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Yarnall MTN, Ioannidi EI, Schmitt-Ulms C, Krajeski RN, Lim J, Villiger L, Zhou W, Jiang K, Garushyants SK, Roberts N, Zhang L, Vakulskas CA, Walker JA, Kadina AP, Zepeda AE, Holden K, Ma H, Xie J, Gao G, Foquet L, Bial G, Donnelly SK, Miyata Y, Radiloff DR, Henderson JM, Ujita A, Abudayyeh OO, Gootenberg JS. Drag-and-drop genome insertion of large sequences without double-strand DNA cleavage using CRISPR-directed integrases. Nat Biotechnol 2023; 41:500-512. [PMID: 36424489 PMCID: PMC10257351 DOI: 10.1038/s41587-022-01527-4] [Citation(s) in RCA: 88] [Impact Index Per Article: 88.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 09/23/2022] [Indexed: 11/26/2022]
Abstract
Programmable genome integration of large, diverse DNA cargo without DNA repair of exposed DNA double-strand breaks remains an unsolved challenge in genome editing. We present programmable addition via site-specific targeting elements (PASTE), which uses a CRISPR-Cas9 nickase fused to both a reverse transcriptase and serine integrase for targeted genomic recruitment and integration of desired payloads. We demonstrate integration of sequences as large as ~36 kilobases at multiple genomic loci across three human cell lines, primary T cells and non-dividing primary human hepatocytes. To augment PASTE, we discovered 25,614 serine integrases and cognate attachment sites from metagenomes and engineered orthologs with higher activity and shorter recognition sequences for efficient programmable integration. PASTE has editing efficiencies similar to or exceeding those of homology-directed repair and non-homologous end joining-based methods, with activity in non-dividing cells and in vivo with fewer detectable off-target events. PASTE expands the capabilities of genome editing by allowing large, multiplexed gene insertion without reliance on DNA repair pathways.
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Affiliation(s)
- Matthew T N Yarnall
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eleonora I Ioannidi
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- ETH Zürich, Zürich, Switzerland
| | - Cian Schmitt-Ulms
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rohan N Krajeski
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Justin Lim
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lukas Villiger
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Wenyuan Zhou
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kaiyi Jiang
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sofya K Garushyants
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Liyang Zhang
- Integrated DNA Technologies, Coralville, IA, USA
| | | | | | | | | | | | - Hong Ma
- University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jun Xie
- University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Guangping Gao
- University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Greg Bial
- Yecuris Corporation, Tualatin, OR, USA
| | | | | | | | | | | | - Omar O Abudayyeh
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Robarts DR, Paine-Cabrera D, Kotulkar M, Venneman KK, Gunewardena S, Corton JC, Lau C, Foquet L, Bial G, Apte U. Identifying Human Specific Adverse Outcome Pathways of Per- and Polyfluoroalkyl Substances Using Liver-Chimeric Humanized Mice. bioRxiv 2023:2023.02.01.526711. [PMID: 36778348 PMCID: PMC9915685 DOI: 10.1101/2023.02.01.526711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Background Per- and polyfluoroalkyl substances (PFAS) are persistent organic pollutants with myriad adverse effects. While perfluorooctanoic acid (PFOA) and perfluorooctane sulfonic acid (PFOS) are the most common contaminants, levels of replacement PFAS, such as perfluoro-2-methyl-3-oxahexanoic acid (GenX), are increasing. In rodents, PFOA, PFOS, and GenX have several adverse effects on the liver, including nonalcoholic fatty liver disease. Objective We aimed to determine human-relevant mechanisms of PFAS induced adverse hepatic effects using FRG liver-chimeric humanized mice with livers repopulated with functional human hepatocytes. Methods Male humanized mice were treated with 0.067 mg/L of PFOA, 0.145 mg/L of PFOS, or 1 mg/L of GenX in drinking water for 28 days. Liver and serum were collected for pathology and clinical chemistry, respectively. RNA-sequencing coupled with pathway analysis was used to determine molecular mechanisms. Results PFOS caused a significant decrease in total serum cholesterol and LDL/VLDL, whereas GenX caused a significant elevation in LDL/VLDL with no change in total cholesterol and HDL. PFOA had no significant changes in serum LDL/VLDL and total cholesterol. All three PFAS induced significant hepatocyte proliferation. RNA-sequencing with alignment to the human genome showed a total of 240, 162, and 619 differentially expressed genes after PFOA, PFOS, and GenX exposure, respectively. Upstream regulator analysis revealed inhibition of NR1D1, a transcriptional repressor important in circadian rhythm, as the major common molecular change in all PFAS treatments. PFAS treated mice had significant nuclear localization of NR1D1. In silico modeling showed PFOA, PFOS, and GenX potentially interact with the DNA-binding domain of NR1D1. Discussion These data implicate PFAS in circadian rhythm disruption via inhibition of NR1D1. These studies show that FRG humanized mice are a useful tool for studying the adverse outcome pathways of environmental pollutants on human hepatocytes in situ.
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Affiliation(s)
- Dakota R. Robarts
- Department of Pharmacology, Toxicology, and Therapeutics, University of Kansas Medical Center, Kansas City, KS
| | - Diego Paine-Cabrera
- Department of Pharmacology, Toxicology, and Therapeutics, University of Kansas Medical Center, Kansas City, KS
| | - Manasi Kotulkar
- Department of Pharmacology, Toxicology, and Therapeutics, University of Kansas Medical Center, Kansas City, KS
| | - Kaitlyn K. Venneman
- Department of Pharmacology, Toxicology, and Therapeutics, University of Kansas Medical Center, Kansas City, KS
| | - Sumedha Gunewardena
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS
| | - J. Christopher Corton
- Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. EPA, Research Triangle Park, NC
| | - Christopher Lau
- Center for Public Health and Environmental Assessment, Office of Research and Development, US EPA, Research Triangle Park, NC
| | | | | | - Udayan Apte
- Department of Pharmacology, Toxicology, and Therapeutics, University of Kansas Medical Center, Kansas City, KS
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Kessler K, Giannisis A, Bial G, Foquet L, Nielsen HM, Raber J. Behavioral and cognitive performance of humanized APOEε3/ε3 liver mice in relation to plasma apolipoprotein E levels. Sci Rep 2023; 13:1728. [PMID: 36720957 PMCID: PMC9889814 DOI: 10.1038/s41598-023-28165-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 01/13/2023] [Indexed: 02/01/2023] Open
Abstract
Plasma apolipoprotein E levels were previously associated with the risk of developing Alzheimer's disease (AD), levels of cerebrospinal fluid AD biomarkers, cognition and imaging brain measures. Outside the brain, the liver is the primary source of apoE and liver transplantation studies have demonstrated that liver-derived apoE does not cross the blood-brain-barrier. How hepatic apoE may be implicated in behavioral and cognitive performance is not clear. In the current study, we behaviorally tested FRGN mice with humanized liver harboring the ε3/ε3 genotype (E3-human liver (HL)) and compared their behavioral and cognitive performance with that of age-matched ε3/ε3 targeted replacement (E3-TR) mice, the latter produces human apoE3 throughout the body whereas the E3-HL mice endogenously produce human apoE3 only in the liver. We also compared the liver weights and plasma apoE levels, and assessed whether plasma apoE levels were correlated with behavioral or cognitive measures in both models. E3-HL were more active but performed cognitively worse than E3-TR mice. E3-HL mice moved more in the open field containing objects, showed higher activity levels in the Y maze, showed higher activity levels during the baseline period in the fear conditioning test than E3-TR mice, and swam faster than E3-TR mice during training to locate the visible platform in the water maze. However, E3-HL mice showed reduced spatial memory retention in the water maze and reduced fear learning and contextual and cued fear memory than E3-TR mice. Liver weights were greater in E3-HL than E3-TR mice and sex-dependent only in the latter model. Plasma apoE3 levels were similar to those found in humans and comparable in female and male E3-TR mice but higher in female E3-HL mice. Finally, we found correlations between plasma apoE levels and behavioral and cognitive measures which were predominantly model-dependent. Our study demonstrates mouse-model dependent associations between plasma apoE levels, behavior and cognition in an 'AD-neutral' setting and suggests that a humanized liver might be sufficient to induce mouse behavioral and cognitive phenotypes.
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Affiliation(s)
- Kat Kessler
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Andreas Giannisis
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
| | - Greg Bial
- Yecuris Corporation, Tualatin, OR, 97062, USA
| | | | - Henrietta M Nielsen
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden.
| | - Jacob Raber
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, 97239, USA. .,Departments of Neurology and Radiation Medicine, Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Portland, OR, 97239, USA.
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Giannisis A, Patra K, Edlund AK, Nieto LA, Benedicto-Gras J, Moussaud S, de la Rosa A, Twohig D, Bengtsson T, Fu Y, Bu G, Bial G, Foquet L, Hammarstedt C, Strom S, Kannisto K, Raber J, Ellis E, Nielsen HM. Brain integrity is altered by hepatic APOE ε4 in humanized-liver mice. Mol Psychiatry 2022; 27:3533-3543. [PMID: 35418601 PMCID: PMC9708568 DOI: 10.1038/s41380-022-01548-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 12/12/2022]
Abstract
Liver-generated plasma apolipoprotein E (apoE) does not enter the brain but nonetheless correlates with Alzheimer's disease (AD) risk and AD biomarker levels. Carriers of APOEε4, the strongest genetic AD risk factor, exhibit lower plasma apoE and altered brain integrity already at mid-life versus non-APOEε4 carriers. Whether altered plasma liver-derived apoE or specifically an APOEε4 liver phenotype promotes neurodegeneration is unknown. Here we investigated the brains of Fah-/-, Rag2-/-, Il2rg-/- mice on the Non-Obese Diabetic (NOD) background (FRGN) with humanized-livers of an AD risk-associated APOE ε4/ε4 versus an APOE ε2/ε3 genotype. Reduced endogenous mouse apoE levels in the brains of APOE ε4/ε4 liver mice were accompanied by various changes in markers of synaptic integrity, neuroinflammation and insulin signaling. Plasma apoE4 levels were associated with unfavorable changes in several of the assessed markers. These results propose a previously unexplored role of the liver in the APOEε4-associated risk of neurodegenerative disease.
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Affiliation(s)
- Andreas Giannisis
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, 10691, Sweden
| | - Kalicharan Patra
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, 10691, Sweden
| | - Anna K Edlund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, 10691, Sweden
| | - Lur Agirrezabala Nieto
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, 10691, Sweden
| | - Joan Benedicto-Gras
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, 10691, Sweden
| | - Simon Moussaud
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, 10691, Sweden
| | - Andrés de la Rosa
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, 10691, Sweden
| | - Daniel Twohig
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, 10691, Sweden
| | - Tore Bengtsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm, 10691, Sweden
| | - Yuan Fu
- Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, FL, 32224, USA
| | - Guojun Bu
- Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, FL, 32224, USA
| | - Greg Bial
- Yecuris Corporation, Tualatin, OR, 97062, USA
| | | | - Christina Hammarstedt
- Department of Laboratory Medicine (LABMED), Karolinska Institutet, Stockholm, 17177, Sweden
| | - Stephen Strom
- Department of Laboratory Medicine (LABMED), Karolinska Institutet, Stockholm, 17177, Sweden
| | - Kristina Kannisto
- Department of Laboratory Medicine (LABMED), Karolinska Institutet, Stockholm, 17177, Sweden
| | - Jacob Raber
- Departments of Behavioral Neuroscience, Neurology, and Radiation Medicine, and Division of Neuroscience, ONPPRC, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Ewa Ellis
- Department of Clinical Science, Intervention and Technology, (CLINTEC), Division of Transplantation surgery, Karolinska Institutet, Huddinge, 14152, Sweden
| | - Henrietta M Nielsen
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, 10691, Sweden.
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Giannisis A, Patra K, Edlund AK, Rosa ADL, Nieto LA, Gras JB, Moussaud S, Bengtsson T, Fu Y, Bu G, Bial G, Foquet L, Hammarstedt C, Strom S, Kannisto K, Ellis E, Nielsen HM. Effects of a liver
APOEε4
‐genotype on synaptic integrity, gliosis and insulin signaling in the brain. Alzheimers Dement 2020. [DOI: 10.1002/alz.042463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | - Yuan Fu
- Mayo Clinic Jacksonville FL USA
| | | | | | | | | | | | | | - Ewa Ellis
- Karolinska Institutet Stockholm Sweden
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Edlund AK, Giannisis A, Patra K, Morrema TH, Hoozemans JJ, Bial G, Foquet L, Nielsen HM. Effects of a high‐fat diet on the brain in FRGN mice with humanized livers. Alzheimers Dement 2020. [DOI: 10.1002/alz.046198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Wilson EM, Bial J, Tarlow B, Bial G, Jensen B, Greiner DL, Brehm MA, Grompe M. Extensive double humanization of both liver and hematopoiesis in FRGN mice. Stem Cell Res 2014; 13:404-12. [PMID: 25310256 PMCID: PMC7275629 DOI: 10.1016/j.scr.2014.08.006] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 08/21/2014] [Accepted: 08/27/2014] [Indexed: 11/21/2022] Open
Abstract
Preclinical research in animals often fails to adequately predict the outcomes observed in human patients. Chimeric animals bearing individual human tissues have been developed to provide improved models of human-specific cellular processes. Mice transplanted with human hematopoietic stem cells can be used to study human immune responses, infections of blood cells and processes of hematopoiesis. Animals with humanized livers are useful for modeling hepatotropic infections as well as drug metabolism and hepatotoxicity. However, many pathophysiologic processes involve both the liver and the hematolymphoid system. Examples include hepatitis C/HIV co-infection, immune mediated liver diseases, liver injuries with inflammation such as steatohepatitis and alcoholic liver disease. We developed a robust protocol enabling the concurrent double-humanization of mice with mature hepatocytes and human blood. Immune-deficient, fumarylacetoacetate hydrolase (Fah−/−), Rag2−/− and Il2rg−/− deficient animals on the NOD-strain background (FRGN) were simultaneously co-transplanted with adult human hepatocytes and hematopoietic stem cells after busulfan and Ad:uPA pre-conditioning. Four months after transplantation the average human liver repopulation exceeded 80% and hematopoietic chimerism also was high (40–80% in bone marrow). Importantly, human macrophages (Kupffer cells) were present in the chimeric livers. Double-chimeric FRGN mice will serve as a new model for disease processes that involve interactions between hepatocytes and hematolymphoid cells.
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Affiliation(s)
| | - J Bial
- Yecuris Corp., Tigard, OR, USA
| | | | - G Bial
- Yecuris Corp., Tigard, OR, USA
| | | | - D L Greiner
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - M A Brehm
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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