we confirmed that the G72V mutation was effective in minimising background expression in the absence of an inducer, resulting in an increase in fold-expression. Loss of responsiveness due to the G72V mutation was compensated through the incorporation of four sensitivity enhancing (SE) mutations, without compromising promoter tightness. However, SE mutations alone (without G72V) led to undesirable leakiness. Although cryptic splice site removal from rtTA did not alter the inducible control of the luciferase reporter gene in this simplified vector system, this is still recommended as a precaution in more complex multi-gene elements that contain rtTA. The optimized expression construct containing G72V and SE mutations currently provides the best improvement of fold-induction mediated by the rtTA-M2 activator in a mammalian system.
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Affiliation(s)
- Sarah C. Saunderson
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
- Correspondence:
| | - SM Ali Hosseini-Rad
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
- Centre of Excellence in Immunology and Immune-Mediated Diseases, University of Chulalongkorn, Bangkok 10330, Thailand
| | - Alexander D. McLellan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
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37
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Schrevens S, Sanglard D. A novel Candida glabrata doxycycline-inducible system for in vitro/in vivo use. FEMS Yeast Res 2022; 22:6680246. [PMID: 36047937 PMCID: PMC9508828 DOI: 10.1093/femsyr/foac046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022] Open
Abstract
Candida glabrata is an important pathogen causing superficial to invasive disease in human. Conditional expression systems are helpful in addressing the function of genes and especially when they can be applied to in vivo studies. Tetracycline-dependent regulation systems have been used in diverse fungi to turn-on (Tet-on) or turn-off (Tet-off) gene expression either in vitro but also in vivo in animal models. Up to now, only a Tet-off expression has been constructed for gene expression in C. glabrata. Here, we report a Tet-on gene expression system which can be used in vitro and in vivo in any C. glabrata genetic background. This system was used in a mice model of systemic infection to demonstrate that the general amino acid permease Gap1 is important for C. glabrata virulence.
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Affiliation(s)
- S Schrevens
- Institute of Microbiology, University of Lausanne and University Hospital, CH-1011 Lausanne, Switzerland
| | - D Sanglard
- Institute of Microbiology, University of Lausanne and University Hospital, CH-1011 Lausanne, Switzerland
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38
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Rethi-Nagy Z, Abraham E, Udvardy K, Klement E, Darula Z, Pal M, Katona RL, Tubak V, Pali T, Kota Z, Sinka R, Udvardy A, Lipinszki Z. STABILON, a Novel Sequence Motif That Enhances the Expression and Accumulation of Intracellular and Secreted Proteins. Int J Mol Sci 2022; 23:ijms23158168. [PMID: 35897744 PMCID: PMC9332151 DOI: 10.3390/ijms23158168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/17/2022] [Accepted: 07/22/2022] [Indexed: 12/10/2022] Open
Abstract
The dynamic balance of transcriptional and translational regulation together with degron-controlled proteolysis shapes the ever-changing cellular proteome. While a large variety of degradation signals has been characterized, our knowledge of cis-acting protein motifs that can in vivo stabilize otherwise short-lived proteins is very limited. We have identified and characterized a conserved 13-mer protein segment derived from the p54/Rpn10 ubiquitin receptor subunit of the Drosophila 26S proteasome, which fulfills all the characteristics of a protein stabilization motif (STABILON). Attachment of STABILON to various intracellular as well as medically relevant secreted model proteins resulted in a significant increase in their cellular or extracellular concentration in mammalian cells. We demonstrate that STABILON acts as a universal and dual function motif that, on the one hand, increases the concentration of the corresponding mRNAs and, on the other hand, prevents the degradation of short-lived fusion proteins. Therefore, STABILON may lead to a breakthrough in biomedical recombinant protein production.
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Affiliation(s)
- Zsuzsanna Rethi-Nagy
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Edit Abraham
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
| | - Katalin Udvardy
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
| | - Eva Klement
- Single Cell Omics Advanced Core Facility, Hungarian Centre of Excellence for Molecular Medicine (HCEMM), H-6726 Szeged, Hungary; (E.K.); (Z.D.)
- Biological Research Centre, Laboratory of Proteomics Research, ELKH, H-6726 Szeged, Hungary
| | - Zsuzsanna Darula
- Single Cell Omics Advanced Core Facility, Hungarian Centre of Excellence for Molecular Medicine (HCEMM), H-6726 Szeged, Hungary; (E.K.); (Z.D.)
- Biological Research Centre, Laboratory of Proteomics Research, ELKH, H-6726 Szeged, Hungary
| | - Margit Pal
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
| | | | - Vilmos Tubak
- Creative Laboratory Ltd., H-6726 Szeged, Hungary;
| | - Tibor Pali
- Biological Research Centre, Institute of Biophysics, ELKH, H-6726 Szeged, Hungary; (T.P.); (Z.K.)
| | - Zoltan Kota
- Biological Research Centre, Institute of Biophysics, ELKH, H-6726 Szeged, Hungary; (T.P.); (Z.K.)
| | - Rita Sinka
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary
- Correspondence: (R.S.); (A.U.); (Z.L.)
| | - Andor Udvardy
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
- Correspondence: (R.S.); (A.U.); (Z.L.)
| | - Zoltan Lipinszki
- Biological Research Centre, Institute of Biochemistry, MTA SZBK Lendület Laboratory of Cell Cycle Regulation, ELKH, H-6726 Szeged, Hungary; (Z.R.-N.); (E.A.); (K.U.); (M.P.)
- Correspondence: (R.S.); (A.U.); (Z.L.)
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39
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Duran AG, Schwestka M, Nazari-Shafti TZ, Neuber S, Stamm C, Gossen M. Limiting Transactivator Amounts Contribute to Transgene Mosaicism in Tet-On All-in-One Systems. ACS Synth Biol 2022; 11:2623-2635. [PMID: 35815862 DOI: 10.1021/acssynbio.2c00036] [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: 11/28/2022]
Abstract
MicroRNAs play an essential role in cell homeostasis and have been proposed as therapeutic agents. One strategy to deliver microRNAs is to genetically engineer target cells to express microRNAs of interest. However, to control dosage and timing, as well as to limit potential side-effects, microRNAs' expression should ideally be under exogenous, inducible control. Conditional expression of miRNA-based short hairpin RNAs (shRNAmirs) via gene regulatory circuits such as the Tet-system is therefore a promising strategy to control shRNAmirs' expression in research and therapy. Single vector approaches like Tet-On all-in-one designs are more compatible with potential clinical applications by providing the Tet-On system components in a single round of genetic engineering. However, all-in-one systems often come at the expense of heterogeneous and unstable expression. In this study, we aimed to understand the causes that lead to such erratic transgene expression. By using a reporter cell, we found that the degree of heterogeneity mostly correlated with reverse tetracycline transactivator (rtTA) expression levels. Moreover, the targeted integration of a potent rtTA expression cassette into a genomic safe harbor locus functionally rescued previously silenced rtTA-responsive transcription units. Overall, our results suggest that ensuring homogenous and stable rtTA expression is essential for the robust and reliable performance of future Tet-On all-in-one designs.
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Affiliation(s)
- Ana G Duran
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany.,Berlin-Brandenburg School for Regenerative Therapies (BSRT), 13353 Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353 Berlin, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin-Brandenburg Center for Regenerative Therapies, Berlin 13353, Germany
| | - Marko Schwestka
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353 Berlin, Germany
| | - Timo Z Nazari-Shafti
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353 Berlin, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies, 13353 Berlin, Germany.,German Centre for Cardiovascular Research, Partner Site Berlin, 13353 Berlin, Germany
| | - Sebastian Neuber
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353 Berlin, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies, 13353 Berlin, Germany.,German Centre for Cardiovascular Research, Partner Site Berlin, 13353 Berlin, Germany
| | - Christof Stamm
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany.,Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353 Berlin, Germany.,German Centre for Cardiovascular Research, Partner Site Berlin, 13353 Berlin, Germany
| | - Manfred Gossen
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353 Berlin, Germany
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40
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Lewis KT, Oles LR, MacDougald OA. Tetracycline response element driven Cre causes ectopic recombinase activity independent of transactivator element. Mol Metab 2022; 61:101501. [PMID: 35452876 PMCID: PMC9170755 DOI: 10.1016/j.molmet.2022.101501] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/06/2022] [Accepted: 04/14/2022] [Indexed: 12/03/2022] Open
Abstract
OBJECTIVE Tamoxifen is widely used for inducible Cre-LoxP systems but has several undesirable side effects for researchers investigating metabolism or energy balance, including weight loss, lipoatrophy, and drug incorporation into lipid stores. For this reason, we sought to determine whether a doxycycline-inducible system would be more advantageous for adipocyte-specific Cre mouse models, but serendipitously discovered widespread ectopic tetracycline response element Cre (TRE-Cre) recombinase activity. METHODS Adipocyte-specific tamoxifen- and doxycycline-inducible Cre mice were crossed to fluorescent Cre reporter mice and visualized by confocal microscopy to assess efficiency and background activity. TRE-Cre mice were crossed to stop-floxed diphtheria toxin mice to selectively ablate cells with background Cre activity. RESULTS Tamoxifen- and doxycycline-inducible systems performed similarly in adipose tissues, but ectopic Cre recombination was evident in numerous other cell types of the latter, most notably neurons. The source of ectopic Cre activity was isolated to the TRE-Cre transgene, driven by the pTet (tetO7) tetracycline-inducible promoter. Ablation of cells with ectopic recombination in mice led to stunted growth, diminished survival, and reduced brain mass. CONCLUSIONS These results indicate that tamoxifen- and doxycycline-inducible adipocyte-specific Cre mouse models are similarly efficient, but the TRE-Cre component of the latter is inherently leaky. TRE-Cre background activity is especially pronounced in the brain and peripheral nerve fibers, and selective ablation of these cells impairs mouse development and survival. Caution should be taken when pairing TRE-Cre with floxed alleles that have defined roles in neural function, and additional controls should be included when using this model system.
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Affiliation(s)
- Kenneth T Lewis
- University of Michigan Medical School, Department of Molecular & Integrative Physiology, Ann Arbor, MI, USA
| | - Lily R Oles
- University of Michigan Medical School, Department of Molecular & Integrative Physiology, Ann Arbor, MI, USA
| | - Ormond A MacDougald
- University of Michigan Medical School, Department of Molecular & Integrative Physiology, Ann Arbor, MI, USA; University of Michigan Medical School, Department of Internal Medicine, Ann Arbor, MI, USA.
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41
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Watson-Levings RS, Palmer GD, Levings PP, Dacanay EA, Evans CH, Ghivizzani SC. Gene Therapy in Orthopaedics: Progress and Challenges in Pre-Clinical Development and Translation. Front Bioeng Biotechnol 2022; 10:901317. [PMID: 35837555 PMCID: PMC9274665 DOI: 10.3389/fbioe.2022.901317] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/27/2022] [Indexed: 11/25/2022] Open
Abstract
In orthopaedics, gene-based treatment approaches are being investigated for an array of common -yet medically challenging- pathologic conditions of the skeletal connective tissues and structures (bone, cartilage, ligament, tendon, joints, intervertebral discs etc.). As the skeletal system protects the vital organs and provides weight-bearing structural support, the various tissues are principally composed of dense extracellular matrix (ECM), often with minimal cellularity and vasculature. Due to their functional roles, composition, and distribution throughout the body the skeletal tissues are prone to traumatic injury, and/or structural failure from chronic inflammation and matrix degradation. Due to a mixture of environment and endogenous factors repair processes are often slow and fail to restore the native quality of the ECM and its function. In other cases, large-scale lesions from severe trauma or tumor surgery, exceed the body’s healing and regenerative capacity. Although a wide range of exogenous gene products (proteins and RNAs) have the potential to enhance tissue repair/regeneration and inhibit degenerative disease their clinical use is hindered by the absence of practical methods for safe, effective delivery. Cumulatively, a large body of evidence demonstrates the capacity to transfer coding sequences for biologic agents to cells in the skeletal tissues to achieve prolonged delivery at functional levels to augment local repair or inhibit pathologic processes. With an eye toward clinical translation, we discuss the research progress in the primary injury and disease targets in orthopaedic gene therapy. Technical considerations important to the exploration and pre-clinical development are presented, with an emphasis on vector technologies and delivery strategies whose capacity to generate and sustain functional transgene expression in vivo is well-established.
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Affiliation(s)
- Rachael S. Watson-Levings
- Department of Orthopaedic Surgery and Sports Medicine, University of Florida College of Medicine, Gainesville, FL, United States
| | - Glyn D. Palmer
- Department of Orthopaedic Surgery and Sports Medicine, University of Florida College of Medicine, Gainesville, FL, United States
| | - Padraic P. Levings
- Department of Orthopaedic Surgery and Sports Medicine, University of Florida College of Medicine, Gainesville, FL, United States
| | - E. Anthony Dacanay
- Department of Orthopaedic Surgery and Sports Medicine, University of Florida College of Medicine, Gainesville, FL, United States
| | - Christopher H. Evans
- Rehabilitation Medicine Research Center, Mayo Clinic, Rochester, MI, United States
| | - Steven C. Ghivizzani
- Department of Orthopaedic Surgery and Sports Medicine, University of Florida College of Medicine, Gainesville, FL, United States
- *Correspondence: Steven C. Ghivizzani,
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42
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Park SB, Uchida T, Tilson S, Hu Z, Ma CD, Leek M, Eichner M, Hong SG, Liang TJ. A dual conditional CRISPR-Cas9 system to activate gene editing and reduce off-target effects in human stem cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 28:656-669. [PMID: 35615005 PMCID: PMC9112054 DOI: 10.1016/j.omtn.2022.04.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 04/22/2022] [Indexed: 12/26/2022]
Abstract
The CRISPR-Cas9 system has emerged as a powerful and efficient tool for genome editing. An important drawback of the CRISPR-Cas9 system is the constitutive endonuclease activity when Cas9 endonuclease and its sgRNA are co-expressed. This constitutive activity results in undesirable off-target effects that hinder studies using the system, such as probing gene functions or its therapeutic use in humans. Here, we describe a convenient method that allows temporal and tight control of CRISPR-Cas9 activity by combining transcriptional regulation of Cas9 expression and protein stability control of Cas9 in human stem cells. To achieve this dual control, we combined the doxycycline-inducible system for transcriptional regulation and FKBP12-derived destabilizing domain fused to Cas9 for protein stability regulation. We showed that approximately 5%–10% of Cas9 expression was observed when only one of the two controls was applied. By combining two systems, we markedly lowered the baseline Cas9 expression and limited the exposure time of Cas9 endonuclease in the cell, resulting in little or no undesirable on- or off-target effects. We anticipate that this dual conditional CRISPR-Cas9 system can serve as a valuable tool for systematic characterization and identification of genes for various pathological processes.
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Affiliation(s)
- Seung Bum Park
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD 20814, USA
| | - Takuro Uchida
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD 20814, USA
| | - Samantha Tilson
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD 20814, USA
| | - Zongyi Hu
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD 20814, USA
| | - Christopher D Ma
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD 20814, USA
| | - Madeleine Leek
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD 20814, USA
| | - Michael Eichner
- Division of Veterinary Resources, National Institutes of Health, Bethesda, MD 20814, USA
| | - So Gun Hong
- Translational Stem Cell Biology Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD 20814, USA
| | - T Jake Liang
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, MD 20814, USA
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43
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Smith SS, Chu D, Qu T, Aggleton JA, Schneider RA. Species-specific sensitivity to TGFβ signaling and changes to the Mmp13 promoter underlie avian jaw development and evolution. eLife 2022; 11:e66005. [PMID: 35666955 PMCID: PMC9246370 DOI: 10.7554/elife.66005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/03/2022] [Indexed: 12/02/2022] Open
Abstract
Precise developmental control of jaw length is critical for survival, but underlying molecular mechanisms remain poorly understood. The jaw skeleton arises from neural crest mesenchyme (NCM), and we previously demonstrated that these progenitor cells express more bone-resorbing enzymes including Matrix metalloproteinase 13 (Mmp13) when they generate shorter jaws in quail embryos versus longer jaws in duck. Moreover, if we inhibit bone resorption or Mmp13, we can increase jaw length. In the current study, we uncover mechanisms establishing species-specific levels of Mmp13 and bone resorption. Quail show greater activation of and sensitivity to transforming growth factor beta (TGFβ) signaling than duck; where intracellular mediators like SMADs and targets like Runt-related transcription factor 2 (Runx2), which bind Mmp13, become elevated. Inhibiting TGFβ signaling decreases bone resorption, and overexpressing Mmp13 in NCM shortens the duck lower jaw. To elucidate the basis for this differential regulation, we examine the Mmp13 promoter. We discover a SMAD-binding element and single nucleotide polymorphisms (SNPs) near a RUNX2-binding element that distinguish quail from duck. Altering the SMAD site and switching the SNPs abolish TGFβ sensitivity in the quail Mmp13 promoter but make the duck promoter responsive. Thus, differential regulation of TGFβ signaling and Mmp13 promoter structure underlie avian jaw development and evolution.
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Affiliation(s)
- Spenser S Smith
- Department of Orthopaedic Surgery, University of California, San FranciscoSan FranciscoUnited States
| | - Daniel Chu
- Department of Orthopaedic Surgery, University of California, San FranciscoSan FranciscoUnited States
| | - Tiange Qu
- Department of Orthopaedic Surgery, University of California, San FranciscoSan FranciscoUnited States
| | - Jessye A Aggleton
- Department of Orthopaedic Surgery, University of California, San FranciscoSan FranciscoUnited States
| | - Richard A Schneider
- Department of Orthopaedic Surgery, University of California, San FranciscoSan FranciscoUnited States
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44
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Johnson S, Karpova Y, Guo D, Ghatak A, Markov DA, Tulin AV. PARG suppresses tumorigenesis and downregulates genes controlling angiogenesis, inflammatory response, and immune cell recruitment. BMC Cancer 2022; 22:557. [PMID: 35585513 PMCID: PMC9118775 DOI: 10.1186/s12885-022-09651-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 05/09/2022] [Indexed: 12/20/2022] Open
Abstract
Chemokines are highly expressed in tumor microenvironment and play a critical role in all aspects of tumorigenesis, including the recruitment of tumor-promoting immune cells, activation of cancer-associated fibroblasts, angiogenesis, metastasis, and growth. Poly (ADP-ribose) polymerase (PARP) is a multi-target transcription regulator with high levels of poly(ADP-ribose) (pADPr) being reported in a variety of cancers. Furthermore, poly (ADP-ribose) glycohydrolase (PARG), an enzyme that degrades pADPr, has been reported to be downregulated in tumor tissues with abnormally high levels of pADPr. In conjunction to this, we have recently reported that the reduction of pADPr, by either pharmacological inhibition of PARP or PARG's overexpression, disrupts renal carcinoma cell malignancy in vitro. Here, we use 3 T3 mouse embryonic fibroblasts, a universal model for malignant transformation, to follow the effect of PARG upregulation on cells' tumorigenicity in vivo. We found that the overexpression of PARG in mouse allografts produces significantly smaller tumors with a delay in tumor onset. As downregulation of PARG has also been implicated in promoting the activation of pro-inflammatory genes, we also followed the gene expression profile of PARG-overexpressing 3 T3 cells using RNA-seq approach and observed that chemokine transcripts are significantly reduced in those cells. Our data suggest that the upregulation of PARG may be potentially useful for the tumor growth inhibition in cancer treatment and as anti-inflammatory intervention.
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Affiliation(s)
- Sarah Johnson
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202 USA
| | - Yaroslava Karpova
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202 USA
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, 119334 Russia
| | - Danping Guo
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202 USA
| | - Atreyi Ghatak
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202 USA
| | - Dmitriy A. Markov
- Department of Cell Biology and Neuroscience, School of Osteopathic Medicine, Rowan University, Stratford, NJ 08084 USA
| | - Alexei V. Tulin
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58202 USA
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45
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Engineering of Synthetic Transcriptional Switches in Yeast. Life (Basel) 2022; 12:life12040557. [PMID: 35455048 PMCID: PMC9030632 DOI: 10.3390/life12040557] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/31/2022] [Accepted: 04/03/2022] [Indexed: 02/04/2023] Open
Abstract
Transcriptional switches can be utilized for many purposes in synthetic biology, including the assembly of complex genetic circuits to achieve sophisticated cellular systems and the construction of biosensors for real-time monitoring of intracellular metabolite concentrations. Although to date such switches have mainly been developed in prokaryotes, those for eukaryotes are increasingly being reported as both rational and random engineering technologies mature. In this review, we describe yeast transcriptional switches with different modes of action and how to alter their properties. We also discuss directed evolution technologies for the rapid and robust construction of yeast transcriptional switches.
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46
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Hindul NL, Jhita A, Oprea DG, Hussain TA, Gonchar O, Campillo MAM, O'Regan L, Kanemaki MT, Fry AM, Hirota K, Tanaka K. Construction of a human hTERT RPE-1 cell line with inducible Cre for editing of endogenous genes. Biol Open 2022; 11:274087. [PMID: 35067715 PMCID: PMC8864296 DOI: 10.1242/bio.059056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/11/2022] [Indexed: 11/20/2022] Open
Abstract
The human retinal pigment epithelial RPE-1 cell line immortalized with hTERT retains a stable karyotype with a modal chromosome number of 46 and has been widely used to study physiological events in human cell culture systems. To facilitate inducible knock-out or knock-in experiments in this cell line, we have modified the AAVS1 locus to harbour a DNA fragment encoding ERT2-Cre-ERT2 fusion protein under regulation of a Tet-On expression system. In the generated cell line, active Cre recombinase was induced by simple addition of doxycycline and tamoxifen to the culture medium. As proof of concept, we successfully introduced an oncogenic point mutation to the endogenous KRAS gene locus of this cell line. The cell line will serve as a powerful tool to conduct functional analyses of human genes. Summary: A near wild-type human hTERT RPE-1 cell line with inducible Cre recombinase integrated at the AAVS1 was generated for inducible genetic knock-in and knock-out. It facilitates human gene functional studies.
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Affiliation(s)
- Naushin L. Hindul
- Department of Molecular and Cell Biology, University of Leicester, UK
| | - Amarjot Jhita
- Department of Molecular and Cell Biology, University of Leicester, UK
| | - Daiana G. Oprea
- Department of Molecular and Cell Biology, University of Leicester, UK
| | | | - Oksana Gonchar
- Department of Molecular and Cell Biology, University of Leicester, UK
| | | | - Laura O'Regan
- Department of Molecular and Cell Biology, University of Leicester, UK
| | - Masato T. Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Andrew M. Fry
- Department of Molecular and Cell Biology, University of Leicester, UK
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - Kayoko Tanaka
- Department of Molecular and Cell Biology, University of Leicester, UK
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47
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Vardapour R, Kehl T, Kneitz S, Ludwig N, Meese E, Lenhof HP, Gessler M. The DGCR8 E518K mutation found in Wilms tumors leads to a partial miRNA processing defect that alters gene expression patterns and biological processes. Carcinogenesis 2021; 43:82-93. [PMID: 34919667 DOI: 10.1093/carcin/bgab110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 11/01/2021] [Accepted: 11/25/2021] [Indexed: 11/14/2022] Open
Abstract
Wilms tumor (WT) is the most common renal tumor in childhood. We and others have previously identified oncogenic driver mutations affecting the microprocessor genes DROSHA and DGCR8 that lead to altered miRNA expression patterns. In the case of DGCR8, a single recurrent hotspot mutation (E518K) was found in the RNA binding domain. To functionally assess this mutation in vitro, we generated mouse Dgcr8-KO embryonic stem cell (mESC) lines with an inducible expression of wild-type or mutant DGCR8, mirroring the hemizygous mutant expression seen in WT. RNA-seq analysis revealed significant differences of miRNA expression profiles in DGCR8-E518K compared to DGCR8-wild-type mESCs. The E518K mutation only led to a partial rescue of the reported miRNA processing defect in Dgcr8-KO, with selectively reduced expression of numerous canonical miRNAs. Nevertheless, DGCR8-E518K retained significant activity given its ability to still process many miRNAs. Subsequent to altered miRNA levels, the expression of mRNA targets was likewise changed. Functional assays showed that DGCR8-E518K cells still have a partial proliferation and differentiation defect but were able to rescue critical biological processes in embryoid body development. The stem cell program could be shut down and all three germ layers were formed. These findings suggest that the E518K mutation leads to a partial reduction of microprocessor activity and altered specificity with selective impairment only in certain developmental contexts, apparently including nephrogenesis.
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Affiliation(s)
- Romina Vardapour
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, Wuerzburg University, 97074 Wuerzburg, Germany
| | - Tim Kehl
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany
| | - Susanne Kneitz
- Theodor-Boveri-Institute/Biocenter, Physiological Chemistry, Wuerzburg University, 97074 Wuerzburg, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany
| | - Manfred Gessler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry, Wuerzburg University, 97074 Wuerzburg, Germany.,Comprehensive Cancer Center Mainfranken, 97078 Wuerzburg, Germany
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48
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Lee AQ, Li Y, Gong Z. Inducible Liver Cancer Models in Transgenic Zebrafish to Investigate Cancer Biology. Cancers (Basel) 2021; 13:5148. [PMID: 34680297 PMCID: PMC8533791 DOI: 10.3390/cancers13205148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/08/2021] [Accepted: 10/09/2021] [Indexed: 12/20/2022] Open
Abstract
Primary liver cancer is one of the most prevalent and deadly cancers, which incidence continues to increase while treatment response remains poor; thus, in-depth understanding of tumour events is necessary to develop more effective therapies. Animal models for liver cancer are powerful tools to reach this goal. Over the past decade, our laboratory has established multiple oncogene transgenic zebrafish lines that can be robustly induced to develop liver cancer. Histological, transcriptomic and molecular analyses validate the use of these transgenic zebrafish as experimental models for liver cancer. In this review, we provide a comprehensive summary of our findings with these inducible zebrafish liver cancer models in tumour initiation, oncogene addiction, tumour microenvironment, gender disparity, cancer cachexia, drug screening and others. Induced oncogene expression causes a rapid change of the tumour microenvironment such as inflammatory responses, increased vascularisation and rapid hepatic growth. In several models, histologically-proven carcinoma can be induced within one week of chemical inducer administration. Interestingly, the induced liver tumours show the ability to regress when the transgenic oncogene is suppressed by the withdrawal of the chemical inducer. Like human liver cancer, there is a strong bias of liver cancer severity in male zebrafish. After long-term tumour progression, liver cancer-bearing zebrafish also show symptoms of cancer cachexia such as muscle-wasting. In addition, the zebrafish models have been used to screen for anti-metastasis drugs as well as to evaluate environmental toxicants in carcinogenesis. These findings demonstrated that these inducible zebrafish liver cancer models provide rapid and convenient experimental tools for further investigation of fundamental cancer biology, with the potential for the discovery of new therapeutic approaches.
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Affiliation(s)
| | | | - Zhiyuan Gong
- Department of Biological Sciences, National University of Singapore, Singapore 119077, Singapore; (A.Q.L.); (Y.L.)
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49
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Lyons SK, Plenker D, Trotman LC. Advances in preclinical evaluation of experimental antibody-drug conjugates. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2021; 4:745-754. [PMID: 34532655 PMCID: PMC8443155 DOI: 10.20517/cdr.2021.37] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The ability to chemically modify monoclonal antibodies with the attachment of specific functional groups has opened up an enormous range of possibilities for the targeted treatment and diagnosis of cancer in the clinic. As the number of such antibody-based drug candidates has increased, so too has the need for more stringent and robust preclinical evaluation of their in vivo performance to maximize the likelihood that time, research effort, and money are only spent developing the most effective and promising candidate molecules for translation to the clinic. Concurrent with the development of antibody-drug conjugate (ADC) technology, several recent advances in preclinical research stand to greatly increase the experimental rigor by which promising candidate molecules can be evaluated. These include advances in preclinical tumor modeling with the development of patient-derived tumor organoid models that far better recapitulate many aspects of the human disease than conventional subcutaneous xenograft models. Such models are amenable to genetic manipulation, which will greatly improve our understanding of the relationship between ADC and antigen and stringently evaluate mechanisms of therapeutic response. Finally, tumor development is often not visible in these in vivo models. We discuss how the application of several preclinical molecular imaging techniques will greatly enhance the quality of experimental data, enabling quantitative pre- and post-treatment tumor measurements or the precise assessment of ADCs as effective diagnostics. In our opinion, when taken together, these advances in preclinical cancer research will greatly improve the identification of effective candidate ADC molecules with the best chance of clinical translation and cancer patient benefit.
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Affiliation(s)
- Scott K Lyons
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Dennis Plenker
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Lloyd C Trotman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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50
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Moya-Torres A, Gupta M, Heide F, Krahn N, Legare S, Nikodemus D, Imhof T, Meier M, Koch M, Stetefeld J. Homogenous overexpression of the extracellular matrix protein Netrin-1 in a hollow fiber bioreactor. Appl Microbiol Biotechnol 2021; 105:6047-6057. [PMID: 34342709 PMCID: PMC8390410 DOI: 10.1007/s00253-021-11438-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/24/2021] [Accepted: 07/03/2021] [Indexed: 12/14/2022]
Abstract
The production of recombinant proteins for functional and biophysical studies, especially in the field of structural determination, still represents a challenge as high quality and quantities are needed to adequately perform experiments. This is in part solved by optimizing protein constructs and expression conditions to maximize the yields in regular flask expression systems. Still, work flow and effort can be substantial with no guarantee to obtain improvements. This study presents a combination of workflows that can be used to dramatically increase protein production and improve processing results, specifically for the extracellular matrix protein Netrin-1. This proteoglycan is an axon guidance cue which interacts with various receptors to initiate downstream signaling cascades affecting cell differentiation, proliferation, metabolism, and survival. We were able to produce large glycoprotein quantities in mammalian cells, which were engineered for protein overexpression and secretion into the media using the controlled environment provided by a hollow fiber bioreactor. Close monitoring of the internal bioreactor conditions allowed for stable production over an extended period of time. In addition to this, Netrin-1 concentrations were monitored in expression media through biolayer interferometry which allowed us to increase Netrin-1 media concentrations tenfold over our current flask systems while preserving excellent protein quality and in solution behavior. Our particular combination of genetic engineering, cell culture system, protein purification, and biophysical characterization permitted us to establish an efficient and continuous production of high-quality protein suitable for structural biology studies that can be translated to various biological systems. KEY POINTS: • Hollow fiber bioreactor produces substantial yields of homogenous Netrin-1 • Biolayer interferometry allows target protein quantitation in expression media • High production yields in the bioreactor do not impair Netrin-1 proteoglycan quality.
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Affiliation(s)
- Aniel Moya-Torres
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Monika Gupta
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Fabian Heide
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada.
| | - Natalie Krahn
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Scott Legare
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Denise Nikodemus
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Imhof
- Institute for Dental Research and Oral Musculoskeletal Biology, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany
| | - Markus Meier
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology, Center for Biochemistry, Center for Molecular Medicine, Medical Faculty, University of Cologne, Cologne, Germany
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada.
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