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Catalán-Tatjer D, Tzimou K, Nielsen LK, Lavado-García J. Unravelling the essential elements for recombinant adeno-associated virus (rAAV) production in animal cell-based platforms. Biotechnol Adv 2024; 73:108370. [PMID: 38692443 DOI: 10.1016/j.biotechadv.2024.108370] [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: 01/16/2024] [Revised: 04/05/2024] [Accepted: 04/27/2024] [Indexed: 05/03/2024]
Abstract
Recombinant adeno-associated viruses (rAAVs) stand at the forefront of gene therapy applications, holding immense significance for their safe and efficient gene delivery capabilities. The constantly increasing and unmet demand for rAAVs underscores the need for a more comprehensive understanding of AAV biology and its impact on rAAV production. In this literature review, we delved into AAV biology and rAAV manufacturing bioprocesses, unravelling the functions and essentiality of proteins involved in rAAV production. We discuss the interconnections between these proteins and how they affect the choice of rAAV production platform. By addressing existing inconsistencies, literature gaps and limitations, this review aims to define a minimal set of genes that are essential for rAAV production, providing the potential to advance rAAV biomanufacturing, with a focus on minimizing the genetic load within rAAV-producing cells.
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Affiliation(s)
- David Catalán-Tatjer
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Konstantina Tzimou
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Lars K Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark; Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Australia
| | - Jesús Lavado-García
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark.
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2
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Göttig L, Schreiner S. E4orf1: The triple agent of adenovirus - Unraveling its roles in oncogenesis, infectious obesity and immune responses in virus replication and vector therapy. Tumour Virus Res 2024; 17:200277. [PMID: 38428735 PMCID: PMC10937242 DOI: 10.1016/j.tvr.2024.200277] [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: 01/22/2024] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 03/03/2024] Open
Abstract
Human Adenoviruses (HAdV) are nearly ubiquitous pathogens comprising numerous sub-types that infect various tissues and organs. Among many encoded proteins that facilitate viral replication and subversion of host cellular processes, the viral E4orf1 protein has emerged as an intriguing yet under-investigated player in the complex interplay between the virus and its host. E4orf1 has gained attention as a metabolism activator and oncogenic agent, while recent research is showing that E4orf1 may play a more important role in modulating cellular pathways such as PI3K-Akt-mTOR, Ras, the immune response and further HAdV replication stages than previously anticipated. In this review, we aim to explore the structure, molecular mechanisms, and biological functions of E4orf1, shedding light on its potentially multifaceted roles during HAdV infection, including metabolic diseases and oncogenesis. Furthermore, we discuss the role of functional E4orf1 in biotechnological applications such as Adenovirus (AdV) vaccine vectors and oncolytic AdV. By dissecting the intricate relationships between HAdV types and E4orf1 proteins, this review provides valuable insights into viral pathogenesis and points to promising areas of future research.
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Affiliation(s)
- Lilian Göttig
- Institute of Virology, School of Medicine, Technical University of Munich, Germany
| | - Sabrina Schreiner
- Institute of Virology, School of Medicine, Technical University of Munich, Germany; Institute of Virology, Hannover Medical School, Hannover, Germany; Cluster of Excellence RESIST (Resolving Infection Susceptibility; EXC 2155), Hannover, Germany; Institute of Virology, Medical Center - University of Freiburg, Freiburg, Germany.
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3
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Yuan Y, Liu P, Zheng Y, Li Q, Bian J, Liang Q, Su T, Dian L, Qi Q. Unique Raoultella species isolated from petroleum contaminated soil degrades polystyrene and polyethylene. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 263:115232. [PMID: 37429089 DOI: 10.1016/j.ecoenv.2023.115232] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/12/2023] [Accepted: 07/04/2023] [Indexed: 07/12/2023]
Abstract
Polyolefin plastics, such as polyethylene (PE) and polystyrene (PS), are the most widely used synthetic plastics in our daily life. However, the chemical structure of polyolefin plastics is composed of carbon-carbon (C-C) bonds, which is extremely stable and makes polyolefin plastics recalcitrant to degradation. The growing accumulation of plastic waste has caused serious environmental pollution and has become a global environmental concern. In this study, we isolated a unique Raoultella sp. DY2415 strain from petroleum-contaminated soil that can degrade PE and PS film. After 60 d of incubation with strain DY2415, the weight of the UV-irradiated PE (UVPE) film and PS film decreased by 8% and 2%, respectively. Apparent microbial colonization and holes on the surface of the films were observed by scanning electron microscopy (SEM). Furthermore, the Fourier transform infrared spectrometer (FTIR) results showed that new oxygen-containing functional groups such as -OH and -CO were introduced into the polyolefin molecular structure. Potential enzymes that may be involved in the biodegradation of polyolefin plastics were analyzed. These results demonstrate that Raoultella sp. DY2415 has the ability to degrade polyolefin plastics and provide a basis for further investigating the biodegradation mechanism.
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Affiliation(s)
- Yingbo Yuan
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Pan Liu
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Yi Zheng
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Qingbin Li
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Junling Bian
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China.
| | - Longyang Dian
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China.
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, 72 Binhai Road, Qingdao 266237, China
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Hierarchical regulation of autophagy during adipocyte differentiation. PLoS One 2022; 17:e0250865. [PMID: 35081114 PMCID: PMC8791469 DOI: 10.1371/journal.pone.0250865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 12/05/2021] [Indexed: 11/19/2022] Open
Abstract
We previously showed that some adipogenic transcription factors such as CEBPB and PPARG directly and indirectly regulate autophagy gene expression in adipogenesis. The order and effect of these events are undetermined. In this study, we modeled the gene expression, DNA-binding of transcriptional regulators, and histone modifications during adipocyte differentiation and evaluated the effect of the regulators on gene expression in terms of direction and magnitude. Then, we identified the overlap of the transcription factors and co-factors binding sites and targets. Finally, we built a chromatin state model based on the histone marks and studied their relation to the factors’ binding. Adipogenic factors differentially regulated autophagy genes as part of the differentiation program. Co-regulators associated with specific transcription factors and preceded them to the regulatory regions. Transcription factors differed in the binding time and location, and their effect on expression was either localized or long-lasting. Adipogenic factors disproportionately targeted genes coding for autophagy-specific transcription factors. In sum, a hierarchical arrangement between adipogenic transcription factors and co-factors drives the regulation of autophagy during adipocyte differentiation.
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Ahmed M, Lai TH, Kim DR. A Small Fraction of Progenitors Differentiate Into Mature Adipocytes by Escaping the Constraints on the Cell Structure. Front Cell Dev Biol 2021; 9:753042. [PMID: 34708046 PMCID: PMC8542793 DOI: 10.3389/fcell.2021.753042] [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: 08/13/2021] [Accepted: 09/10/2021] [Indexed: 11/13/2022] Open
Abstract
Differentiating 3T3-L1 pre-adipocytes are a mixture of non-identical culture cells. It is vital to identify the cell types that respond to the induction stimulus to understand the pre-adipocyte potential and the mature adipocyte behavior. To test this hypothesis, we deconvoluted the gene expression profiles of the cell culture of MDI-induced 3T3-L1 cells. Then we estimated the fractions of the sub-populations and their changes in time. We characterized the sub-populations based on their specific expression profiles. Initial cell cultures comprised three distinct phenotypes. A small fraction of the starting cells responded to the induction and developed into mature adipocytes. Unresponsive cells were probably under structural constraints or were committed to differentiating into alternative phenotypes. Using the same population gene markers, similar proportions were found in induced human primary adipocyte cell cultures. The three sub-populations had diverse responses to treatment with various drugs and compounds. Only the response of the maturating sub-population resembled that estimated from the profiles of the mixture. We then showed that even at a low division rate, a small fraction of cells could increase its share in a dynamic two-populations model. Finally, we used a cell cycle expression index to validate that model. To sum, pre-adipocytes are a mixture of different cells of which a limited fraction become mature adipocytes.
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Affiliation(s)
- Mahmoud Ahmed
- Department of Biochemistry and Convergence Medical Sciences, Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, South Korea
| | - Trang Huyen Lai
- Department of Biochemistry and Convergence Medical Sciences, Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, South Korea
| | - Deok Ryong Kim
- Department of Biochemistry and Convergence Medical Sciences, Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, South Korea
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Girdhar K, Powis A, Raisingani A, Chrudinová M, Huang R, Tran T, Sevgi K, Dogus Dogru Y, Altindis E. Viruses and Metabolism: The Effects of Viral Infections and Viral Insulins on Host Metabolism. Annu Rev Virol 2021; 8:373-391. [PMID: 34586876 PMCID: PMC9175272 DOI: 10.1146/annurev-virology-091919-102416] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Over the past decades, there have been tremendous efforts to understand the cross-talk between viruses and host metabolism. Several studies have elucidated the mechanisms through which viral infections manipulate metabolic pathways including glucose, fatty acid, protein, and nucleotide metabolism. These pathways are evolutionarily conserved across the tree of life and extremely important for the host's nutrient utilization and energy production. In this review, we focus on host glucose, glutamine, and fatty acid metabolism and highlight the pathways manipulated by the different classes of viruses to increase their replication. We also explore a new system of viral hormones in which viruses mimic host hormones to manipulate the host endocrine system. We discuss viral insulin/IGF-1-like peptides and their potential effects on host metabolism. Together, these pathogenesis mechanisms targeting cellular signaling pathways create a multidimensional network of interactions between host and viral proteins. Defining and better understanding these mechanisms will help us to develop new therapeutic tools to prevent and treat viral infections.
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Affiliation(s)
- Khyati Girdhar
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, USA;
| | - Amaya Powis
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, USA;
| | - Amol Raisingani
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, USA;
| | - Martina Chrudinová
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, USA;
| | - Ruixu Huang
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, USA;
| | - Tu Tran
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, USA;
| | - Kaan Sevgi
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, USA;
| | - Yusuf Dogus Dogru
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, USA;
| | - Emrah Altindis
- Department of Biology, Boston College, Chestnut Hill, Massachusetts 02467, USA;
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Orré T, Joly A, Karatas Z, Kastberger B, Cabriel C, Böttcher RT, Lévêque-Fort S, Sibarita JB, Fässler R, Wehrle-Haller B, Rossier O, Giannone G. Molecular motion and tridimensional nanoscale localization of kindlin control integrin activation in focal adhesions. Nat Commun 2021; 12:3104. [PMID: 34035280 PMCID: PMC8149821 DOI: 10.1038/s41467-021-23372-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 04/21/2021] [Indexed: 12/20/2022] Open
Abstract
Focal adhesions (FAs) initiate chemical and mechanical signals involved in cell polarity, migration, proliferation and differentiation. Super-resolution microscopy revealed that FAs are organized at the nanoscale into functional layers from the lower plasma membrane to the upper actin cytoskeleton. Yet, how FAs proteins are guided into specific nano-layers to promote interaction with given targets is unknown. Using single protein tracking, super-resolution microscopy and functional assays, we link the molecular behavior and 3D nanoscale localization of kindlin with its function in integrin activation inside FAs. We show that immobilization of integrins in FAs depends on interaction with kindlin. Unlike talin, kindlin displays free diffusion along the plasma membrane outside and inside FAs. We demonstrate that the kindlin Pleckstrin Homology domain promotes membrane diffusion and localization to the membrane-proximal integrin nano-layer, necessary for kindlin enrichment and function in FAs. Using kindlin-deficient cells, we show that kindlin membrane localization and diffusion are crucial for integrin activation, cell spreading and FAs formation. Thus, kindlin uses a different route than talin to reach and activate integrins, providing a possible molecular basis for their complementarity during integrin activation.
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Affiliation(s)
- Thomas Orré
- University Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR, Bordeaux, France
| | - Adrien Joly
- University Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR, Bordeaux, France
| | - Zeynep Karatas
- University Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR, Bordeaux, France
| | - Birgit Kastberger
- Department of Cell Physiology and Metabolism, Centre Médical Universitaire, Geneva 4, Switzerland
| | - Clément Cabriel
- Institut des Sciences Moléculaires d'Orsay, CNRS UMR8214, Univ. Paris-Sud, Université Paris Saclay, Orsay, Cedex, France
| | | | - Sandrine Lévêque-Fort
- Institut des Sciences Moléculaires d'Orsay, CNRS UMR8214, Univ. Paris-Sud, Université Paris Saclay, Orsay, Cedex, France
| | - Jean-Baptiste Sibarita
- University Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR, Bordeaux, France
| | | | - Bernhard Wehrle-Haller
- Department of Cell Physiology and Metabolism, Centre Médical Universitaire, Geneva 4, Switzerland
| | - Olivier Rossier
- University Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR, Bordeaux, France.
| | - Grégory Giannone
- University Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, IINS, UMR, Bordeaux, France.
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Li X, Wang J, Jia Y, Reheman A, Yan Y. The Genome Analysis of Methylobacterium populi YC-XJ1 with Diverse Xenobiotics Biodegrading Capacity and Degradation Characteristics of Related Hydrolase. Int J Mol Sci 2020; 21:ijms21124436. [PMID: 32580446 PMCID: PMC7352507 DOI: 10.3390/ijms21124436] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 11/16/2022] Open
Abstract
Methylobacterium populi YC-XJ1 isolated from desert soil exhibited a diverse degrading ability towards aromatic oxyphenoxypropionic acid esters (AOPPs) herbicide, phthalate esters (PAEs), organophosphorus flame retardants (OPFRs), chlorpyrifos and phoxim. The genome of YC-XJ1 was sequenced and analyzed systematically. YC-XJ1 contained a large number of exogenous compounds degradation pathways and hydrolase resources. The quizalofop-p-ethyl (QPE) degrading gene qpeh2 and diethyl phthalate (DEP) degrading gene deph1 were cloned and expressed. The characteristics of corresponding hydrolases were investigated. The specific activity of recombinant QPEH2 was 0.1 ± 0.02 U mg-1 for QPE with kcat/Km values of 1.8 ± 0.016 (mM-1·s-1). The specific activity of recombinant DEPH1 was 0.1 ± 0.02 U mg-1 for DEP with kcat/Km values of 0.8 ± 0.02 (mM-1·s-1). This work systematically illuminated the metabolic versatility of strain YC-XJ1 via the combination of genomics analysis and laboratory experiments. These results suggested that strain YC-XJ1 with diverse xenobiotics biodegrading capacity was a promising candidate for the bioremediation of polluted sites.
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Affiliation(s)
- Xianjun Li
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (J.W.); (Y.J.)
| | - Junhuan Wang
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (J.W.); (Y.J.)
| | - Yang Jia
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (J.W.); (Y.J.)
| | - Aikebaier Reheman
- Key Laboratory of Toxicology, Ningde Normal University, Ningde 352100, China
- Correspondence: (A.R.); (Y.Y.); Tel.: +86-10-82109685 (Y.Y.)
| | - Yanchun Yan
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.L.); (J.W.); (Y.J.)
- Correspondence: (A.R.); (Y.Y.); Tel.: +86-10-82109685 (Y.Y.)
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Abstract
The 3T3-L1 pre-adipocyte cell line is widely used to study the fat cell differentiation in vitro. Researchers also use this cell model to study obesity and insulin resistance. We surveyed the literature, the gene expression omnibus and the sequence read archive for RNA-Seq and ChIP-Seq datasets of MDI-induced 3T3-L1 differentiating cells sampled at one or more time points. The metadata of the relevant datasets were manually curated using unified language across the original studies. The raw reads were collected and pre-processed using a reproducible state-of-the-art pipeline. The final datasets are presented as reads count in genes for the RNA-Seq and reads count in peaks for the ChIP-Seq dataset. The curated datasets are available as two Bioconductor experimental data packages curatedAdipoRNA and curatedAdipoChIP. In addition, the packages document the source code of the data collection and the pre-processing pipelines. Here, we provide a descriptive analysis of the datasets with context and technical validation.
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Affiliation(s)
- Mahmoud Ahmed
- Department of Biochemistry and Convergence Medical Sciences and Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, Republic of Korea
| | - Deok Ryong Kim
- Department of Biochemistry and Convergence Medical Sciences and Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, Republic of Korea
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Beg M, Abdullah N, Thowfeik FS, Altorki NK, McGraw TE. Distinct Akt phosphorylation states are required for insulin regulated Glut4 and Glut1-mediated glucose uptake. eLife 2017; 6. [PMID: 28589878 PMCID: PMC5462539 DOI: 10.7554/elife.26896] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/22/2017] [Indexed: 01/01/2023] Open
Abstract
Insulin, downstream of Akt activation, promotes glucose uptake into fat and muscle cells to lower postprandial blood glucose, an enforced change in cellular metabolism to maintain glucose homeostasis. This effect is mediated by the Glut4 glucose transporter. Growth factors also enhance glucose uptake to fuel an anabolic metabolism required for tissue growth and repair. This activity is predominantly mediated by the Glut1. Akt is activated by phosphorylation of its kinase and hydrophobic motif (HM) domains. We show that insulin-stimulated Glut4-mediated glucose uptake requires PDPK1 phosphorylation of the kinase domain but not mTORC2 phosphorylation of the HM domain. Nonetheless, an intact HM domain is required for Glut4-mediated glucose uptake. Whereas, Glut1-mediated glucose uptake also requires mTORC2 phosphorylation of the HM domain, demonstrating both phosphorylation-dependent and independent roles of the HM domain in regulating glucose uptake. Thus, mTORC2 links Akt to the distinct physiologic programs related to Glut4 and Glut1-mediated glucose uptake. DOI:http://dx.doi.org/10.7554/eLife.26896.001
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Affiliation(s)
- Muheeb Beg
- Department of Biochemistry, Weill Cornell Medicine, New York, United States
| | - Nazish Abdullah
- Department of Biochemistry, Weill Cornell Medicine, New York, United States
| | - Fathima Shazna Thowfeik
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, United States.,Lung Cancer Program, Meyer Cancer Center, Weill Cornell Medicine, New York, United States
| | - Nasser K Altorki
- Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, United States.,Lung Cancer Program, Meyer Cancer Center, Weill Cornell Medicine, New York, United States
| | - Timothy E McGraw
- Department of Biochemistry, Weill Cornell Medicine, New York, United States.,Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, United States.,Lung Cancer Program, Meyer Cancer Center, Weill Cornell Medicine, New York, United States
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