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Patra AT, Tan E, Kok YJ, Ng SK, Bi X. Temporal insights into molecular and cellular responses during rAAV production in HEK293T cells. Mol Ther Methods Clin Dev 2024; 32:101278. [PMID: 39022743 PMCID: PMC11253160 DOI: 10.1016/j.omtm.2024.101278] [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: 12/16/2023] [Accepted: 06/04/2024] [Indexed: 07/20/2024]
Abstract
The gene therapy field seeks cost-effective, large-scale production of recombinant adeno-associated virus (rAAV) vectors for high-dosage therapeutic applications. Although strategies like suspension cell culture and transfection optimization have shown moderate success, challenges persist for large-scale applications. To unravel molecular and cellular mechanisms influencing rAAV production, we conducted an SWATH-MS proteomic analysis of HEK293T cells transfected using standard, sub-optimal, and optimal conditions. Gene Ontology and pathway analysis revealed significant protein expression variations, particularly in processes related to cellular homeostasis, metabolic regulation, vesicular transport, ribosomal biogenesis, and cellular proliferation under optimal transfection conditions. This resulted in a 50% increase in rAAV titer compared with the standard protocol. Additionally, we identified modifications in host cell proteins crucial for AAV mRNA stability and gene translation, particularly regarding AAV capsid transcripts under optimal transfection conditions. Our study identified 124 host proteins associated with AAV replication and assembly, each exhibiting distinct expression pattern throughout rAAV production stages in optimal transfection condition. This investigation sheds light on the cellular mechanisms involved in rAAV production in HEK293T cells and proposes promising avenues for further enhancing rAAV titer during production.
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Affiliation(s)
- Alok Tanala Patra
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A∗STAR), Singapore 138668, Singapore
| | - Evan Tan
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A∗STAR), Singapore 138668, Singapore
| | - Yee Jiun Kok
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A∗STAR), Singapore 138668, Singapore
| | - Say Kong Ng
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A∗STAR), Singapore 138668, Singapore
| | - Xuezhi Bi
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A∗STAR), Singapore 138668, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
- Food, Chemical and Biotechnology Cluster, Singapore Institute of Technology, Singapore 138683, Singapore
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Jiang W, Xiao D, Wu C, Yang J, Peng X, Chen L, Zhang J, Zha G, Li W, Ju R, Xiang M, Xie Z. Circular RNA-based therapy provides sustained and robust neuroprotection for retinal ganglion cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102258. [PMID: 39045516 PMCID: PMC11264179 DOI: 10.1016/j.omtn.2024.102258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/14/2024] [Indexed: 07/25/2024]
Abstract
Ocular neurodegenerative diseases like glaucoma lead to progressive retinal ganglion cell (RGC) loss, causing irreversible vision impairment. Neuroprotection is needed to preserve RGCs across debilitating conditions. Nerve growth factor (NGF) protein therapy shows efficacy, but struggles with limited bioavailability and a short half-life. Here we explore a novel approach to address this deficiency by utilizing circular RNA (circRNA)-based therapy. We show that circRNAs exhibit an exceptional capacity for prolonged protein expression and circRNA-expressed NGF protects cells from glucose deprivation. In a mouse optic nerve crush model, lipid nanoparticle (LNP)-formulated circNGF administered intravitreally protects RGCs and axons from injury-induced degeneration. It also significantly outperforms NGF protein therapy without detectable retinal toxicity. Furthermore, single-cell transcriptomics revealed LNP-circNGF's multifaceted therapeutic effects, enhancing genes related to visual perception while reducing trauma-associated changes. This study signifies the promise of circRNA-based therapies for treating ocular neurodegenerative diseases and provides an innovative intervention platform for other ocular diseases.
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Affiliation(s)
- Wenbing Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Dongchang Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Cheng Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Jiaqi Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Xinghua Peng
- Research and Development Center, Shenzhen MagicRNA Biotech, Shenzhen 518107, China
| | - Linfeng Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Jiamin Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Gaofeng Zha
- Scientific Research Center, The Seventh Affiliated Hospital. Sun Yat-sen University, Shenzhen 518107, China
| | - Wei Li
- Retinal Neurophysiology Section, National Eye Institute, NIH, Bethesda, MD 20892, USA
| | - Rong Ju
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Mengqing Xiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
- Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
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Marupudi N, Xiong MP. Genetic Targets and Applications of Iron Chelators for Neurodegeneration with Brain Iron Accumulation. ACS BIO & MED CHEM AU 2024; 4:119-130. [PMID: 38911909 PMCID: PMC11191567 DOI: 10.1021/acsbiomedchemau.3c00066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 06/25/2024]
Abstract
Neurodegeneration with brain iron accumulation (NBIA) is a group of neurodegenerative diseases that are typically caused by a monogenetic mutation, leading to development of disordered movement symptoms such as dystonia, hyperreflexia, etc. Brain iron accumulation can be diagnosed through MRI imaging and is hypothesized to be the cause of oxidative stress, leading to the degeneration of brain tissue. There are four main types of NBIA: pantothenate kinase-associated neurodegeneration (PKAN), PLA2G6-associated neurodegeneration (PLAN), mitochondrial membrane protein-associated neurodegeneration (MKAN), and beta-propeller protein-associated neurodegeneration (BPAN). There are no causative therapies for these diseases, but iron chelators have been shown to have potential toward treating NBIA. Three chelators are investigated in this Review: deferoxamine (DFO), desferasirox (DFS), and deferiprone (DFP). DFO has been investigated to treat neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD); however, dose-related toxicity in these studies, as well as in PKAN studies, have shown that the drug still requires more development before it can be applied toward NBIA cases. Iron chelation therapies other than the ones currently in clinical use have not yet reached clinical studies, but they may possess characteristics that would allow them to access the brain in ways that current chelators cannot. Intranasal formulations are an attractive dosage form to study for chelation therapy, as this method of delivery can bypass the blood-brain barrier and access the CNS. Gene therapy differs from iron chelation therapy as it is a causal treatment of the disease, whereas iron chelators only target the disease progression of NBIA. Because the pathophysiology of NBIA diseases is still unclear, future courses of action should be focused on causative treatment; however, iron chelation therapy is the current best course of action.
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Affiliation(s)
- Neharika Marupudi
- Department of Pharmaceutical
& Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602-2352, United States
| | - May P. Xiong
- Department of Pharmaceutical
& Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia 30602-2352, United States
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Fu X, Suo H, Zhang J, Chen D. Machine-learning-guided Directed Evolution for AAV Capsid Engineering. Curr Pharm Des 2024; 30:811-824. [PMID: 38445704 DOI: 10.2174/0113816128286593240226060318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 03/07/2024]
Abstract
Target gene delivery is crucial to gene therapy. Adeno-associated virus (AAV) has emerged as a primary gene therapy vector due to its broad host range, long-term expression, and low pathogenicity. However, AAV vectors have some limitations, such as immunogenicity and insufficient targeting. Designing or modifying capsids is a potential method of improving the efficacy of gene delivery, but hindered by weak biological basis of AAV, complexity of the capsids, and limitations of current screening methods. Artificial intelligence (AI), especially machine learning (ML), has great potential to accelerate and improve the optimization of capsid properties as well as decrease their development time and manufacturing costs. This review introduces the traditional methods of designing AAV capsids and the general steps of building a sequence-function ML model, highlights the applications of ML in the development workflow, and summarizes its advantages and challenges.
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Affiliation(s)
- Xianrong Fu
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Hairui Suo
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Jiachen Zhang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Dongmei Chen
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China
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Bao Y, Lu W. Targeting cerebral diseases with enhanced delivery of therapeutic proteins across the blood-brain barrier. Expert Opin Drug Deliv 2023; 20:1681-1698. [PMID: 36945117 DOI: 10.1080/17425247.2023.2193390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 03/16/2023] [Indexed: 03/23/2023]
Abstract
INTRODUCTION Cerebral diseases have been threatening public physical and psychological health in the recent years. With the existence of the blood-brain barrier (BBB), it is particularly hard for therapeutic proteins like peptides, enzymes, antibodies, etc. to enter the central nervous system (CNS) and function in diagnosis and treatment in cerebral diseases. Fortunately, the past decade has witnessed some emerging strategies of delivering macromolecular therapeutic proteins across the BBB. AREAS COVERED Based on the structure, functions, and substances transport mechanisms, various enhanced delivery strategies of therapeutic proteins were reviewed, categorized by molecule-mediated delivery strategies, carrier-mediated delivery strategies, and other delivery strategies. EXPERT OPINION As for molecule-mediated delivery strategies, development of genetic engineering technology, optimization of protein expression and purification techniques, and mature of quality control systems all help to realize large-scale production of recombinant antibodies, making it possible to apply to the clinical practice. In terms of carrier-mediated delivery strategies and others, although nano-carriers/adeno-associated virus (AAV) are also promising candidates for delivering therapeutic proteins or genes across the BBB, some issues still remain to be further investigated, including safety concerns related to applied materials, large-scale production costs, quality control standards, combination therapies with auxiliary delivery strategies like focused ultrasound, etc.
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Affiliation(s)
- Yanning Bao
- Department of Pharmaceutics, School of Pharmacy, Fudan University & Key Laboratory of Smart Drug Delivery (Fudan University), Ministry of Education, Shanghai, China
| | - Weiyue Lu
- Department of Pharmaceutics, School of Pharmacy, Fudan University & Key Laboratory of Smart Drug Delivery (Fudan University), Ministry of Education, Shanghai, China
- Shanghai Engineering Technology Research Center for Pharmaceutical Intelligent Equipment, and Shanghai Frontiers Science Center for Druggability of Cardiovascular non-coding RNA, Institute for Frontier Medical Technology, Shanghai University of Engineering Science, Shanghai, China
- Department of Research and Development, Shanghai Tayzen PharmLab Co., Ltd. Lingang of Shanghai, China
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Quach TT, Stratton HJ, Khanna R, Mackey-Alfonso S, Deems N, Honnorat J, Meyer K, Duchemin AM. Neurodegenerative Diseases: From Dysproteostasis, Altered Calcium Signalosome to Selective Neuronal Vulnerability to AAV-Mediated Gene Therapy. Int J Mol Sci 2022; 23:ijms232214188. [PMID: 36430666 PMCID: PMC9694178 DOI: 10.3390/ijms232214188] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 11/18/2022] Open
Abstract
Despite intense research into the multifaceted etiology of neurodegenerative diseases (ND), they remain incurable. Here we provide a brief overview of several major ND and explore novel therapeutic approaches. Although the cause (s) of ND are not fully understood, the accumulation of misfolded/aggregated proteins in the brain is a common pathological feature. This aggregation may initiate disruption of Ca++ signaling, which is an early pathological event leading to altered dendritic structure, neuronal dysfunction, and cell death. Presently, ND gene therapies remain unidimensional, elusive, and limited to modifying one pathological feature while ignoring others. Considering the complexity of signaling cascades in ND, we discuss emerging therapeutic concepts and suggest that deciphering the molecular mechanisms involved in dendritic pathology may broaden the phenotypic spectrum of ND treatment. An innovative multiplexed gene transfer strategy that employs silencing and/or over-expressing multiple effectors could preserve vulnerable neurons before they are lost. Such therapeutic approaches may extend brain health span and ameliorate burdensome chronic disease states.
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Affiliation(s)
- Tam T. Quach
- Institute for Behavioral Medicine Research, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, USA
- INSERM U1217/CNRS UMR5310, Université de Lyon, Université Claude Bernard Lyon 1, 69677 Lyon, France
| | | | - Rajesh Khanna
- Department of Molecular Pathobiology, New York University, New York, NY 10010, USA
| | - Sabrina Mackey-Alfonso
- Institute for Behavioral Medicine Research, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, USA
| | - Nicolas Deems
- Institute for Behavioral Medicine Research, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, USA
| | - Jérome Honnorat
- INSERM U1217/CNRS UMR5310, Université de Lyon, Université Claude Bernard Lyon 1, 69677 Lyon, France
- French Reference Center on Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon, 69677 Lyon, France
- SynatAc Team, Institut NeuroMyoGène, 69677 Lyon, France
| | - Kathrin Meyer
- The Research Institute of Nationwide Children Hospital, Columbus, OH 43205, USA
- Department of Pediatric, The Ohio State University, Columbus, OH 43210, USA
| | - Anne-Marie Duchemin
- Department of Psychiatry and Behavioral Health, The Ohio State University, Columbus, OH 43210, USA
- Correspondence: ; Tel.: +1-614-293-5517; Fax: +1-614-293-7599
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Tkatch T, Rysevaite-Kyguoliene K, Sabeckis I, Sabeckiene D, Pauza DH, Baranauskas G. An efficient rAAV vector for protein expression in cortical parvalbumin expressing interneurons. Sci Rep 2022; 12:17851. [PMID: 36284123 PMCID: PMC9596399 DOI: 10.1038/s41598-022-21867-0] [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: 12/29/2021] [Accepted: 10/04/2022] [Indexed: 01/20/2023] Open
Abstract
Recombinant adeno-associated viruses (rAAV) are extensively used in both research and clinical applications. Despite significant advances, there is a lack of short promoters able to drive the expression of virus delivered genes in specific classes of neurons. We designed an efficient rAAV vector suitable for the rAAV-mediated gene expression in cortical interneurons, mainly in the parvalbumin expressing cells. The vector includes a short parvalbumin promoter and a specialized poly(A) sequence. The degree of conservation of the parvalbumin gene adjoining non-coding regions was used in both the promoter design and the selection of the poly(A) sequence. The specificity was established by co-localizing the fluorescence of the virus delivered eGFP and the antibody for a neuronal marker. rAAV particles were injected in the visual cortex area V1/V2 of adult rats (2-4 months old). Neurons expressing the virus delivered eGFP were mainly positive for interneuronal markers: 66.5 ± 2.8% for parvalbumin, 14.6 ± 2.4% for somatostatin, 7.1 ± 1.2% for vasoactive intestinal peptide, 2.8 ± 0.6% for cholecystokinin. Meanwhile, only 2.1 ± 0.5% were positive for CaMKII, a marker for principal cells in the cortex. The efficiency of the construct was verified by optogenetic experiments: the expression of the virus delivered ChR2 channels was sufficient to evoke by blue light laser high frequency bursts of action potentials in putative fast spiking neurons. We conclude that our promoter allows highly specific expression of the rAAV delivered cDNAs in cortical interneurons with a strong preference for the parvalbumin positive cells.
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Affiliation(s)
- Tatiana Tkatch
- grid.45083.3a0000 0004 0432 6841Neurophysiology Laboratory, Neuroscience Institute, Lithuanian University of Health Sciences, Kaunas, Lithuania ,grid.16753.360000 0001 2299 3507Present Address: Department of Physiology, Northwestern University, Chicago, IL USA
| | | | - Ignas Sabeckis
- grid.45083.3a0000 0004 0432 6841Anatomy Institute, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Deimante Sabeckiene
- grid.45083.3a0000 0004 0432 6841Anatomy Institute, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Dainius H. Pauza
- grid.45083.3a0000 0004 0432 6841Anatomy Institute, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Gytis Baranauskas
- grid.45083.3a0000 0004 0432 6841Neurophysiology Laboratory, Neuroscience Institute, Lithuanian University of Health Sciences, Kaunas, Lithuania
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Wang L, Yuan PQ, Challis C, Ravindra Kumar S, Taché Y. Transduction of Systemically Administered Adeno-Associated Virus in the Colonic Enteric Nervous System and c-Kit Cells of Adult Mice. Front Neuroanat 2022; 16:884280. [PMID: 35734536 PMCID: PMC9207206 DOI: 10.3389/fnana.2022.884280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Systemic delivery of adeno-associated virus (AAV) vectors transduces the enteric nervous system. However, less is known on the mapping and morphological and neurochemical characterization in the adult mouse colon. We used AAV9-CAG-GFP (AAV9) and AAV-PHP.S-hSyn1-tdTomato farnesylated (PHP.S-tdTf) to investigate the segmental distribution, morphologies and neurochemical coding of the transduction. The vectors were retro-orbitally injected in male and female adult mice, and 3 weeks later, the colon was prepared for microcopy with or without immunohistochemistry for neuronal and non-neuronal markers. In contrast to the distributions in neonatal and juvenile rodents, the AAV transduction in neurons and/or nerve fibers was the highest in the proximal colon, decreased gradually in the transverse, and was sparse in the distal colon without difference between sexes. In the proximal colon, the AAV9-transduced myenteric neurons were unevenly distributed. The majority of enteric neurons did not have AAV9 expression in their processes, except those with big soma with or without variously shaped dendrites, and a long axon. Immunolabeling demonstrated that about 31% neurons were transduced by AAV9, and the transduction was in 50, 28, and 31% of cholinergic, nitrergic, and calbindin-positive myenteric neurons, respectively. The nerve fiber markers, calcitonin gene-related peptide alpha, tyrosine hydroxylase or vasoactive intestinal polypeptide co-localized with AAV9 or PHP.S-tdTf in the mucosa, and rarely in the myenteric plexus. Unexpectedly, AAV9 expression appeared also in a few c-Kit immunoreactive cells among the heavily populated interstitial cells of Cajal (ICC). In the distal colon, the AAV transduction appeared in a few nerve fibers mostly the interganglionic strands. Other types of AAV9 and AAV-PHP vectors induced a similar colonic segmental difference which is not colon specific since neurons were transduced in the small intestine and gastric antrum, while little in the gastric corpus and none in the lower esophagus. Conclusion These findings demonstrate that in adult mice colon that there is a rostro-caudal decrease in the transduction of systemic delivery of AAV9 and its variants independent of sex. The characterization of AAV transduction in the proximal colon in cholinergic and nitrergic myenteric neurons along with a few ICC suggests implications in circuitries regulating motility.
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Affiliation(s)
- Lixin Wang
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, CURE/Digestive Diseases Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA, United States
| | - Pu-Qing Yuan
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, CURE/Digestive Diseases Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA, United States
| | - Collin Challis
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Sripriya Ravindra Kumar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Yvette Taché
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, CURE/Digestive Diseases Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, CA, United States
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