1
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Chang TY, Waxman DJ. HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo. RESEARCH SQUARE 2024:rs.3.rs-4559581. [PMID: 38978599 PMCID: PMC11230509 DOI: 10.21203/rs.3.rs-4559581/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Background STARR-seq and other massively-parallel reporter assays are widely used to discover functional enhancers in transfected cell models, which can be confounded by plasmid vector-induced type-I interferon immune responses and lack the multicellular environment and endogenous chromatin state of complex mammalian tissues. Results Here, we describe HDI-STARR-seq, which combines STARR-seq plasmid library delivery to the liver, by hydrodynamic tail vein injection (HDI), with reporter RNA transcriptional initiation driven by a minimal Albumin promoter, which we show is essential for mouse liver STARR-seq enhancer activity assayed 7 days after HDI. Importantly, little or no vector-induced innate type-I interferon responses were observed. Comparisons of HDI-STARR-seq activity between male and female mouse livers and in livers from males treated with an activating ligand of the transcription factor CAR (Nr1i3) identified many condition-dependent enhancers linked to condition-specific gene expression. Further, thousands of active liver enhancers were identified using a high complexity STARR-seq library comprised of ~ 50,000 genomic regions released by DNase-I digestion of mouse liver nuclei. When compared to stringently inactive library sequences, the active enhancer sequences identified were highly enriched for liver open chromatin regions with activating histone marks (H3K27ac, H3K4me1, H3K4me3), were significantly closer to gene transcriptional start sites, and were significantly depleted of repressive (H3K27me3, H3K9me3) and transcribed region histone marks (H3K36me3). Conclusions HDI-STARR-seq offers substantial improvements over current methodologies for large scale, functional profiling of enhancers, including condition-dependent enhancers, in liver tissue in vivo, and can be adapted to characterize enhancer activities in a variety of species and tissues by selecting suitable tissue- and species-specific promoter sequences.
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2
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Chang TY, Waxman DJ. HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598329. [PMID: 38915578 PMCID: PMC11195054 DOI: 10.1101/2024.06.10.598329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
STARR-seq and other massively-parallel reporter assays are widely used to discover functional enhancers in transfected cell models, which can be confounded by plasmid vector-induced type-I interferon immune responses and lack the multicellular environment and endogenous chromatin state of complex mammalian tissues. Here, we describe HDI-STARR-seq, which combines STARR-seq plasmid library delivery to the liver, by hydrodynamic tail vein injection (HDI), with reporter RNA transcriptional initiation driven by a minimal Albumin promoter, which we show is essential for mouse liver STARR-seq enhancer activity assayed 7 days after HDI. Importantly, little or no vector-induced innate type-I interferon responses were observed. Comparisons of HDI-STARR-seq activity between male and female mouse livers and in livers from males treated with an activating ligand of the transcription factor CAR (Nr1i3) identified many condition-dependent enhancers linked to condition-specific gene expression. Further, thousands of active liver enhancers were identified using a high complexity STARR-seq library comprised of ~50,000 genomic regions released by DNase-I digestion of mouse liver nuclei. When compared to stringently inactive library sequences, the active enhancer sequences identified were highly enriched for liver open chromatin regions with activating histone marks (H3K27ac, H3K4me1, H3K4me3), were significantly closer to gene transcriptional start sites, and were significantly depleted of repressive (H3K27me3, H3K9me3) and transcribed region histone marks (H3K36me3). HDI-STARR-seq offers substantial improvements over current methodologies for large scale, functional profiling of enhancers, including condition-dependent enhancers, in liver tissue in vivo, and can be adapted to characterize enhancer activities in a variety of species and tissues by selecting suitable tissue- and species-specific promoter sequences.
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Affiliation(s)
- Ting-Ya Chang
- Departments of Biology and Biomedical Engineering, and Bioinformatics program, Boston University, Boston, MA 02215
| | - David J Waxman
- Departments of Biology and Biomedical Engineering, and Bioinformatics program, Boston University, Boston, MA 02215
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3
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Marques-da-Silva C, Schmidt-Silva C, Baptista RP, Kurup SP. Inherently Reduced Expression of ASC Restricts Caspase-1 Processing in Hepatocytes and Promotes Plasmodium Infection. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:596-606. [PMID: 38149914 PMCID: PMC10872340 DOI: 10.4049/jimmunol.2300440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/06/2023] [Indexed: 12/28/2023]
Abstract
Inflammasome-mediated caspase-1 activation facilitates innate immune control of Plasmodium in the liver, thereby limiting the incidence and severity of clinical malaria. However, caspase-1 processing occurs incompletely in both mouse and human hepatocytes and precludes the generation of mature IL-1β or IL-18, unlike in other cells. Why this is so or how it impacts Plasmodium control in the liver has remained unknown. We show that an inherently reduced expression of the inflammasome adaptor molecule apoptosis-associated specklike protein containing CARD (ASC) is responsible for the incomplete proteolytic processing of caspase-1 in murine hepatocytes. Transgenically enhancing ASC expression in hepatocytes enabled complete caspase-1 processing, enhanced pyroptotic cell death, maturation of the proinflammatory cytokines IL-1β and IL-18 that was otherwise absent, and better overall control of Plasmodium infection in the liver of mice. This, however, impeded the protection offered by live attenuated antimalarial vaccination. Tempering ASC expression in mouse macrophages, on the other hand, resulted in incomplete processing of caspase-1. Our work shows how caspase-1 activation and function in host cells are fundamentally defined by ASC expression and offers a potential new pathway to create better disease and vaccination outcomes by modifying the latter.
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Affiliation(s)
- Camila Marques-da-Silva
- Department of Cellular Biology, University of Georgia, Athens, GA
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA
| | - Clyde Schmidt-Silva
- Department of Cellular Biology, University of Georgia, Athens, GA
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA
| | - Rodrigo P Baptista
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA
| | - Samarchith P Kurup
- Department of Cellular Biology, University of Georgia, Athens, GA
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA
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4
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Yin W, Sun L, Liang Y, Luo C, Feng T, Zhang Y, Zhang W, Yin Y. Maternal intermittent fasting deteriorates offspring metabolism via suppression of hepatic mTORC1 signaling. FASEB J 2023; 37:e22831. [PMID: 36856728 DOI: 10.1096/fj.202201907r] [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: 11/16/2022] [Revised: 01/10/2023] [Accepted: 02/08/2023] [Indexed: 03/02/2023]
Abstract
The metabolic benefits of intermittent fasting (IF) have been well recognized. However, limited studies have examined the relationship between long-term maternal IF before pregnancy and offspring health. In this study, a C57BL/6J mouse model of long-term IF before pregnancy was established: 4-week-old female mice were subjected to alternate-day fasting for 12 weeks and resumed normal diet after mating. Female mice in the control group were fed ad libitum. Offspring mice were weaned at 6 weeks of age and fed a normal chow diet or a 60% high-fat diet. The effects of long-term pre-pregnancy IF on offspring metabolism and its underlying mechanism were examined. We found that neonatal IF offspring weighted significantly less relevant to control mice. This difference gradually disappeared as a result of catch-up growth. In the IF offspring, adipose tissue mass was significantly increased. This alteration was associated with a considerable deterioration in glucose tolerance. No significant difference in food intake was observed. Further, lipid deposition as well as triglyceride contents in the liver were greatly increased. Maternal IF significantly decreased levels of DNA methyltransferase in the liver of offspring. DNA methylation modifications of molecules associated with the mTORC1 signaling pathway were significantly altered, leading to the significant inhibition of mTORC1 signaling. Overexpression of S6K1 activated hepatic mTORC1 signaling and reversed the metabolic dysfunction in IF offspring. In conclusion, long-term pre-pregnancy IF increases hepatic steatosis and adiposity, as well as impairs glucose metabolism in adult offspring. This occurs through DNA methylation-dependent suppression of hepatic mTORC1 signaling activity.
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Affiliation(s)
- Wenzhen Yin
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, and Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, Beijing, China.,Clinical Translational Science Center, Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing, China
| | - Lijun Sun
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, and Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, Beijing, China
| | - Yuan Liang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, and Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, Beijing, China
| | - Chao Luo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, and Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, Beijing, China
| | - Tiange Feng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, and Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, Beijing, China
| | - Yunhua Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, and Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, Beijing, China
| | - Weizhen Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, and Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, Beijing, China.,Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Yue Yin
- Department of Pharmacology, School of Basic Medical Sciences, and Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Peking University, Beijing, China
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5
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Gallego Romero I, Lea AJ. Leveraging massively parallel reporter assays for evolutionary questions. Genome Biol 2023; 24:26. [PMID: 36788564 PMCID: PMC9926830 DOI: 10.1186/s13059-023-02856-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 01/17/2023] [Indexed: 02/16/2023] Open
Abstract
A long-standing goal of evolutionary biology is to decode how gene regulation contributes to organismal diversity. Doing so is challenging because it is hard to predict function from non-coding sequence and to perform molecular research with non-model taxa. Massively parallel reporter assays (MPRAs) enable the testing of thousands to millions of sequences for regulatory activity simultaneously. Here, we discuss the execution, advantages, and limitations of MPRAs, with a focus on evolutionary questions. We propose solutions for extending MPRAs to rare taxa and those with limited genomic resources, and we underscore MPRA's broad potential for driving genome-scale, functional studies across organisms.
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Affiliation(s)
- Irene Gallego Romero
- Melbourne Integrative Genomics, University of Melbourne, Royal Parade, Parkville, Victoria, 3010, Australia. .,School of BioSciences, The University of Melbourne, Royal Parade, Parkville, 3010, Australia. .,The Centre for Stem Cell Systems, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, 30 Royal Parade, Parkville, Victoria, 3010, Australia. .,Center for Genomics, Evolution and Medicine, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia.
| | - Amanda J. Lea
- grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN 37240 USA ,grid.152326.10000 0001 2264 7217Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37240 USA ,grid.152326.10000 0001 2264 7217Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37240 USA ,Child and Brain Development Program, Canadian Institute for Advanced Study, Toronto, Canada
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6
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Marques-da-Silva C, Poudel B, Baptista RP, Peissig K, Hancox LS, Shiau JC, Pewe LL, Shears MJ, Kanneganti TD, Sinnis P, Kyle DE, Gurung P, Harty JT, Kurup SP. AIM2 sensors mediate immunity to Plasmodium infection in hepatocytes. Proc Natl Acad Sci U S A 2023; 120:e2210181120. [PMID: 36595704 PMCID: PMC9926219 DOI: 10.1073/pnas.2210181120] [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: 06/15/2022] [Accepted: 11/18/2022] [Indexed: 01/05/2023] Open
Abstract
Malaria, caused by Plasmodium parasites is a severe disease affecting millions of people around the world. Plasmodium undergoes obligatory development and replication in the hepatocytes, before initiating the life-threatening blood-stage of malaria. Although the natural immune responses impeding Plasmodium infection and development in the liver are key to controlling clinical malaria and transmission, those remain relatively unknown. Here we demonstrate that the DNA of Plasmodium parasites is sensed by cytosolic AIM2 (absent in melanoma 2) receptors in the infected hepatocytes, resulting in Caspase-1 activation. Remarkably, Caspase-1 was observed to undergo unconventional proteolytic processing in hepatocytes, resulting in the activation of the membrane pore-forming protein, Gasdermin D, but not inflammasome-associated proinflammatory cytokines. Nevertheless, this resulted in the elimination of Plasmodium-infected hepatocytes and the control of malaria infection in the liver. Our study uncovers a pathway of natural immunity critical for the control of malaria in the liver.
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Affiliation(s)
- Camila Marques-da-Silva
- Department of Cellular Biology, University of Georgia, Athens, GA30605
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA30605
| | - Barun Poudel
- Department of Internal Medicine, University of Iowa, Iowa City, IA52242
| | - Rodrigo P. Baptista
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA30605
- Institute of Bioinformatics, University of Georgia, Athens, GA30605
| | - Kristen Peissig
- Department of Cellular Biology, University of Georgia, Athens, GA30605
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA30605
| | - Lisa S. Hancox
- Department of Pathology, University of Iowa, Iowa City, IA52242
| | - Justine C. Shiau
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA30605
- Department of Infectious Diseases, University of Georgia, Athens, GA30605
| | - Lecia L. Pewe
- Department of Pathology, University of Iowa, Iowa City, IA52242
| | - Melanie J. Shears
- Johns Hopkins Malaria Research Institute, Johns Hopkins University, Baltimore, MD21205
- Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, MD21205
| | | | - Photini Sinnis
- Johns Hopkins Malaria Research Institute, Johns Hopkins University, Baltimore, MD21205
- Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, MD21205
| | - Dennis E. Kyle
- Department of Cellular Biology, University of Georgia, Athens, GA30605
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA30605
- Department of Infectious Diseases, University of Georgia, Athens, GA30605
| | - Prajwal Gurung
- Department of Internal Medicine, University of Iowa, Iowa City, IA52242
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA52242
| | - John T. Harty
- Department of Pathology, University of Iowa, Iowa City, IA52242
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA52242
| | - Samarchith P. Kurup
- Department of Cellular Biology, University of Georgia, Athens, GA30605
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA30605
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7
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Lv S, Zhou Y, Chen J, Yuan H, Zhang ZN, Luan B. Hepatic ER stress suppresses adipose browning through ATF4-CIRP-ANGPTL3 cascade. Cell Rep 2022; 40:111422. [PMID: 36170814 DOI: 10.1016/j.celrep.2022.111422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 07/28/2022] [Accepted: 09/07/2022] [Indexed: 12/01/2022] Open
Abstract
Hepatic endoplasmic reticulum (ER) stress is a hallmark of obesity-induced liver steatosis and contributes to the progress of steatosis and insulin resistance in liver. However, its influence on adipose function is still unclear. Here, we identify a hepatic ER stress-induced activating transcription factor 4 (ATF4)-cold-inducible RNA-binding protein (CIRP)-angiopoietin-related protein3 (ANGPTL3) cascade critical for the regulation of adipose browning. We find that obesity increases CIRP expression in liver through ER stress-induced ATF4. CIRP in turn binds to the 3' UTR and increases mRNA stability of ANGPTL3. ANGPTL3 secreted from liver suppresses uncoupling protein 1 expression through integrin αvβ3 and c-Jun N-terminal kinase in adipose tissue. While hepatic expression of either ATF4, CIRP, or ANGPTL3 suppresses adipose browning, knockdown of CIRP and ANGPTL3 in liver or administration of integrin αvβ3 inhibitor cilengitide increases adipose browning process. Taken together, we identify a communication mechanism to link hepatic ER stress and adipose browning that may imply a reciprocal regulation of obesity and liver steatosis.
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Affiliation(s)
- Sihan Lv
- Department of Endocrinology, Tongji Hospital Affiliated to Tongji University, School of Medicine, Tongji University, Shanghai 200072, China
| | - Yingqun Zhou
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China
| | - Jiaojiao Chen
- Department of Gastroenterology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China; School of Clinical Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Huiwen Yuan
- Department of Endocrinology, Tongji Hospital Affiliated to Tongji University, School of Medicine, Tongji University, Shanghai 200072, China
| | - Zhen-Ning Zhang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Bing Luan
- Department of Endocrinology, Tongji Hospital Affiliated to Tongji University, School of Medicine, Tongji University, Shanghai 200072, China.
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8
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Braun CJ, Adames AC, Saur D, Rad R. Tutorial: design and execution of CRISPR in vivo screens. Nat Protoc 2022; 17:1903-1925. [PMID: 35840661 DOI: 10.1038/s41596-022-00700-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 03/22/2022] [Indexed: 11/09/2022]
Abstract
Here we provide a detailed tutorial on CRISPR in vivo screening. Using the mouse as the model organism, we introduce a range of CRISPR tools and applications, delineate general considerations for 'transplantation-based' or 'direct in vivo' screening design, and provide details on technical execution, sequencing readouts, computational analyses and data interpretation. In vivo screens face unique pitfalls and limitations, such as delivery issues or library bottlenecking, which must be counteracted to avoid screening failure or flawed conclusions. A broad variety of in vivo phenotypes can be interrogated such as organ development, hematopoietic lineage decision and evolutionary licensing in oncogenesis. We describe experimental strategies to address various biological questions and provide an outlook on emerging CRISPR applications, such as genetic interaction screening. These technological advances create potent new opportunities to dissect the molecular underpinnings of complex organismal phenotypes.
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Affiliation(s)
- Christian J Braun
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany. .,Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany. .,Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Andrés Carbonell Adames
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Dieter Saur
- Institute of Experimental Cancer Therapy, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany. .,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany. .,Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany. .,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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9
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Giri J, Basu M, Roy S, Mishra T, Jana K, Chande A, Ukil A. Translationally Controlled Tumor Protein-Mediated Stabilization of Host Antiapoptotic Protein MCL-1 Is Critical for Establishment of Infection by Intramacrophage Parasite Leishmania donovani. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:2540-2548. [PMID: 35562118 DOI: 10.4049/jimmunol.2100748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 03/21/2022] [Indexed: 06/15/2023]
Abstract
In the early phase of infection, the intramacrophage pathogen Leishmania donovani protects its niche with the help of the antiapoptotic protein myeloid cell leukemia-1 (MCL-1). Whether Leishmania could exploit MCL-1, an extremely labile protein, at the late phase is still unclear. A steady translational level of MCL-1 observed up to 48 h postinfection and increased caspase-3 activity in MCL-1-silenced infected macrophages documented its importance in the late hours of infection. The transcript level of MCL-1 showed a sharp decline at 6 h postinfection, and persistent MCL-1 expression in cyclohexamide-treated cells negates the possibility of de novo protein synthesis, thereby suggesting infection-induced stability. Increased ubiquitination, a prerequisite for proteasomal degradation of MCL-1, was also found to be absent in the late hours of infection. Lack of interaction with its specific E3 ubiquitin ligase MULE (MCL-1 ubiquitin ligase E3) and specific deubiquitinase USP9X prompted us to search for blockade of the ubiquitin-binding site in MCL-1. To this end, TCTP (translationally controlled tumor protein), a well-known binding partner of MCL-1 and antiapoptotic regulator, was found to be strongly associated with MCL-1 during infection. Phosphorylation of TCTP, a requirement for MCL-1 binding, was also increased in infected macrophages. Knockdown of TCTP decreased MCL-1 expression and short hairpin RNA-mediated silencing of TCTP in an infected mouse model of visceral leishmaniasis showed decreased parasite burden and induction of liver cell apoptosis. Collectively, our investigation revealed a key mechanism of how L. donovani exploits TCTP to establish infection within the host.
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Affiliation(s)
- Jayeeta Giri
- Department of Biochemistry, University of Calcutta, Kolkata, India
| | - Moumita Basu
- Biosciences and Bioengineering Department, Indian Institute of Technology, Mumbai, India
| | - Shalini Roy
- Department of Biochemistry, University of Calcutta, Kolkata, India
| | - Tarun Mishra
- Molecular Virology Laboratory, Indian Institute of Science Education and Research Bhopal, Bhopal, India; and
| | - Kuladip Jana
- Division of Molecular Medicine, Bose Institute, P1/12 Calcutta Improvement Trust Scheme VIIM, Kolkata, India
| | - Ajit Chande
- Molecular Virology Laboratory, Indian Institute of Science Education and Research Bhopal, Bhopal, India; and
| | - Anindita Ukil
- Department of Biochemistry, University of Calcutta, Kolkata, India;
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10
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Rouatbi N, McGlynn T, Al-Jamal KT. Pre-clinical non-viral vectors exploited for in vivo CRISPR/Cas9 gene editing: an overview. Biomater Sci 2022; 10:3410-3432. [PMID: 35604372 DOI: 10.1039/d1bm01452h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Clustered regulatory interspaced short palindromic repeats or CRISPR/Cas9 has emerged as a potent and versatile tool for efficient genome editing. This technology has been exploited for several applications including disease modelling, cell therapy, diagnosis, and treatment of many diseases including cancer. The in vivo application of CRISPR/Cas9 is hindered by poor stability, pharmacokinetic profile, and the limited ability of the CRISPR payloads to cross biological barriers. Although viral vectors have been implemented as delivery tools for efficient in vivo gene editing, their application is associated with high immunogenicity and toxicity, limiting their clinical translation. Hence, there is a need to explore new delivery methods that can guarantee safe and efficient delivery of the CRISPR/Cas9 components to target cells. In this review, we first provide a brief history and principles of nuclease-mediated gene editing, we then focus on the different CRISPR/Cas9 formats outlining their potentials and limitations. Finally, we discuss the alternative non-viral delivery strategies currently adopted for in vivo CRISPR/Cas9 gene editing.
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Affiliation(s)
- Nadia Rouatbi
- Institute of Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK.
| | - Tasneem McGlynn
- Institute of Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK.
| | - Khuloud T Al-Jamal
- Institute of Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, UK.
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11
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Kaltenbacher T, Löprich J, Maresch R, Weber J, Müller S, Oellinger R, Groß N, Griger J, de Andrade Krätzig N, Avramopoulos P, Ramanujam D, Brummer S, Widholz SA, Bärthel S, Falcomatà C, Pfaus A, Alnatsha A, Mayerle J, Schmidt-Supprian M, Reichert M, Schneider G, Ehmer U, Braun CJ, Saur D, Engelhardt S, Rad R. CRISPR somatic genome engineering and cancer modeling in the mouse pancreas and liver. Nat Protoc 2022; 17:1142-1188. [PMID: 35288718 DOI: 10.1038/s41596-021-00677-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/07/2021] [Indexed: 12/23/2022]
Abstract
Genetically engineered mouse models (GEMMs) transformed the study of organismal disease phenotypes but are limited by their lengthy generation in embryonic stem cells. Here, we describe methods for rapid and scalable genome engineering in somatic cells of the liver and pancreas through delivery of CRISPR components into living mice. We introduce the spectrum of genetic tools, delineate viral and nonviral CRISPR delivery strategies and describe a series of applications, ranging from gene editing and cancer modeling to chromosome engineering or CRISPR multiplexing and its spatio-temporal control. Beyond experimental design and execution, the protocol describes quantification of genetic and functional editing outcomes, including sequencing approaches, data analysis and interpretation. Compared to traditional knockout mice, somatic GEMMs face an increased risk for mouse-to-mouse variability because of the higher experimental demands of the procedures. The robust protocols described here will help unleash the full potential of somatic genome manipulation. Depending on the delivery method and envisaged application, the protocol takes 3-5 weeks.
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Affiliation(s)
- Thorsten Kaltenbacher
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Jessica Löprich
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Roman Maresch
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Julia Weber
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Sebastian Müller
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Rupert Oellinger
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Nina Groß
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Joscha Griger
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Niklas de Andrade Krätzig
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Petros Avramopoulos
- Institute of Pharmacology and Toxicology, Technical University of Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Deepak Ramanujam
- Institute of Pharmacology and Toxicology, Technical University of Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Sabine Brummer
- Institute of Pharmacology and Toxicology, Technical University of Munich, Munich, Germany
| | - Sebastian A Widholz
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Stefanie Bärthel
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Experimental Cancer Therapy, Technical University of Munich, Munich, Germany
| | - Chiara Falcomatà
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Experimental Cancer Therapy, Technical University of Munich, Munich, Germany
| | - Anja Pfaus
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Ahmed Alnatsha
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Julia Mayerle
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marc Schmidt-Supprian
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Experimental Hematology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Maximilian Reichert
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Günter Schneider
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Ursula Ehmer
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Christian J Braun
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany.,Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Experimental Cancer Therapy, Technical University of Munich, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Stefan Engelhardt
- Institute of Pharmacology and Toxicology, Technical University of Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany. .,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany. .,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.
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12
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Wang H, Chen X. Hydrodynamic Injection for Developing NASH Model. Methods Mol Biol 2022; 2455:31-39. [PMID: 35212983 PMCID: PMC8939306 DOI: 10.1007/978-1-0716-2128-8_3] [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: 01/03/2023]
Abstract
The hydrodynamic tail vein injection (HTVi) is a technique that is used to deliver plasmid genes into live mice or rats. The HTVi leads to the in vivo transfection of exogenous DNA primarily in the liver, serving as a reliable approach of establishing animal models for the study of liver diseases. The nonalcoholic steatohepatitis (NASH) is liver inflammation and damage resulting from an accumulation of fat in the liver. With the rising prevalence of obesity worldwide, NASH is becoming an increasingly common health problem. The pathogenesis of NASH is a multi-step process involving complicated pathways. The molecular mechanisms of NASH remain poorly understood. Here, we describe the use of HTVi to establish animal models for the study of NASH.
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Affiliation(s)
- Haichuan Wang
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, CA, USA
| | - Xin Chen
- Department of Bioengineering and Therapeutic Sciences and Liver Center, University of California, San Francisco, CA, USA.
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13
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Romanov SE, Kalashnikova DA, Laktionov PP. Methods of massive parallel reporter assays for investigation of enhancers. Vavilovskii Zhurnal Genet Selektsii 2021; 25:344-355. [PMID: 34901731 PMCID: PMC8627875 DOI: 10.18699/vj21.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 03/28/2021] [Accepted: 03/28/2021] [Indexed: 11/19/2022] Open
Abstract
The correct deployment of genetic programs for development and differentiation relies on finely coordinated regulation of specific gene sets. Genomic regulatory elements play an exceptional role in this process. There are few types of gene regulatory elements, including promoters, enhancers, insulators and silencers. Alterations of gene regulatory elements may cause various pathologies, including cancer, congenital disorders and autoimmune diseases. The development of high-throughput genomic assays has made it possible to significantly accelerate the accumulation of information about the characteristic epigenetic properties of regulatory elements. In combination with high-throughput studies focused on the genome-wide distribution of epigenetic marks, regulatory proteins and the spatial structure of chromatin, this significantly expands the understanding of the principles of epigenetic regulation of genes and allows potential regulatory elements to be searched for in silico. However, common experimental approaches used to study the local characteristics of chromatin have a number of technical limitations that may reduce the reliability of computational identification of genomic regulatory sequences. Taking into account the variability of the functions of epigenetic determinants and complex multicomponent regulation of genomic elements activity, their functional verification is often required. A plethora of methods have been developed to study the functional role of regulatory elements on the genome scale. Common experimental approaches for in silico identification of regulatory elements and their inherent technical limitations will be described. The present review is focused on original high-throughput methods of enhancer activity reporter analysis that are currently used to validate predicted regulatory elements and to perform de novo searches. The methods described allow assessing the functional role of the nucleotide sequence of a regulatory element, to determine its exact boundaries and to assess the influence of the local state of chromatin on the activity of enhancers and gene expression. These approaches have contributed substantially to the understanding of the fundamental principles of gene regulation.
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Affiliation(s)
- S E Romanov
- Novosibirsk State University, Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk, Russia Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Genomics Laboratory, Novosibirsk, Russia
| | - D A Kalashnikova
- Novosibirsk State University, Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk, Russia Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Genomics Laboratory, Novosibirsk, Russia
| | - P P Laktionov
- Novosibirsk State University, Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk, Russia Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Genomics Laboratory, Novosibirsk, Russia
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14
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Gendron WAC, Rubin JD, Hansen MJ, Nace RA, Simone BW, Ekker SC, Barry MA. Unlocking loxP to Track Genome Editing In Vivo. Genes (Basel) 2021; 12:1204. [PMID: 34440379 PMCID: PMC8394901 DOI: 10.3390/genes12081204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/05/2021] [Accepted: 07/22/2021] [Indexed: 11/16/2022] Open
Abstract
The development of CRISPR-associated proteins, such as Cas9, has led to increased accessibility and ease of use in genome editing. However, additional tools are needed to quantify and identify successful genome editing events in living animals. We developed a method to rapidly quantify and monitor gene editing activity non-invasively in living animals that also facilitates confocal microscopy and nucleotide level analyses. Here we report a new CRISPR "fingerprinting" approach to activating luciferase and fluorescent proteins in mice as a function of gene editing. This system is based on experience with our prior cre recombinase (cre)-detector system and is designed for Cas editors able to target loxP including gRNAs for SaCas9 and ErCas12a. These CRISPRs cut specifically within loxP, an approach that is a departure from previous gene editing in vivo activity detection techniques that targeted adjacent stop sequences. In this sensor paradigm, CRISPR activity was monitored non-invasively in living cre reporter mice (FVB.129S6(B6)-Gt(ROSA)26Sortm1(Luc)Kael/J and Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J, which will be referred to as LSL-luciferase and mT/mG throughout the paper) after intramuscular or intravenous hydrodynamic plasmid injections, demonstrating utility in two diverse organ systems. The same genome-editing event was examined at the cellular level in specific tissues by confocal microscopy to determine the identity and frequency of successfully genome-edited cells. Further, SaCas9 induced targeted editing at efficiencies that were comparable to cre, demonstrating high effective delivery and activity in a whole animal. This work establishes genome editing tools and models to track CRISPR editing in vivo non-invasively and to fingerprint the identity of targeted cells. This approach also enables similar utility for any of the thousands of previously generated loxP animal models.
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Affiliation(s)
- William A. C. Gendron
- Virology and Gene Therapy Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA; (W.A.C.G.); (J.D.R.); (M.J.H.); (R.A.N.)
| | - Jeffrey D. Rubin
- Virology and Gene Therapy Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA; (W.A.C.G.); (J.D.R.); (M.J.H.); (R.A.N.)
| | - Michael J. Hansen
- Virology and Gene Therapy Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA; (W.A.C.G.); (J.D.R.); (M.J.H.); (R.A.N.)
| | - Rebecca A. Nace
- Virology and Gene Therapy Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA; (W.A.C.G.); (J.D.R.); (M.J.H.); (R.A.N.)
| | - Brandon W. Simone
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (B.W.S.); (S.C.E.)
| | - Stephen C. Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (B.W.S.); (S.C.E.)
| | - Michael A. Barry
- Department of Medicine, Division of Infectious Diseases, Mayo Clinic, Rochester, MN 55905, USA
- Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
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15
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Hunt C, Hartford SA, White D, Pefanis E, Hanna T, Herman C, Wiley J, Brown H, Su Q, Xin Y, Voronin D, Nguyen H, Altarejos J, Crosby K, Haines J, Cancelarich S, Drummond M, Moller-Tank S, Malpass R, Buckley J, Del Pilar Molina-Portela M, Droguett G, Frendewey D, Chiao E, Zambrowicz B, Gong G. Tissue-specific activation of gene expression by the Synergistic Activation Mediator (SAM) CRISPRa system in mice. Nat Commun 2021; 12:2770. [PMID: 33986266 PMCID: PMC8119962 DOI: 10.1038/s41467-021-22932-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/06/2021] [Indexed: 02/03/2023] Open
Abstract
CRISPR-based transcriptional activation is a powerful tool for functional gene interrogation; however, delivery difficulties have limited its applications in vivo. Here, we created a mouse model expressing all components of the CRISPR-Cas9 guide RNA-directed Synergistic Activation Mediator (SAM) from a single transcript that is capable of activating target genes in a tissue-specific manner. We optimized Lipid Nanoparticles and Adeno-Associated Virus guide RNA delivery approaches to achieve expression modulation of one or more genes in vivo. We utilized the SAM mouse model to generate a hypercholesteremia disease state that we could bidirectionally modulate with various guide RNAs. Additionally, we applied SAM to optimize gene expression in a humanized Transthyretin mouse model to recapitulate human expression levels. These results demonstrate that the SAM gene activation platform can facilitate in vivo research and drug discovery.
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Affiliation(s)
| | | | - Derek White
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | | | | | | | | | | | - Qi Su
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | - Yurong Xin
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | | | - Hien Nguyen
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | | | - Keith Crosby
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | | | | | | | | | - Ryan Malpass
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | | | | | | | | | - Eric Chiao
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | | | - Guochun Gong
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA.
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16
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Ghassemi B, Jamalkhah M, Shokri G, Kehtari M, Soleimani M, Shamsara M, Kiani J. Improved efficiency of genome editing by constitutive expression of Cas9 endonuclease in genetically-modified mice. 3 Biotech 2021; 11:56. [PMID: 33489675 DOI: 10.1007/s13205-020-02580-z] [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: 07/27/2020] [Accepted: 12/01/2020] [Indexed: 11/30/2022] Open
Abstract
Despite its convenience and precision, CRISPR-based gene editing approaches still suffer from off-target effects and low efficiencies, which are partially rooted in Cas9, the nuclease component of the CRISPR/Cas9 system. In this study, we showed how mouse genome editing efficiency can be improved by constitutive and inheritable expression of Cas9 nuclease. For this goal, a transgenic mouse line expressing the Cas9 protein (Cas9-mouse) was generated. For in vitro assessment of gene editing efficiency, the Cas9-mice were crossed with the EGFP-mice to obtain mouse embryonic fibroblasts (MEF) expressing both EGFP and Cas9 (MEFCas9-EGFP). Transfection of these cells with in vitro transcribed (IVT) EGFP sgRNA or phU6-EGFPsgRNA plasmid led to robust decrease of Mean Fluorescent Intensity (MFI) to 8500 ± 1025 a.u. and 13,200 ± 1006 a.u. respectively. However, in the control group, in which the MEFEGFP cells were transfected with a pX330-EGFPsgRNA plasmid, the measured MFI was 16,800 ± 2254 a.u. For in vivo assessment, the Cas9-zygotes at two pronuclei stage (2PN) were microinjected with a phU6-HhexsgRNA vector and the gene mutation efficiency was compared with the wild-type (WT) zygotes microinjected with a pX330-HhexsgRNA plasmid. The analysis of born mice showed that while the injection of Cas9-zygotes resulted in 43.75% Hhex gene mutated mice, it was just 15.79% for the WT zygotes. In conclusion, the inheritable and constitutive expression of Cas9 in mice provides an efficient platform for gene editing, which can facilitate the production of genetically-modified cells and animals.
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Affiliation(s)
- Bita Ghassemi
- Division of Continuing Education, University of California Irvine, Irvine, CA USA
| | - Monire Jamalkhah
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Gelareh Shokri
- Department of Molecular Biology and Genetic Engineering, Stem Cell Technology Research Center, Tehran, Iran
| | - Mousa Kehtari
- Department of Stem Cell Biology, Stem Cell Technology Research Center, Tehran, Iran
| | - Masoud Soleimani
- Hematology Department, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mehdi Shamsara
- Department of Animal Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Jafar Kiani
- Cellular and Molecular Research Centre, Iran University of Medical Sciences, Iran University of Medical Sciences, Shahid Hemmat Highway, Tehran, Iran
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
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17
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Whitlock RS, Yang T, Vasudevan SA, Woodfield SE. Animal Modeling of Pediatric Liver Cancer. Cancers (Basel) 2020; 12:cancers12020273. [PMID: 31979130 PMCID: PMC7072332 DOI: 10.3390/cancers12020273] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/19/2020] [Accepted: 01/19/2020] [Indexed: 01/09/2023] Open
Abstract
Hepatoblastoma (HB) is the most common pediatric liver malignancy. Management of HB requires multidisciplinary efforts. The 5-year overall survival of this disease is about 80% in developed countries. Despite advances in the care of these patients, survival in recurrent or treatment-refractory disease is lower than 50%. This is due to more complex tumor biology, including hepatocellular carcinoma (HCC)-like mutations and expression of aggressive gene signatures leading to chemoresistance, vascular invasion, and metastatic spread. The current treatment protocols for pediatric liver cancer do not incorporate targeted therapies, and the ability to test these therapies is limited due to the inaccessibility of cell lines and mouse models. In this review, we discuss the current status of preclinical animal modeling in pediatric liver cancer, primarily HB. Although HB is a rare cancer, the research community has worked together to develop a range of interesting and relevant mouse models for diverse preclinical studies.
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Affiliation(s)
- Richard S. Whitlock
- Divisions of Pediatric Surgery and Surgical Research, Michael E. DeBakey Department of Surgery, Pediatric Surgical Oncology Laboratory, Texas Children’s Surgical Oncology Program, Texas Children’s Liver Tumor Program, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; (R.S.W.); (S.A.V.)
| | - Tianyou Yang
- Department of Pediatric Surgery, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Sanjeev A. Vasudevan
- Divisions of Pediatric Surgery and Surgical Research, Michael E. DeBakey Department of Surgery, Pediatric Surgical Oncology Laboratory, Texas Children’s Surgical Oncology Program, Texas Children’s Liver Tumor Program, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; (R.S.W.); (S.A.V.)
| | - Sarah E. Woodfield
- Divisions of Pediatric Surgery and Surgical Research, Michael E. DeBakey Department of Surgery, Pediatric Surgical Oncology Laboratory, Texas Children’s Surgical Oncology Program, Texas Children’s Liver Tumor Program, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; (R.S.W.); (S.A.V.)
- Correspondence: ; Tel.: +1-832-824-4591
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18
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Takada S, Watanabe T, Mizuta R. DNase γ-dependent DNA fragmentation causes karyolysis in necrotic hepatocyte. J Vet Med Sci 2019; 82:23-26. [PMID: 31735730 PMCID: PMC6983664 DOI: 10.1292/jvms.19-0499] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Karyolysis is the complete dissolution of nuclear components of a dying cell. However, the generation mechanism has not been clarified. We studied a necrotic DNA fragmentation factor DNase γ (also known as DNase1L3) and previously found that karyolysis was inhibited in DNase γ deficient (DNase γ−/−) mice. To confirm this, we transiently expressed DNase γ in the liver of DNase γ−/− mice and caused hepatocyte necrosis by acetaminophen overdose. As expected, karyolysis was induced in the necrotic hepatocytes. We also found that the depletion of Kupffer cells from wild type mice reduced the expression and activity of DNase γ in the liver. Thus, we concluded that DNase γ produced from Kupffer cells caused karyolysis of necrotic hepatocytes.
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Affiliation(s)
- Shuhei Takada
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba 278-0022, Japan
| | - Taiki Watanabe
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba 278-0022, Japan
| | - Ryushin Mizuta
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba 278-0022, Japan
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19
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Torresi J, Tran BM, Christiansen D, Earnest-Silveira L, Schwab RHM, Vincan E. HBV-related hepatocarcinogenesis: the role of signalling pathways and innovative ex vivo research models. BMC Cancer 2019; 19:707. [PMID: 31319796 PMCID: PMC6637598 DOI: 10.1186/s12885-019-5916-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 07/09/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) is the leading cause of liver cancer, but the mechanisms by which HBV causes liver cancer are poorly understood and chemotherapeutic strategies to cure liver cancer are not available. A better understanding of how HBV requisitions cellular components in the liver will identify novel therapeutic targets for HBV associated hepatocellular carcinoma (HCC). MAIN BODY The development of HCC involves deregulation in several cellular signalling pathways including Wnt/FZD/β-catenin, PI3K/Akt/mTOR, IRS1/IGF, and Ras/Raf/MAPK. HBV is known to dysregulate several hepatocyte pathways and cell cycle regulation resulting in HCC development. A number of these HBV induced changes are also mediated through the Wnt/FZD/β-catenin pathway. The lack of a suitable human liver model for the study of HBV has hampered research into understanding pathogenesis of HBV. Primary human hepatocytes provide one option; however, these cells are prone to losing their hepatic functionality and their ability to support HBV replication. Another approach involves induced-pluripotent stem (iPS) cell-derived hepatocytes. However, iPS technology relies on retroviruses or lentiviruses for effective gene delivery and pose the risk of activating a range of oncogenes. Liver organoids developed from patient-derived liver tissues provide a significant advance in HCC research. Liver organoids retain the characteristics of their original tissue, undergo unlimited expansion, can be differentiated into mature hepatocytes and are susceptible to natural infection with HBV. CONCLUSION By utilizing new ex vivo techniques like liver organoids it will become possible to develop improved and personalized therapeutic approaches that will improve HCC outcomes and potentially lead to a cure for HBV.
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Affiliation(s)
- Joseph Torresi
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010 Australia
| | - Bang Manh Tran
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010 Australia
| | - Dale Christiansen
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010 Australia
| | - Linda Earnest-Silveira
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010 Australia
| | - Renate Hilda Marianne Schwab
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010 Australia
| | - Elizabeth Vincan
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010 Australia
- Victorian Infectious Diseases Reference Laboratory, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010 Australia
- School of Pharmacy and Biomedical Sciences, Curtin University, Perth, WA 6845 Australia
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20
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Yamamoto M, Xin B, Nishikawa Y. Mouse Model for Hepatocellular Carcinoma and Cholangiocarcinoma Originated from Mature Hepatocytes. Methods Mol Biol 2019; 1905:221-236. [PMID: 30536104 DOI: 10.1007/978-1-4939-8961-4_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Liver cancer consists of two main histological subtypes, hepatocellular carcinoma and cholangiocarcinoma, both of which have poor prognosis. Therefore, in searching for new therapeutic targets, adequate mouse models to develop and validate therapeutic strategies are urgently needed. Although there are mouse models of liver cancer, each model has shortcomings. To overcome these shortcomings, a mouse model using a hydrodynamic tail vein injection and the Sleeping Beauty transposon was developed. By inducing stable expression of oncogenes in mouse hepatocytes in vivo, the model can easily induce liver cancer with specific characteristics that depend on the oncogenes used to induce carcinogenesis. Here, we describe the details of the methods to induce hepatocellular carcinoma or cholangiocarcinoma from mouse hepatocytes.
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Affiliation(s)
- Masahiro Yamamoto
- Division of Tumor Pathology, Department of Pathology, Asahikawa Medical University, Asahikawa, Hokkaido, Japan.
| | - Bing Xin
- Division of Tumor Pathology, Department of Pathology, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
| | - Yuji Nishikawa
- Division of Tumor Pathology, Department of Pathology, Asahikawa Medical University, Asahikawa, Hokkaido, Japan
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21
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Olsen TM, Stone BC, Chuenchob V, Murphy SC. Prime-and-Trap Malaria Vaccination To Generate Protective CD8 + Liver-Resident Memory T Cells. THE JOURNAL OF IMMUNOLOGY 2018; 201:1984-1993. [PMID: 30127085 DOI: 10.4049/jimmunol.1800740] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/02/2018] [Indexed: 11/19/2022]
Abstract
Tissue-resident memory CD8+ T (Trm) cells in the liver are critical for long-term protection against pre-erythrocytic Plasmodium infection. Such protection can usually be induced with three to five doses of i.v. administered radiation-attenuated sporozoites (RAS). To simplify and accelerate vaccination, we tested a DNA vaccine designed to induce potent T cell responses against the SYVPSAEQI epitope of Plasmodium yoelii circumsporozoite protein. In a heterologous "prime-and-trap" regimen, priming using gene gun-administered DNA and boosting with one dose of RAS attracted expanding Ag-specific CD8+ T cell populations to the liver, where they became Trm cells. Vaccinated in this manner, BALB/c mice were completely protected against challenge, an outcome not reliably achieved following one dose of RAS or following DNA-only vaccination. This study demonstrates that the combination of CD8+ T cell priming by DNA and boosting with liver-homing RAS enhances formation of a completely protective liver Trm cell response and suggests novel approaches for enhancing T cell-based pre-erythrocytic malaria vaccines.
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Affiliation(s)
- Tayla M Olsen
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98109.,Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, WA 98109
| | - Brad C Stone
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98109.,Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, WA 98109
| | - Vorada Chuenchob
- Center for Infectious Disease Research, University of Washington, Seattle, WA 98109; and
| | - Sean C Murphy
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98109; .,Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, WA 98109.,Department of Microbiology, University of Washington, Seattle, WA 98195
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Synthetic cytokine receptors transmit biological signals using artificial ligands. Nat Commun 2018; 9:2034. [PMID: 29789554 PMCID: PMC5964073 DOI: 10.1038/s41467-018-04454-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/23/2018] [Indexed: 11/25/2022] Open
Abstract
Cytokine-induced signal transduction is executed by natural biological switches, which among many others control immune-related processes. Here, we show that synthetic cytokine receptors (SyCyRs) can induce cytokine signaling using non-physiological ligands. High-affinity GFP- and mCherry-nanobodies were fused to transmembrane and intracellular domains of the IL-6/IL-11 and IL-23 cytokine receptors gp130 and IL-12Rβ1/IL-23R, respectively. Homo- and heterodimeric GFP:mCherry fusion proteins as synthetic cytokine-like ligands were able to induce canonical signaling in vitro and in vivo. Using SyCyR ligands, we show that IL-23 receptor homodimerization results in its activation and IL-23-like signal transduction. Moreover, trimeric receptor assembly induces trans-phosphorylation among cytokine receptors with associated Janus kinases. The SyCyR technology allows biochemical analyses of transmembrane receptor signaling in vitro and in vivo, cell-specific activation through SyCyR ligands using transgenic animals and possible therapeutic regimes involving non-physiological targets during immunotherapy. Cytokine-induced signaling acts as an ON/OFF switch dependent on the presence of ligands. Here the authors construct synthetic cytokine receptors responsive to synthetic ligands able to activate canonical signaling pathways.
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Eclov RJ, Kim MJ, Chhibber A, Smith RP, Ahituv N, Kroetz DL. ABCG2 regulatory single-nucleotide polymorphisms alter in vivo enhancer activity and expression. Pharmacogenet Genomics 2018; 27:454-463. [PMID: 28930109 DOI: 10.1097/fpc.0000000000000312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
OBJECTIVES The expression and activity of the breast cancer resistance protein (ABCG2) contributes toward the pharmacokinetics of endogenous and xenobiotic substrates. The effect of genetic variation on the activity of cis-regulatory elements and nuclear response elements in the ABCG2 locus and their contribution toward ABCG2 expression have not been investigated systematically. In this study, the effect of genetic variation on the in vitro and in vivo enhancer activity of six previously identified liver enhancers in the ABCG2 locus was examined. METHODS Reference and variant liver enhancers were tested for their ability to alter luciferase activity in vitro in HepG2 and HEK293T cell lines and in vivo using a hydrodynamic tail vein assay. Positive in vivo single-nucleotide polymorphisms (SNPs) were tested for association with gene expression and for altered protein binding in electrophoretic mobility shift assays. RESULTS Multiple SNPs were found to alter enhancer activity in vitro. Four of these variants (rs9999111, rs12508471, ABCG2RE1*2, and rs149713212) decreased and one (rs2725263) increased enhancer activity in vivo. In addition, rs9999111 and rs12508471 were associated with ABCG2 expression in lymphoblastoid cell lines, lymphocytes, and T cells, and showed increased HepG2 nuclear protein binding. CONCLUSION This study identifies SNPs within regulatory regions of the ABCG2 locus that alter enhancer activity in vitro and in vivo. Several of these SNPs correlate with tissue-specific ABCG2 expression and alter DNA/protein binding. These SNPs could contribute toward reported tissue-specific variability in ABCG2 expression and may influence the correlation between ABCG2 expression and disease risk or the pharmacokinetics and pharmacodynamics of breast cancer resistance protein substrates.
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Affiliation(s)
- Rachel J Eclov
- aDepartment of Bioengineering and Therapeutic Sciences bInstitute for Human Genetics, University of California San Francisco, San Francisco, California, USA
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Tat-enhanced delivery of the C terminus of HDAg-L inhibits assembly and secretion of hepatitis D virus. Antiviral Res 2017; 150:69-78. [PMID: 29247673 DOI: 10.1016/j.antiviral.2017.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/30/2017] [Accepted: 12/12/2017] [Indexed: 12/18/2022]
Abstract
Hepatitis D virus (HDV) contains a single-stranded circular RNA genome that encodes two forms of hepatitis delta antigen (HDAg), the small delta antigen (HDAg-S) and the large delta antigen (HDAg-L). The two proteins have an identical amino acid sequence, except that HDAg-L has a 19-amino-acid extension at the C terminus. The domain spanning amino acid residues 198-210 of the HDAg-L (HDAg-L(198-210)) contains a nuclear export signal (NES), which is important for the nuclear export of HDV ribonucleoprotein to the cytoplasm. In this study, we established a cell permeable TAT-HA-HDAg-L(198-210) fusion protein using an E. coli protein expression system, to determine its function during HDV infection. The cytotoxicity of the TAT-HA-HDAg-L(198-210) fusion protein was investigated using an MTT assay, while a GST pull-down assay revealed that the TAT-HA-HDAg-L(198-210) fusion protein interfered with the interaction between HDAg-L and clathrin heavy chain (CHC). In addition, the cellular distribution of HDAg-L, in the presence of HBsAg, was observed by immunofluorescence staining and the TAT-HA-HDAg-L(198-210) fusion protein was found to impede the nuclear export of HDAg-L. Furthermore, assembly of HDV virus-like particles (VLPs) was decreased by the expression of the TAT-HDAg-L(198-210) fusion protein. The TAT-HA-HDAg-L(198-210) fusion protein also inhibited virus particle assembly and HDV secretion in a mouse model. These results suggest that the TAT-HA-HDAg-L(198-210) fusion protein inhibits the nuclear export of HDAg-L and competes with the C terminus of HDAg-L for interaction with CHC, and may have potential as a therapeutic agent for HDV infection.
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Meyer-Kovac J, Kolbe I, Ehrhardt L, Leliavski A, Husse J, Salinas G, Lingner T, Tsang AH, Barclay JL, Oster H. Hepatic gene therapy rescues high-fat diet responses in circadian Clock mutant mice. Mol Metab 2017; 6:512-523. [PMID: 28580282 PMCID: PMC5444075 DOI: 10.1016/j.molmet.2017.03.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 03/16/2017] [Accepted: 03/22/2017] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE Circadian Clock gene mutant mice show dampened 24-h feeding rhythms and an increased sensitivity to high-fat diet (HFD) feeding. Restricting HFD access to the dark phase counteracts its obesogenic effect in wild-type mice. The extent to which altered feeding rhythms are causative for the obesogenic phenotype of Clock mutant mice, however, remains unknown. METHODS Metabolic parameters of wild-type (WT) and ClockΔ19 mutant mice (MT) were investigated under ad libitum and nighttime restricted HFD feeding. Liver circadian clock function was partially rescued by hydrodynamic tail vein delivery of WT-Clock DNA vectors in mutant mice and transcriptional, metabolic, endocrine and behavioral rhythms studied. RESULTS Nighttime-restricted feeding restored food intake, but not body weight regulation in MT mice under HFD, suggesting Clock-dependent metabolic dysregulation downstream of circadian appetite control. Liver-directed Clock gene therapy partially restored liver circadian oscillator function and transcriptome regulation without affecting centrally controlled circadian behaviors. Under HFD, MT mice with partially restored liver clock function (MT-LR) showed normalized body weight gain, rescued 24-h food intake rhythms, and WT-like energy expenditure. This was associated with decreased nighttime leptin and daytime ghrelin levels, reduced hepatic lipid accumulation, and improved glucose tolerance. Transcriptome analysis revealed that hepatic Clock rescue in MT mice affected a range of metabolic pathways. CONCLUSION Liver Clock gene therapy improves resistance against HFD-induced metabolic impairments in mice with circadian clock disruption. Restoring or stabilizing liver clock function might be a promising target for therapeutic interventions in obesity and metabolic disorders.
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Affiliation(s)
- Judit Meyer-Kovac
- Circadian Rhythms Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Isa Kolbe
- Chronophysiology Group, Medical Department 1, University of Lübeck, Lübeck, Germany
| | - Lea Ehrhardt
- Circadian Rhythms Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Alexei Leliavski
- Chronophysiology Group, Medical Department 1, University of Lübeck, Lübeck, Germany
- Institute for Nutrition Medicine, University of Lübeck, Lübeck, Germany
| | - Jana Husse
- Circadian Rhythms Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Gabriela Salinas
- Microarray and Deep-Sequencing Core Facility, Institute Developmental Biochemistry, University Medical Center, Göttingen, Germany
| | - Thomas Lingner
- Microarray and Deep-Sequencing Core Facility, Institute Developmental Biochemistry, University Medical Center, Göttingen, Germany
| | - Anthony H. Tsang
- Circadian Rhythms Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Chronophysiology Group, Medical Department 1, University of Lübeck, Lübeck, Germany
| | | | - Henrik Oster
- Circadian Rhythms Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Chronophysiology Group, Medical Department 1, University of Lübeck, Lübeck, Germany
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Eclov RJ, Kim MJ, Smith RP, Liang X, Ahituv N, Kroetz DL. In Vivo Hepatic Enhancer Elements in the Human ABCG2 Locus. Drug Metab Dispos 2016; 45:208-215. [PMID: 27856528 DOI: 10.1124/dmd.116.072033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 11/02/2016] [Indexed: 12/21/2022] Open
Abstract
ABCG2 encodes the mitoxantrone resistance protein (MXR; breast cancer resistance protein), an ATP-binding cassette (ABC) efflux membrane transporter. Computational analysis of the ∼300 kb region of DNA surrounding ABCG2 (chr4:88911376-89220011, hg19) identified 30 regions with potential cis-regulatory capabilities. These putative regulatory regions were tested for their enhancer and suppressor activity in a human liver cell line using luciferase reporter assays. The in vitro enhancer and suppressor assays identified four regions that decreased gene expression and five regions that increased expression >1.6-fold. Four of five human hepatic in vitro enhancers were confirmed as in vivo liver enhancers using the mouse hydrodynamic tail vein injection assay. Two of the in vivo liver enhancers (ABCG2RE1 and ABCG2RE9) responded to 17β-estradiol or rifampin in human cell lines, and ABCG2RE9 had ChIP-seq evidence to support the binding of several transcription factors and the transcriptional coactivator p300 in human hepatocytes. This study identified genomic regions surrounding human ABCG2 that can function as regulatory elements, some with the capacity to alter gene expression upon environmental stimulus. The results from this research will drive future investigations of interindividual variation in ABCG2 expression and function that contribute to differences in drug response.
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Affiliation(s)
- Rachel J Eclov
- Department of Bioengineering and Therapeutic Sciences (R.J.E., M.J.K., R.P.S., X.L., N.A., D.L.K.); and Institute for Human Genetics (M.J.K., R.P.S., N.A., D.L.K.), University of California, San Francisco, San Francisco, California
| | - Mee J Kim
- Department of Bioengineering and Therapeutic Sciences (R.J.E., M.J.K., R.P.S., X.L., N.A., D.L.K.); and Institute for Human Genetics (M.J.K., R.P.S., N.A., D.L.K.), University of California, San Francisco, San Francisco, California
| | - Robin P Smith
- Department of Bioengineering and Therapeutic Sciences (R.J.E., M.J.K., R.P.S., X.L., N.A., D.L.K.); and Institute for Human Genetics (M.J.K., R.P.S., N.A., D.L.K.), University of California, San Francisco, San Francisco, California
| | - Xiaomin Liang
- Department of Bioengineering and Therapeutic Sciences (R.J.E., M.J.K., R.P.S., X.L., N.A., D.L.K.); and Institute for Human Genetics (M.J.K., R.P.S., N.A., D.L.K.), University of California, San Francisco, San Francisco, California
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences (R.J.E., M.J.K., R.P.S., X.L., N.A., D.L.K.); and Institute for Human Genetics (M.J.K., R.P.S., N.A., D.L.K.), University of California, San Francisco, San Francisco, California
| | - Deanna L Kroetz
- Department of Bioengineering and Therapeutic Sciences (R.J.E., M.J.K., R.P.S., X.L., N.A., D.L.K.); and Institute for Human Genetics (M.J.K., R.P.S., N.A., D.L.K.), University of California, San Francisco, San Francisco, California
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Inoue F, Ahituv N. Decoding enhancers using massively parallel reporter assays. Genomics 2015; 106:159-164. [PMID: 26072433 DOI: 10.1016/j.ygeno.2015.06.005] [Citation(s) in RCA: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/22/2015] [Accepted: 06/08/2015] [Indexed: 10/23/2022]
Abstract
Enhancers control the timing, location and expression levels of their target genes. Nucleotide variation in enhancers has been shown to lead to numerous phenotypes, including human disease. While putative enhancer sequences and nucleotide variation within them can now be detected in a rapid manner using various genomic technologies, the understanding of the functional consequences of these variants still remains largely unknown. Massively parallel reporter assays (MPRAs) can overcome this hurdle by providing the ability to test thousands of sequences and nucleotide variants within them for enhancer activity en masse. Here, we describe this technology and specifically focus on how it is being used to obtain an increased understanding of enhancer regulatory code and grammar.
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Affiliation(s)
- Fumitaka Inoue
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA.
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94158, USA.
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Systematic dissection of coding exons at single nucleotide resolution supports an additional role in cell-specific transcriptional regulation. PLoS Genet 2014; 10:e1004592. [PMID: 25340400 PMCID: PMC4207465 DOI: 10.1371/journal.pgen.1004592] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 07/09/2014] [Indexed: 12/22/2022] Open
Abstract
In addition to their protein coding function, exons can also serve as transcriptional enhancers. Mutations in these exonic-enhancers (eExons) could alter both protein function and transcription. However, the functional consequence of eExon mutations is not well known. Here, using massively parallel reporter assays, we dissect the enhancer activity of three liver eExons (SORL1 exon 17, TRAF3IP2 exon 2, PPARG exon 6) at single nucleotide resolution in the mouse liver. We find that both synonymous and non-synonymous mutations have similar effects on enhancer activity and many of the deleterious mutation clusters overlap known liver-associated transcription factor binding sites. Carrying a similar massively parallel reporter assay in HeLa cells with these three eExons found differences in their mutation profiles compared to the liver, suggesting that enhancers could have distinct operating profiles in different tissues. Our results demonstrate that eExon mutations could lead to multiple phenotypes by disrupting both the protein sequence and enhancer activity and that enhancers can have distinct mutation profiles in different cell types. Exons that code for protein can also have additional functions, such as regulating gene transcription through enhancer activity. Here, we changed every nucleotide in three different exons that also function as enhancers, and examined their enhancer activity to test whether nucleotide changes in these exons can affect both the protein sequence and enhancer function. We found that mutations with a significant effect on enhancer function can reside both in regions that change the protein sequence (non-synonymous) and regions that do not change it (synonymous). When we conducted a similar analysis in a different cell type, we observed a difference in the nucleotide changes that cause a significant effect on enhancer activity, suggesting that the enhancer functional units can differ between tissues.
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Zhang S, Li L, Kendrick SL, Gerard RD, Zhu H. TALEN-mediated somatic mutagenesis in murine models of cancer. Cancer Res 2014; 74:5311-21. [PMID: 25070752 DOI: 10.1158/0008-5472.can-14-0529] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cancer genome sequencing has identified numerous somatic mutations whose biologic relevance is uncertain. In this study, we used genome-editing tools to create and analyze targeted somatic mutations in murine models of liver cancer. Transcription activator-like effector nucleases (TALEN) were designed against β-catenin (Ctnnb1) and adenomatous polyposis coli (Apc), two commonly mutated genes in hepatocellular carcinoma (HCC), to generate isogenic HCC cell lines. Both mutant cell lines exhibited evidence of Wnt pathway dysregulation. We asked whether these TALENs could create targeted somatic mutations after hydrodynamic transfection into mouse liver. TALENs targeting β-catenin promoted endogenous HCC carrying the intended gain-of-function mutations. However, TALENs targeting Apc were not as efficient in inducing in vivo homozygous loss-of-function mutations. We hypothesized that hepatocyte polyploidy might be protective against TALEN-induced loss of heterozygosity, and indeed Apc gene editing was less efficient in tetraploid than in diploid hepatocytes. To increase efficiency, we administered adenoviral Apc TALENs and found that we could achieve a higher mutagenesis rate in vivo. Our results demonstrate that genome-editing tools can enable the in vivo study of cancer genes and faithfully recapitulate the mosaic nature of mutagenesis in mouse cancer models. Cancer Res; 74(18); 5311-21. ©2014 AACR.
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Affiliation(s)
- Shuyuan Zhang
- Department of Pediatrics, Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas. Department of Internal Medicine, Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Lin Li
- Department of Pediatrics, Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas. Department of Internal Medicine, Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Sara L Kendrick
- Department of Pediatrics, Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas. Department of Internal Medicine, Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Robert D Gerard
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Hao Zhu
- Department of Pediatrics, Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas. Department of Internal Medicine, Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas.
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Bhatia S, Kleinjan DA. Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences. Hum Genet 2014; 133:815-45. [DOI: 10.1007/s00439-014-1424-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 01/18/2014] [Indexed: 01/05/2023]
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