1
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Sniegowski T, Rajasekaran D, Sennoune SR, Sunitha S, Chen F, Fokar M, Kshirsagar S, Reddy PH, Korac K, Mahmud Syed M, Sharker T, Ganapathy V, Bhutia YD. Amino acid transporter SLC38A5 is a tumor promoter and a novel therapeutic target for pancreatic cancer. Sci Rep 2023; 13:16863. [PMID: 37803043 PMCID: PMC10558479 DOI: 10.1038/s41598-023-43983-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/01/2023] [Indexed: 10/08/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) cells have a great demand for nutrients in the form of sugars, amino acids, and lipids. Particularly, amino acids are critical for cancer growth and, as intermediates, connect glucose, lipid and nucleotide metabolism. PDAC cells meet these requirements by upregulating selective amino acid transporters. Here we show that SLC38A5 (SN2/SNAT5), a neutral amino acid transporter is highly upregulated and functional in PDAC cells. Using CRISPR/Cas9-mediated knockout of SLC38A5, we show its tumor promoting role in an in vitro cell line model as well as in a subcutaneous xenograft mouse model. Using metabolomics and RNA sequencing, we show significant reduction in many amino acid substrates of SLC38A5 as well as OXPHOS inactivation in response to SLC38A5 deletion. Experimental validation demonstrates inhibition of mTORC1, glycolysis and mitochondrial respiration in KO cells, suggesting a serious metabolic crisis associated with SLC38A5 deletion. Since many SLC38A5 substrates are activators of mTORC1 as well as TCA cycle intermediates/precursors, we speculate amino acid insufficiency as a possible link between SLC38A5 deletion and inactivation of mTORC1, glycolysis and mitochondrial respiration, and the underlying mechanism for PDAC attenuation. Overall, we show that SLC38A5 promotes PDAC, thereby identifying a novel, hitherto unknown, therapeutic target for PDAC.
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Affiliation(s)
- Tyler Sniegowski
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Devaraja Rajasekaran
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Souad R Sennoune
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Sukumaran Sunitha
- Center for Biotechnology & Genomics, Texas Tech University, Lubbock, TX, 79409, USA
| | - Fang Chen
- Center for Biotechnology & Genomics, Texas Tech University, Lubbock, TX, 79409, USA
| | - Mohamed Fokar
- Center for Biotechnology & Genomics, Texas Tech University, Lubbock, TX, 79409, USA
| | - Sudhir Kshirsagar
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Ksenija Korac
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Mosharaf Mahmud Syed
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Tanima Sharker
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Vadivel Ganapathy
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Yangzom D Bhutia
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA.
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2
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Vanheer L, Fantuzzi F, To SK, Schiavo A, Van Haele M, Ostyn T, Haesen T, Yi X, Janiszewski A, Chappell J, Rihoux A, Sawatani T, Roskams T, Pattou F, Kerr-Conte J, Cnop M, Pasque V. Inferring regulators of cell identity in the human adult pancreas. NAR Genom Bioinform 2023; 5:lqad068. [PMID: 37435358 PMCID: PMC10331937 DOI: 10.1093/nargab/lqad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/17/2023] [Accepted: 06/28/2023] [Indexed: 07/13/2023] Open
Abstract
Cellular identity during development is under the control of transcription factors that form gene regulatory networks. However, the transcription factors and gene regulatory networks underlying cellular identity in the human adult pancreas remain largely unexplored. Here, we integrate multiple single-cell RNA-sequencing datasets of the human adult pancreas, totaling 7393 cells, and comprehensively reconstruct gene regulatory networks. We show that a network of 142 transcription factors forms distinct regulatory modules that characterize pancreatic cell types. We present evidence that our approach identifies regulators of cell identity and cell states in the human adult pancreas. We predict that HEYL, BHLHE41 and JUND are active in acinar, beta and alpha cells, respectively, and show that these proteins are present in the human adult pancreas as well as in human induced pluripotent stem cell (hiPSC)-derived islet cells. Using single-cell transcriptomics, we found that JUND represses beta cell genes in hiPSC-alpha cells. BHLHE41 depletion induced apoptosis in primary pancreatic islets. The comprehensive gene regulatory network atlas can be explored interactively online. We anticipate our analysis to be the starting point for a more sophisticated dissection of how transcription factors regulate cell identity and cell states in the human adult pancreas.
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Affiliation(s)
| | | | - San Kit To
- Department of Development and Regeneration; KU Leuven - University of Leuven; Single-cell Omics Institute and Leuven Stem Cell Institute, Herestraat 49, B-3000 Leuven, Belgium
| | - Andrea Schiavo
- ULB Center for Diabetes Research; Université Libre de Bruxelles; Route de Lennik 808, B-1070 Brussels, Belgium
| | - Matthias Van Haele
- Department of Imaging and Pathology; Translational Cell and Tissue Research, KU Leuven and University Hospitals Leuven; Herestraat 49, B-3000 Leuven, Belgium
| | - Tessa Ostyn
- Department of Imaging and Pathology; Translational Cell and Tissue Research, KU Leuven and University Hospitals Leuven; Herestraat 49, B-3000 Leuven, Belgium
| | - Tine Haesen
- Department of Development and Regeneration; KU Leuven - University of Leuven; Single-cell Omics Institute and Leuven Stem Cell Institute, Herestraat 49, B-3000 Leuven, Belgium
| | - Xiaoyan Yi
- ULB Center for Diabetes Research; Université Libre de Bruxelles; Route de Lennik 808, B-1070 Brussels, Belgium
| | - Adrian Janiszewski
- Department of Development and Regeneration; KU Leuven - University of Leuven; Single-cell Omics Institute and Leuven Stem Cell Institute, Herestraat 49, B-3000 Leuven, Belgium
| | - Joel Chappell
- Department of Development and Regeneration; KU Leuven - University of Leuven; Single-cell Omics Institute and Leuven Stem Cell Institute, Herestraat 49, B-3000 Leuven, Belgium
| | - Adrien Rihoux
- Department of Development and Regeneration; KU Leuven - University of Leuven; Single-cell Omics Institute and Leuven Stem Cell Institute, Herestraat 49, B-3000 Leuven, Belgium
| | - Toshiaki Sawatani
- ULB Center for Diabetes Research; Université Libre de Bruxelles; Route de Lennik 808, B-1070 Brussels, Belgium
| | - Tania Roskams
- Department of Imaging and Pathology; Translational Cell and Tissue Research, KU Leuven and University Hospitals Leuven; Herestraat 49, B-3000 Leuven, Belgium
| | - Francois Pattou
- University of Lille, Inserm, CHU Lille, Institute Pasteur Lille, U1190-EGID, F-59000 Lille, France
- European Genomic Institute for Diabetes, F-59000 Lille, France
- University of Lille, F-59000 Lille, France
| | - Julie Kerr-Conte
- University of Lille, Inserm, CHU Lille, Institute Pasteur Lille, U1190-EGID, F-59000 Lille, France
- European Genomic Institute for Diabetes, F-59000 Lille, France
- University of Lille, F-59000 Lille, France
| | - Miriam Cnop
- Correspondence may also be addressed to Miriam Cnop. Tel: +32 2 555 6305; Fax: +32 2 555 6239;
| | - Vincent Pasque
- To whom correspondence should be addressed. Tel: +32 16 376283; Fax: +32 16 330827;
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3
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Taurino G, Chiu M, Bianchi MG, Griffini E, Bussolati O. The SLC38A5/SNAT5 amino acid transporter: from pathophysiology to pro-cancer roles in the tumor microenvironment. Am J Physiol Cell Physiol 2023; 325:C550-C562. [PMID: 37458433 DOI: 10.1152/ajpcell.00169.2023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 08/09/2023]
Abstract
SLC38A5/SNAT5 is a system N transporter that can mediate net inward or outward transmembrane fluxes of neutral amino acids coupled with Na+ (symport) and H+ (antiport). Its preferential substrates are not only amino acids with side chains containing amide (glutamine and asparagine) or imidazole (histidine) groups, but also serine, glycine, and alanine are transported by the carrier. Expressed in the pancreas, intestinal tract, brain, liver, bone marrow, and placenta, it is regulated at mRNA and protein levels by mTORC1 and WNT/β-catenin pathways, and it is sensitive to pH, nutritional stress, inflammation, and hypoxia. SNAT5 expression has been found to be altered in pathological conditions such as chronic inflammatory diseases, gestational complications, chronic metabolic acidosis, and malnutrition. Growing experimental evidence shows that SNAT5 is overexpressed in several types of cancer cells. Moreover, recently published results indicate that SNAT5 expression in stromal cells can support the metabolic exchanges occurring in the tumor microenvironment of asparagine-auxotroph tumors. We review the functional role of the SNAT5 transporter in pathophysiology and propose that, due to its peculiar operational and regulatory features, SNAT5 may play important pro-cancer roles when expressed either in neoplastic or in stromal cells of glutamine-auxotroph tumors.NEW & NOTEWORTHY The transporter SLC38A5/SNAT5 provides net influx or efflux of glutamine, asparagine, and serine. These amino acids are of particular metabolic relevance in several conditions. Changes in transporter expression or activity have been described in selected types of human cancers, where SNAT5 can mediate amino acid exchanges between tumor and stromal cells, thus providing a potential therapeutic target. This is the first review that recapitulates the characteristics and roles of the transporter in physiology and pathology.
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Affiliation(s)
- Giuseppe Taurino
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
- MRH-Microbiome Research Hub, University of Parma, Parma, Italy
| | - Martina Chiu
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Massimiliano G Bianchi
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
- MRH-Microbiome Research Hub, University of Parma, Parma, Italy
| | - Erika Griffini
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Ovidio Bussolati
- Laboratory of General Pathology, Department of Medicine and Surgery, University of Parma, Parma, Italy
- MRH-Microbiome Research Hub, University of Parma, Parma, Italy
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4
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Xie B, Gao D, Zhou B, Chen S, Wang L. New discoveries in the field of metabolism by applying single-cell and spatial omics. J Pharm Anal 2023; 13:711-725. [PMID: 37577385 PMCID: PMC10422156 DOI: 10.1016/j.jpha.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 05/29/2023] [Accepted: 06/02/2023] [Indexed: 08/15/2023] Open
Abstract
Single-cell multi-Omics (SCM-Omics) and spatial multi-Omics (SM-Omics) technologies provide state-of-the-art methods for exploring the composition and function of cell types in tissues/organs. Since its emergence in 2009, single-cell RNA sequencing (scRNA-seq) has yielded many groundbreaking new discoveries. The combination of this method with the emergence and development of SM-Omics techniques has been a pioneering strategy in neuroscience, developmental biology, and cancer research, especially for assessing tumor heterogeneity and T-cell infiltration. In recent years, the application of these methods in the study of metabolic diseases has also increased. The emerging SCM-Omics and SM-Omics approaches allow the molecular and spatial analysis of cells to explore regulatory states and determine cell fate, and thus provide promising tools for unraveling heterogeneous metabolic processes and making them amenable to intervention. Here, we review the evolution of SCM-Omics and SM-Omics technologies, and describe the progress in the application of SCM-Omics and SM-Omics in metabolism-related diseases, including obesity, diabetes, nonalcoholic fatty liver disease (NAFLD) and cardiovascular disease (CVD). We also conclude that the application of SCM-Omics and SM-Omics approaches can help resolve the molecular mechanisms underlying the pathogenesis of metabolic diseases in the body and facilitate therapeutic measures for metabolism-related diseases. This review concludes with an overview of the current status of this emerging field and the outlook for its future.
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Affiliation(s)
- Baocai Xie
- Department of Critical Care Medicine, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, 518060, China
- Department of Respiratory Diseases, The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450014, China
| | - Dengfeng Gao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Biqiang Zhou
- Department of Geriatric & Spinal Pain Multi-Department Treatment, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen, Guangdong, 518035, China
| | - Shi Chen
- Department of Critical Care Medicine, Shenzhen Institute of Translational Medicine, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, Guangdong, 518060, China
- Department of Gastroenterology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Lianrong Wang
- Department of Respiratory Diseases, The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450014, China
- Department of Gastroenterology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
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5
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Otto R, Detjen KM, Riemer P, Fattohi M, Grötzinger C, Rindi G, Wiedenmann B, Sers C, Leser U. Transcriptomic Deconvolution of Neuroendocrine Neoplasms Predicts Clinically Relevant Characteristics. Cancers (Basel) 2023; 15:cancers15030936. [PMID: 36765893 PMCID: PMC9913692 DOI: 10.3390/cancers15030936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
Pancreatic neuroendocrine neoplasms (panNENs) are a rare yet diverse type of neoplasia whose precise clinical-pathological classification is frequently challenging. Since incorrect classifications can affect treatment decisions, additional tools which support the diagnosis, such as machine learning (ML) techniques, are critically needed but generally unavailable due to the scarcity of suitable ML training data for rare panNENs. Here, we demonstrate that a multi-step ML framework predicts clinically relevant panNEN characteristics while being exclusively trained on widely available data of a healthy origin. The approach classifies panNENs by deconvolving their transcriptomes into cell type proportions based on shared gene expression profiles with healthy pancreatic cell types. The deconvolution results were found to provide a prognostic value with respect to the prediction of the overall patient survival time, neoplastic grading, and carcinoma versus tumor subclassification. The performance with which a proliferation rate agnostic deconvolution ML model could predict the clinical characteristics was found to be comparable to that of a comparative baseline model trained on the proliferation rate-informed MKI67 levels. The approach is novel in that it complements established proliferation rate-oriented classification schemes whose results can be reproduced and further refined by differentiating between identically graded subgroups. By including non-endocrine cell types, the deconvolution approach furthermore provides an in silico quantification of panNEN dedifferentiation, optimizing it for challenging clinical classification tasks in more aggressive panNEN subtypes.
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Affiliation(s)
- Raik Otto
- Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
- Correspondence: ; Tel.: +49-030-2093-3086
| | - Katharina M. Detjen
- Department of Hepatology and Gastroenterology, Charité—Universitätsmedizin Berlin, Campus Virchow-Klinikum and Campus Charité Mitte, 13353 Berlin, Germany
| | - Pamela Riemer
- Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Melanie Fattohi
- Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Carsten Grötzinger
- Department of Hepatology and Gastroenterology, Charité—Universitätsmedizin Berlin, Campus Virchow-Klinikum and Campus Charité Mitte, 13353 Berlin, Germany
| | - Guido Rindi
- Section of Anatomic Pathology, Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy
- Anatomic Pathology Unit, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Roma, Italy
| | - Bertram Wiedenmann
- Department of Hepatology and Gastroenterology, Charité—Universitätsmedizin Berlin, Campus Virchow-Klinikum and Campus Charité Mitte, 13353 Berlin, Germany
| | - Christine Sers
- Laboratory of Molecular Tumor Pathology and Systems Biology, Institute of Pathology, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Ulf Leser
- Knowledge Management in Bioinformatics, Institute for Computer Science, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
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6
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Wang Z, Yemanyi F, Blomfield AK, Bora K, Huang S, Liu CH, Britton WR, Cho SS, Tomita Y, Fu Z, Ma JX, Li WH, Chen J. Amino acid transporter SLC38A5 regulates developmental and pathological retinal angiogenesis. eLife 2022; 11:e73105. [PMID: 36454214 PMCID: PMC9714971 DOI: 10.7554/elife.73105] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
Amino acid (AA) metabolism in vascular endothelium is important for sprouting angiogenesis. SLC38A5 (solute carrier family 38 member 5), an AA transporter, shuttles neutral AAs across cell membrane, including glutamine, which may serve as metabolic fuel for proliferating endothelial cells (ECs) to promote angiogenesis. Here, we found that Slc38a5 is highly enriched in normal retinal vascular endothelium, and more specifically, in pathological sprouting neovessels. Slc38a5 is suppressed in retinal blood vessels from Lrp5-/- and Ndpy/- mice, both genetic models of defective retinal vascular development with Wnt signaling mutations. Additionally, Slc38a5 transcription is regulated by Wnt/β-catenin signaling. Genetic deficiency of Slc38a5 in mice substantially delays retinal vascular development and suppresses pathological neovascularization in oxygen-induced retinopathy modeling ischemic proliferative retinopathies. Inhibition of SLC38A5 in human retinal vascular ECs impairs EC proliferation and angiogenic function, suppresses glutamine uptake, and dampens vascular endothelial growth factor receptor 2. Together these findings suggest that SLC38A5 is a new metabolic regulator of retinal angiogenesis by controlling AA nutrient uptake and homeostasis in ECs.
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Affiliation(s)
- Zhongxiao Wang
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical SchoolBostonUnited States
| | - Felix Yemanyi
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical SchoolBostonUnited States
| | - Alexandra K Blomfield
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical SchoolBostonUnited States
| | - Kiran Bora
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical SchoolBostonUnited States
| | - Shuo Huang
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical SchoolBostonUnited States
| | - Chi-Hsiu Liu
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical SchoolBostonUnited States
| | - William R Britton
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical SchoolBostonUnited States
| | - Steve S Cho
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical SchoolBostonUnited States
| | - Yohei Tomita
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical SchoolBostonUnited States
| | - Zhongjie Fu
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical SchoolBostonUnited States
| | - Jian-xing Ma
- Department of Biochemistry, Wake Forest University School of MedicineWinston-SalemUnited States
| | - Wen-hong Li
- Departments of Cell Biology and of Biochemistry, University of Texas Southwestern Medical CenterDallasUnited States
| | - Jing Chen
- Department of Ophthalmology, Boston Children's Hospital, Harvard Medical SchoolBostonUnited States
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7
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Abstract
Islet dysfunction is central in type 2 diabetes and full-blown type 2 diabetes develops first when the beta cells lose their ability to secrete adequate amounts of insulin in response to raised plasma glucose. Several mechanisms behind beta cell dysfunction have been put forward but many important questions still remain. Furthermore, our understanding of the contribution of each islet cell type in type 2 diabetes pathophysiology has been limited by technical boundaries. Closing this knowledge gap will lead to a leap forward in our understanding of the islet as an organ and potentially lead to improved treatments. The development of single-cell RNA sequencing (scRNAseq) has led to a breakthrough for characterising the transcriptome of each islet cell type and several important observations on the regulation of cell-type-specific gene expression have been made. When it comes to identifying type 2 diabetes disease mechanisms, the outcome is still limited. Several studies have identified differentially expressed genes, although there is very limited consensus between the studies. As with all new techniques, scRNAseq has limitations; in addition to being extremely expensive, genes expressed at low levels may not be detected, noise may not be appropriately filtered and selection biases for certain cell types are at hand. Furthermore, recent advances suggest that commonly used computational tools may be suboptimal for analysis of scRNAseq data in small-scale studies. Fortunately, development of new computational tools holds promise for harnessing the full potential of scRNAseq data. Here we summarise how scRNAseq has contributed to increasing the understanding of various aspects of islet biology as well as type 2 diabetes disease mechanisms. We also focus on challenges that remain and propose steps to promote the utilisation of the full potential of scRNAseq in this area.
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Affiliation(s)
| | - Nils Wierup
- Lund University Diabetes Centre, Malmö, Sweden.
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8
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Jovic D, Liang X, Zeng H, Lin L, Xu F, Luo Y. Single-cell RNA sequencing technologies and applications: A brief overview. Clin Transl Med 2022; 12:e694. [PMID: 35352511 PMCID: PMC8964935 DOI: 10.1002/ctm2.694] [Citation(s) in RCA: 243] [Impact Index Per Article: 121.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 12/09/2021] [Accepted: 12/20/2021] [Indexed: 12/19/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) technology has become the state-of-the-art approach for unravelling the heterogeneity and complexity of RNA transcripts within individual cells, as well as revealing the composition of different cell types and functions within highly organized tissues/organs/organisms. Since its first discovery in 2009, studies based on scRNA-seq provide massive information across different fields making exciting new discoveries in better understanding the composition and interaction of cells within humans, model animals and plants. In this review, we provide a concise overview about the scRNA-seq technology, experimental and computational procedures for transforming the biological and molecular processes into computational and statistical data. We also provide an explanation of the key technological steps in implementing the technology. We highlight a few examples on how scRNA-seq can provide unique information for better understanding health and diseases. One important application of the scRNA-seq technology is to build a better and high-resolution catalogue of cells in all living organism, commonly known as atlas, which is key resource to better understand and provide a solution in treating diseases. While great promises have been demonstrated with the technology in all areas, we further highlight a few remaining challenges to be overcome and its great potentials in transforming current protocols in disease diagnosis and treatment.
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Affiliation(s)
- Dragomirka Jovic
- Lars Bolund Institute of Regenerative MedicineQingdao‐Europe Advanced Institute for Life SciencesQingdaoChina
- BGI‐ShenzhenShenzhenChina
| | - Xue Liang
- Lars Bolund Institute of Regenerative MedicineQingdao‐Europe Advanced Institute for Life SciencesQingdaoChina
- BGI‐ShenzhenShenzhenChina
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Hua Zeng
- Nanjing University of Chinese MedicineNanjingChina
| | - Lin Lin
- Department of BiomedicineAarhus UniversityAarhusDenmark
- Steno Diabetes Center AarhusAarhus University HospitalAarhusDenmark
| | - Fengping Xu
- Lars Bolund Institute of Regenerative MedicineQingdao‐Europe Advanced Institute for Life SciencesQingdaoChina
- BGI‐ShenzhenShenzhenChina
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative MedicineQingdao‐Europe Advanced Institute for Life SciencesQingdaoChina
- BGI‐ShenzhenShenzhenChina
- Department of BiomedicineAarhus UniversityAarhusDenmark
- Steno Diabetes Center AarhusAarhus University HospitalAarhusDenmark
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9
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Janssens J, Aibar S, Taskiran II, Ismail JN, Gomez AE, Aughey G, Spanier KI, De Rop FV, González-Blas CB, Dionne M, Grimes K, Quan XJ, Papasokrati D, Hulselmans G, Makhzami S, De Waegeneer M, Christiaens V, Southall T, Aerts S. Decoding gene regulation in the fly brain. Nature 2022; 601:630-636. [PMID: 34987221 DOI: 10.1038/s41586-021-04262-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 11/17/2021] [Indexed: 12/13/2022]
Abstract
The Drosophila brain is a frequently used model in neuroscience. Single-cell transcriptome analysis1-6, three-dimensional morphological classification7 and electron microscopy mapping of the connectome8,9 have revealed an immense diversity of neuronal and glial cell types that underlie an array of functional and behavioural traits in the fly. The identities of these cell types are controlled by gene regulatory networks (GRNs), involving combinations of transcription factors that bind to genomic enhancers to regulate their target genes. Here, to characterize GRNs at the cell-type level in the fly brain, we profiled the chromatin accessibility of 240,919 single cells spanning 9 developmental timepoints and integrated these data with single-cell transcriptomes. We identify more than 95,000 regulatory regions that are used in different neuronal cell types, of which 70,000 are linked to developmental trajectories involving neurogenesis, reprogramming and maturation. For 40 cell types, uniquely accessible regions were associated with their expressed transcription factors and downstream target genes through a combination of motif discovery, network inference and deep learning, creating enhancer GRNs. The enhancer architectures revealed by DeepFlyBrain lead to a better understanding of neuronal regulatory diversity and can be used to design genetic driver lines for cell types at specific timepoints, facilitating their characterization and manipulation.
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Affiliation(s)
- Jasper Janssens
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Sara Aibar
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Ibrahim Ihsan Taskiran
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Joy N Ismail
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Gabriel Aughey
- Department of Life Sciences, Imperial College London, London, UK
| | - Katina I Spanier
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Florian V De Rop
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Marc Dionne
- Department of Life Sciences, Imperial College London, London, UK
| | - Krista Grimes
- Department of Life Sciences, Imperial College London, London, UK
| | - Xiao Jiang Quan
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Dafni Papasokrati
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Samira Makhzami
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Maxime De Waegeneer
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Tony Southall
- Department of Life Sciences, Imperial College London, London, UK
| | - Stein Aerts
- VIB Center for Brain & Disease Research, Leuven, Belgium. .,Department of Human Genetics, KU Leuven, Leuven, Belgium.
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10
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Alvarez Fallas ME, Pedraza-Arevalo S, Cujba AM, Manea T, Lambert C, Morrugares R, Sancho R. Stem/progenitor cells in normal physiology and disease of the pancreas. Mol Cell Endocrinol 2021; 538:111459. [PMID: 34543699 PMCID: PMC8573583 DOI: 10.1016/j.mce.2021.111459] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 03/19/2021] [Accepted: 09/13/2021] [Indexed: 02/08/2023]
Abstract
Though embryonic pancreas progenitors are well characterised, the existence of stem/progenitor cells in the postnatal mammalian pancreas has been long debated, mainly due to contradicting results on regeneration after injury or disease in mice. Despite these controversies, sequencing advancements combined with lineage tracing and organoid technologies indicate that homeostatic and trigger-induced regenerative responses in mice could occur. The presence of putative progenitor cells in the adult pancreas has been proposed during homeostasis and upon different stress challenges such as inflammation, tissue damage and oncogenic stress. More recently, single cell transcriptomics has revealed a remarkable heterogeneity in all pancreas cell types, with some cells showing the signature of potential progenitors. In this review we provide an overview on embryonic and putative adult pancreas progenitors in homeostasis and disease, with special emphasis on in vitro culture systems and scRNA-seq technology as tools to address the progenitor nature of different pancreatic cells.
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Affiliation(s)
- Mario Enrique Alvarez Fallas
- Centre for Stem Cells and Regenerative Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Sergio Pedraza-Arevalo
- Centre for Stem Cells and Regenerative Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Ana-Maria Cujba
- Centre for Stem Cells and Regenerative Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Teodora Manea
- Centre for Stem Cells and Regenerative Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Christopher Lambert
- Centre for Stem Cells and Regenerative Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Rosario Morrugares
- Instituto Maimonides de Investigacion Biomedica de Cordoba (IMIBIC), Cordoba, Spain; Departamento de Biologia Celular, Fisiologia e Inmunologia, Universidad de Cordoba, Cordoba, Spain; Hospital Universitario Reina Sofia, Cordoba, Spain
| | - Rocio Sancho
- Centre for Stem Cells and Regenerative Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK; Department of Medicine III, University Hospital Carl Gustav Carus, Dresden, Germany.
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11
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Krentz NAJ, Shea LD, Huising MO, Shaw JAM. Restoring normal islet mass and function in type 1 diabetes through regenerative medicine and tissue engineering. Lancet Diabetes Endocrinol 2021; 9:708-724. [PMID: 34480875 PMCID: PMC10881068 DOI: 10.1016/s2213-8587(21)00170-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/17/2021] [Accepted: 06/08/2021] [Indexed: 02/09/2023]
Abstract
Type 1 diabetes is characterised by autoimmune-mediated destruction of pancreatic β-cell mass. With the advent of insulin therapy a century ago, type 1 diabetes changed from a progressive, fatal disease to one that requires lifelong complex self-management. Replacing the lost β-cell mass through transplantation has proven successful, but limited donor supply and need for lifelong immunosuppression restricts widespread use. In this Review, we highlight incremental advances over the past 20 years and remaining challenges in regenerative medicine approaches to restoring β-cell mass and function in type 1 diabetes. We begin by summarising the role of endocrine islets in glucose homoeostasis and how this is altered in disease. We then discuss the potential regenerative capacity of the remaining islet cells and the utility of stem cell-derived β-like cells to restore β-cell function. We conclude with tissue engineering approaches that might improve the engraftment, function, and survival of β-cell replacement therapies.
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Affiliation(s)
- Nicole A J Krentz
- Division of Endocrinology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Lonnie D Shea
- Departments of Biomedical Engineering, Chemical Engineering, and Surgery, College of Engineering and School of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Mark O Huising
- Department of Neurobiology, Physiology and Behavior, College of Biological Sciences, University of California, Davis, Davis, CA, USA; Department of Physiology and Membrane Biology, School of Medicine, University of California, Davis, Davis, CA, USA
| | - James A M Shaw
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK; Institute of Transplantation, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
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12
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Lodestijn SC, van Neerven SM, Vermeulen L, Bijlsma MF. Stem Cells in the Exocrine Pancreas during Homeostasis, Injury, and Cancer. Cancers (Basel) 2021; 13:cancers13133295. [PMID: 34209288 PMCID: PMC8267661 DOI: 10.3390/cancers13133295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/16/2021] [Accepted: 06/26/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Pancreatic cancer is one of the most lethal malignancies. Hence, improved therapies are urgently needed. Recent research indicates that pancreatic cancers depend on cancer stem cells (CSCs) for tumor expansion, metastasis, and therapy resistance. However, the exact functionality of pancreatic CSCs is still unclear. CSCs have much in common with normal pancreatic stem cells that have been better, albeit still incompletely, characterized. In this literature review, we address how pancreatic stem cells influence growth, homeostasis, regeneration, and cancer. Furthermore, we outline which intrinsic and extrinsic factors regulate stem cell functionality during these different processes to explore potential novel targets for treating pancreatic cancer. Abstract Cell generation and renewal are essential processes to develop, maintain, and regenerate tissues. New cells can be generated from immature cell types, such as stem-like cells, or originate from more differentiated pre-existing cells that self-renew or transdifferentiate. The adult pancreas is a dormant organ with limited regeneration capacity, which complicates studying these processes. As a result, there is still discussion about the existence of stem cells in the adult pancreas. Interestingly, in contrast to the classical stem cell concept, stem cell properties seem to be plastic, and, in circumstances of injury, differentiated cells can revert back to a more immature cellular state. Importantly, deregulation of the balance between cellular proliferation and differentiation can lead to disease initiation, in particular to cancer formation. Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with a 5-year survival rate of only ~9%. Unfortunately, metastasis formation often occurs prior to diagnosis, and most tumors are resistant to current treatment strategies. It has been proposed that a specific subpopulation of cells, i.e., cancer stem cells (CSCs), are responsible for tumor expansion, metastasis formation, and therapy resistance. Understanding the underlying mechanisms of pancreatic stem cells during homeostasis and injury might lead to new insights to understand the role of CSCs in PDAC. Therefore, in this review, we present an overview of the current literature regarding the stem cell dynamics in the pancreas during health and disease. Furthermore, we highlight the influence of the tumor microenvironment on the growth behavior of PDAC.
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Affiliation(s)
- Sophie C. Lodestijn
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (S.C.L.); (S.M.v.N.); (L.V.)
- Oncode Institute, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Sanne M. van Neerven
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (S.C.L.); (S.M.v.N.); (L.V.)
- Oncode Institute, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Louis Vermeulen
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (S.C.L.); (S.M.v.N.); (L.V.)
- Oncode Institute, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Maarten F. Bijlsma
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology Endocrinology and Metabolism, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; (S.C.L.); (S.M.v.N.); (L.V.)
- Oncode Institute, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Correspondence:
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13
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Szlachcic WJ, Ziojla N, Kizewska DK, Kempa M, Borowiak M. Endocrine Pancreas Development and Dysfunction Through the Lens of Single-Cell RNA-Sequencing. Front Cell Dev Biol 2021; 9:629212. [PMID: 33996792 PMCID: PMC8116659 DOI: 10.3389/fcell.2021.629212] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 04/06/2021] [Indexed: 12/16/2022] Open
Abstract
A chronic inability to maintain blood glucose homeostasis leads to diabetes, which can damage multiple organs. The pancreatic islets regulate blood glucose levels through the coordinated action of islet cell-secreted hormones, with the insulin released by β-cells playing a crucial role in this process. Diabetes is caused by insufficient insulin secretion due to β-cell loss, or a pancreatic dysfunction. The restoration of a functional β-cell mass might, therefore, offer a cure. To this end, major efforts are underway to generate human β-cells de novo, in vitro, or in vivo. The efficient generation of functional β-cells requires a comprehensive knowledge of pancreas development, including the mechanisms driving cell fate decisions or endocrine cell maturation. Rapid progress in single-cell RNA sequencing (scRNA-Seq) technologies has brought a new dimension to pancreas development research. These methods can capture the transcriptomes of thousands of individual cells, including rare cell types, subtypes, and transient states. With such massive datasets, it is possible to infer the developmental trajectories of cell transitions and gene regulatory pathways. Here, we summarize recent advances in our understanding of endocrine pancreas development and function from scRNA-Seq studies on developing and adult pancreas and human endocrine differentiation models. We also discuss recent scRNA-Seq findings for the pathological pancreas in diabetes, and their implications for better treatment.
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Affiliation(s)
- Wojciech J. Szlachcic
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Natalia Ziojla
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Dorota K. Kizewska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Marcelina Kempa
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Malgorzata Borowiak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, United States
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14
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Sniegowski T, Korac K, Bhutia YD, Ganapathy V. SLC6A14 and SLC38A5 Drive the Glutaminolysis and Serine-Glycine-One-Carbon Pathways in Cancer. Pharmaceuticals (Basel) 2021; 14:ph14030216. [PMID: 33806675 PMCID: PMC8000594 DOI: 10.3390/ph14030216] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 02/06/2023] Open
Abstract
The glutaminolysis and serine–glycine–one-carbon pathways represent metabolic reactions that are reprogramed and upregulated in cancer; these pathways are involved in supporting the growth and proliferation of cancer cells. Glutaminolysis participates in the production of lactate, an oncometabolite, and also in anabolic reactions leading to the synthesis of fatty acids and cholesterol. The serine–glycine–one-carbon pathway is involved in the synthesis of purines and pyrimidines and the control of the epigenetic signature (DNA methylation, histone methylation) in cancer cells. Methionine is obligatory for most of the methyl-transfer reactions in the form of S-adenosylmethionine; here, too, the serine–glycine–one-carbon pathway is necessary for the resynthesis of methionine following the methyl-transfer reaction. Glutamine, serine, glycine, and methionine are obligatory to fuel these metabolic pathways. The first three amino acids can be synthesized endogenously to some extent, but the need for these amino acids in cancer cells is so high that they also have to be acquired from extracellular sources. Methionine is an essential amino acid, thus making it necessary for cancer cells to acquire this amino acid solely from the extracellular milieu. Cancer cells upregulate specific amino acid transporters to meet this increased demand for these four amino acids. SLC6A14 and SLC38A5 are the two transporters that are upregulated in a variety of cancers to mediate the influx of glutamine, serine, glycine, and methionine into cancer cells. SLC6A14 is a Na+/Cl− -coupled transporter for multiple amino acids, including these four amino acids. In contrast, SLC38A5 is a Na+-coupled transporter with rather restricted specificity towards glutamine, serine, glycine, and methionine. Both transporters exhibit unique functional features that are ideal for the rapid proliferation of cancer cells. As such, these two amino acid transporters play a critical role in promoting the survival and growth of cancer cells and hence represent novel, hitherto largely unexplored, targets for cancer therapy.
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15
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Smith DK, Kates L, Durinck S, Patel N, Stawiski EW, Kljavin N, Foreman O, Sipos B, Solloway MJ, Allan BB, Peterson AS. Elevated Serum Amino Acids Induce a Subpopulation of Alpha Cells to Initiate Pancreatic Neuroendocrine Tumor Formation. CELL REPORTS MEDICINE 2020; 1:100058. [PMID: 33205067 PMCID: PMC7659536 DOI: 10.1016/j.xcrm.2020.100058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/06/2020] [Accepted: 06/25/2020] [Indexed: 12/17/2022]
Abstract
The cellular origin of sporadic pancreatic neuroendocrine tumors (PNETs) is obscure. Hormone expression suggests that these tumors arise from glucagon-producing alpha cells or insulin-producing β cells, but instability in hormone expression prevents linage determination. We utilize loss of hepatic glucagon receptor (GCGR) signaling to drive alpha cell hyperproliferation and tumor formation to identify a cell of origin and dissect mechanisms that drive progression. Using a combination of genetically engineered Gcgr knockout mice and GCGR-inhibiting antibodies, we show that elevated plasma amino acids drive the appearance of a proliferative population of SLC38A5+ embryonic progenitor-like alpha cells in mice. Further, we characterize tumors from patients with rare bi-allelic germline GCGR loss-of-function variants and find prominent tumor-cell-associated expression of the SLC38A5 paralog SLC7A8 as well as markers of active mTOR signaling. Thus, progenitor cells arise from adult alpha cells in response to metabolic signals and, when inductive signals are chronically present, drive tumor initiation. GCGR inhibition induces an SLC38A5+ alpha cell population in aged mice An SLC38A5+ alpha cell subpopulation initiates pancreatic tumors in aged Gcgr−/− mice Tumors exhibit low mutational burden and response to mTOR inhibition by rapamycin Tumors in GCGR loss-of-function models lack immune cell infiltration
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Affiliation(s)
- Derek K Smith
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Lance Kates
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Steffen Durinck
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Nisha Patel
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Eric W Stawiski
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Noelyn Kljavin
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Oded Foreman
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Bence Sipos
- University Hospital Tübingen, Internal Medicine VIII, Tübingen 72076, Germany
| | - Mark J Solloway
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Bernard B Allan
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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16
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Lu CJ, Fan XY, Guo YF, Cheng ZC, Dong J, Chen JZ, Li LY, Wang MW, Wu ZK, Wang F, Tong XJ, Luo LF, Tang FC, Zhu ZY, Zhang B. Single-cell analyses identify distinct and intermediate states of zebrafish pancreatic islet development. J Mol Cell Biol 2020; 11:435-447. [PMID: 30407522 PMCID: PMC6604604 DOI: 10.1093/jmcb/mjy064] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 10/31/2018] [Accepted: 11/08/2018] [Indexed: 12/13/2022] Open
Abstract
Pancreatic endocrine islets are vital for glucose homeostasis. However, the islet developmental trajectory and its regulatory network are not well understood. To define the features of these specification and differentiation processes, we isolated individual islet cells from TgBAC(neurod1:EGFP) transgenic zebrafish and analyzed islet developmental dynamics across four different embryonic stages using a single-cell RNA-seq strategy. We identified proliferative endocrine progenitors, which could be further categorized by different cell cycle phases with the G1/S subpopulation displaying a distinct differentiation potential. We identified endocrine precursors, a heterogeneous intermediate-state population consisting of lineage-primed alpha, beta and delta cells that were characterized by the expression of lineage-specific transcription factors and relatively low expression of terminally differentiation markers. The terminally differentiated alpha, beta, and delta cells displayed stage-dependent differentiation states, which were related to their functional maturation. Our data unveiled distinct states, events and molecular features during the islet developmental transition, and provided resources to comprehensively understand the lineage hierarchy of islet development at the single-cell level.
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Affiliation(s)
- Chong-Jian Lu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Xiao-Ying Fan
- Beijing Advanced Innovation Center for Genomics (ICG), College of Life Sciences, Peking University, Beijing, China
| | - Yue-Feng Guo
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Zhen-Chao Cheng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Ji Dong
- Beijing Advanced Innovation Center for Genomics (ICG), College of Life Sciences, Peking University, Beijing, China
| | - Jin-Zi Chen
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing, China
| | - Lian-Yan Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Mei-Wen Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Ze-Kai Wu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Fei Wang
- National Center for Protein Sciences, Peking University, Beijing, China
| | - Xiang-Jun Tong
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Ling-Fei Luo
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing, China
| | - Fu-Chou Tang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics (ICG), College of Life Sciences, Peking University, Beijing, China
| | - Zuo-Yan Zhu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Bo Zhang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
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17
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Yu XX, Xu CR. Understanding generation and regeneration of pancreatic β cells from a single-cell perspective. Development 2020; 147:147/7/dev179051. [PMID: 32280064 DOI: 10.1242/dev.179051] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 02/20/2020] [Indexed: 12/12/2022]
Abstract
Understanding the mechanisms that underlie the generation and regeneration of β cells is crucial for developing treatments for diabetes. However, traditional research methods, which are based on populations of cells, have limitations for defining the precise processes of β-cell differentiation and trans-differentiation, and the associated regulatory mechanisms. The recent development of single-cell technologies has enabled re-examination of these processes at a single-cell resolution to uncover intermediate cell states, cellular heterogeneity and molecular trajectories of cell fate specification. Here, we review recent advances in understanding β-cell generation and regeneration, in vivo and in vitro, from single-cell technologies, which could provide insights for optimization of diabetes therapy strategies.
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Affiliation(s)
- Xin-Xin Yu
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Cheng-Ran Xu
- Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
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18
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Abstract
Glucagon and its partner insulin are dually linked in both their secretion from islet cells and their action in the liver. Glucagon signaling increases hepatic glucose output, and hyperglucagonemia is partly responsible for the hyperglycemia in diabetes, making glucagon an attractive target for therapeutic intervention. Interrupting glucagon signaling lowers blood glucose but also results in hyperglucagonemia and α-cell hyperplasia. Investigation of the mechanism for α-cell proliferation led to the description of a conserved liver-α-cell axis where glucagon is a critical regulator of amino acid homeostasis. In return, amino acids regulate α-cell function and proliferation. New evidence suggests that dysfunction of the axis in humans may result in the hyperglucagonemia observed in diabetes. This discussion outlines important but often overlooked roles for glucagon that extend beyond glycemia and supports a new role for α-cells as amino acid sensors.
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Affiliation(s)
- E Danielle Dean
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, and Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
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19
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Krentz NAJ, Lee MYY, Xu EE, Sproul SLJ, Maslova A, Sasaki S, Lynn FC. Single-Cell Transcriptome Profiling of Mouse and hESC-Derived Pancreatic Progenitors. Stem Cell Reports 2019; 11:1551-1564. [PMID: 30540962 PMCID: PMC6294286 DOI: 10.1016/j.stemcr.2018.11.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 11/09/2018] [Accepted: 11/12/2018] [Indexed: 01/06/2023] Open
Abstract
Human embryonic stem cells (hESCs) are a potential unlimited source of insulin-producing β cells for diabetes treatment. A greater understanding of how β cells form during embryonic development will improve current hESC differentiation protocols. All pancreatic endocrine cells, including β cells, are derived from Neurog3-expressing endocrine progenitors. This study characterizes the single-cell transcriptomes of 6,905 mouse embryonic day (E) 15.5 and 6,626 E18.5 pancreatic cells isolated from Neurog3-Cre; Rosa26mT/mG embryos, allowing for enrichment of endocrine progenitors (yellow; tdTomato + EGFP) and endocrine cells (green; EGFP). Using a NEUROG3-2A-eGFP CyT49 hESC reporter line (N5-5), 4,462 hESC-derived GFP+ cells were sequenced. Differential expression analysis revealed enrichment of markers that are consistent with progenitor, endocrine, or previously undescribed cell-state populations. This study characterizes the single-cell transcriptomes of mouse and hESC-derived endocrine progenitors and serves as a resource (https://lynnlab.shinyapps.io/embryonic_pancreas) for improving the formation of functional β-like cells from hESCs. Single-cell transcriptome of embryonic mouse pancreas and hESC-derived cells Identification of novel cell types during mouse pancreas development Pseudotime analysis reveals developmental trajectories of endocrine cell lineage hESC-derived endocrine cells resemble immature β cells
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Affiliation(s)
- Nicole A J Krentz
- Diabetes Research Group, BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada; Departments of Surgery and Cellular and Physiological Sciences, University of British Columbia, 950 28(th) Avenue West, Vancouver, BC V5Z4H4, Canada.
| | - Michelle Y Y Lee
- Diabetes Research Group, BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Eric E Xu
- Diabetes Research Group, BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada; Departments of Surgery and Cellular and Physiological Sciences, University of British Columbia, 950 28(th) Avenue West, Vancouver, BC V5Z4H4, Canada
| | - Shannon L J Sproul
- Diabetes Research Group, BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada; Departments of Surgery and Cellular and Physiological Sciences, University of British Columbia, 950 28(th) Avenue West, Vancouver, BC V5Z4H4, Canada
| | - Alexandra Maslova
- Graduate Program in Bioinformatics, University of British Columbia, 100-570 7(th) Avenue West, Vancouver, BC V5Z 4S6, Canada
| | - Shugo Sasaki
- Diabetes Research Group, BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada; Departments of Surgery and Cellular and Physiological Sciences, University of British Columbia, 950 28(th) Avenue West, Vancouver, BC V5Z4H4, Canada
| | - Francis C Lynn
- Diabetes Research Group, BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada; Departments of Surgery and Cellular and Physiological Sciences, University of British Columbia, 950 28(th) Avenue West, Vancouver, BC V5Z4H4, Canada.
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20
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Gao C, Peng J. A glimpse of endocrine pancreas development from single-cell analyses. J Mol Cell Biol 2019; 11:433-434. [PMID: 30500955 PMCID: PMC6604600 DOI: 10.1093/jmcb/mjy079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 11/29/2018] [Indexed: 11/23/2022] Open
Affiliation(s)
- Ce Gao
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Jinrong Peng
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China
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21
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Sekiguchi R, Hauser B. Preparation of Cells from Embryonic Organs for Single-Cell RNA Sequencing. CURRENT PROTOCOLS IN CELL BIOLOGY 2019; 83:e86. [PMID: 30957983 PMCID: PMC6506382 DOI: 10.1002/cpcb.86] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Although single-cell RNA sequencing (scRNA-seq) has become one of the most powerful methods available for transcriptome analysis, the quality of scRNA-seq data largely depends on cell preparation. Cell preparation from cultured cells and tissues requires different methods because of the inherent differences between these two categories of cells. Compared to cultured cells, tissues have more extracellular matrix, and the cells are generally more adherent and thus difficult to dissociate. The challenge is to achieve sufficient dissociation, cell counts, and viability all at the same time. This protocol describes approaches that help achieve these goals. These include a cold dissociation technique using cryophilic proteases active at cold temperature, timing of trituration during protease digestion, as well as filtration and washing methods that optimize cell viability and retention. Materials and equipment that optimize the process also discussed. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Rei Sekiguchi
- Department of Oral and Craniofacial Sciences, School of Dentistry, University of Missouri-Kansas City, Kansas City, MO
- Department of Biomedical and Health Informatics, School of Medicine, University of Missouri-Kansas City, Kansas City, MO
| | - Belinda Hauser
- Matrix and Morphogenesis Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD
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22
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Affiliation(s)
- Zhe Liu
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Julie B Sneddon
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
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23
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Bastidas-Ponce A, Tritschler S, Dony L, Scheibner K, Tarquis-Medina M, Salinno C, Schirge S, Burtscher I, Böttcher A, Theis F, Lickert H, Bakhti M. Massive single-cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis. Development 2019; 146:dev.173849. [DOI: 10.1242/dev.173849] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 05/21/2019] [Indexed: 12/21/2022]
Abstract
Deciphering mechanisms of endocrine cell induction, specification and lineage allocation in vivo will provide valuable insights into how the islets of Langerhans are generated. Currently, it is ill defined how endocrine progenitors segregate into different endocrine subtypes during development. Here, we generated a novel Neurogenin3 (Ngn3)-Venus fusion (NVF) reporter mouse line, that closely mirrors the transient endogenous Ngn3 protein expression. To define an in vivo roadmap of endocrinogenesis, we performed single-cell RNA-sequencing of 36,351 pancreatic epithelial and NVF+ cells during secondary transition. This allowed to time-resolve and distinguish Ngn3low endocrine progenitors, Ngn3high endocrine precursors, Fev+ endocrine lineage and hormone+ endocrine subtypes and delineate molecular programs during the stepwise lineage restriction steps. Strikingly, we identified 58 novel signature genes that show the same transient expression dynamics as Ngn3 in the 7,260 profiled Ngn3-expressing cells. The differential expression of these genes in endocrine precursors associated with their cell-fate allocation towards distinct endocrine cell types. Thus, the generation of an accurately regulated NVF reporter allowed us to temporally resolve endocrine lineage development to provide a fine-grained single-cell molecular profile of endocrinogenesis in vivo.
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Affiliation(s)
- Aimée Bastidas-Ponce
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- Technical University of Munich, School of Medicine, Munich, Germany
| | - Sophie Tritschler
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- Technical University of Munich, School of Life Sciences Weihenstephan, Freising, Germany
| | - Leander Dony
- Institute of Computational Biology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804 Munich, Germany
| | - Katharina Scheibner
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- Technical University of Munich, School of Medicine, Munich, Germany
| | - Marta Tarquis-Medina
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- Technical University of Munich, School of Medicine, Munich, Germany
| | - Ciro Salinno
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- Technical University of Munich, School of Medicine, Munich, Germany
| | - Silvia Schirge
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Anika Böttcher
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Fabian Theis
- Institute of Computational Biology, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- Technical University of Munich, Department of Mathematics, Munich, Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- Technical University of Munich, School of Medicine, Munich, Germany
| | - Mostafa Bakhti
- Institute of Diabetes and Regeneration Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), D-85764 Neuherberg, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, D-85764 Neuherberg, Germany
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24
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van Gurp L, Muraro MJ, Dielen T, Seneby L, Dharmadhikari G, Gradwohl G, van Oudenaarden A, de Koning EJP. A transcriptomic roadmap to alpha- and beta cell differentiation in the embryonic pancreas. Development 2019; 146:dev.173716. [DOI: 10.1242/dev.173716] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/24/2019] [Indexed: 12/13/2022]
Abstract
During pancreatic development, endocrine cells appear from the pancreatic epithelium when Neurog3 positive cells delaminate and differentiate into alpha, beta, gamma and delta cells. The mechanisms involved in this process are still incompletely understood. We characterized the temporal, lineage-specific developmental programs during pancreatic development by sequencing the transcriptome of thousands of individual pancreatic cells from embryonic day E12.5 to E18.5 in mice, and identified all known cell types that are present in the embryonic pancreas, but focused specifically on alpha and beta cell differentiation by enrichment of a MIP-GFP reporter. We characterized transcriptomic heterogeneity in the tip domain based on proliferation, and characterized two endocrine precursor clusters marked by expression of Neurog3 and Fev. Pseudotime analysis revealed specific branches for developing alpha- and beta cells, which allowed identification of specific gene regulation patterns. These include some known and many previously unreported genes that appear to define pancreatic cell fate transitions. This resource allows dynamic profiling of embryonic pancreas development at single cell resolution and reveals novel gene signatures during pancreatic differentiation into alpha and beta cells.
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Affiliation(s)
- Léon van Gurp
- Hubrecht Institute\KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
| | - Mauro J. Muraro
- Hubrecht Institute\KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
- Single Cell Discoveries, Utrecht, the Netherlands
| | - Tim Dielen
- Hubrecht Institute\KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
| | - Lina Seneby
- Hubrecht Institute\KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
| | - Gitanjali Dharmadhikari
- Hubrecht Institute\KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
| | - Gerard Gradwohl
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Alexander van Oudenaarden
- Hubrecht Institute\KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
- Single Cell Discoveries, Utrecht, the Netherlands
- Oncode Institute, the Netherlands
| | - Eelco J. P. de Koning
- Hubrecht Institute\KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
- Department of Internal Medicine, Leiden University Medical Center, Leiden, the Netherlands
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25
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Huang XT, Li X, Qin PZ, Zhu Y, Xu SN, Chen JP. Technical Advances in Single-Cell RNA Sequencing and Applications in Normal and Malignant Hematopoiesis. Front Oncol 2018; 8:582. [PMID: 30581771 PMCID: PMC6292934 DOI: 10.3389/fonc.2018.00582] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/19/2018] [Indexed: 12/20/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has been tremendously developed in the past decade owing to overcoming challenges associated with isolation of massive quantities of single cells. Previously, cell heterogeneity and low quantities of available biological material posed significant difficulties to scRNA-seq. Cell-to-cell variation and heterogeneity are fundamental and intrinsic characteristics of normal and malignant hematopoietic cells; this heterogeneity has often been ignored in omics studies. The application of scRNA-seq has profoundly changed our comprehension of many biological phenomena, including organ development and carcinogenesis. Hematopoiesis, is actually a maturation process for more than ten distinct blood and immune cells, and is thought to be critically involved in hematological homeostasis and in sustaining the physiological functions. However, aberrant hematopoiesis directly leads to hematological malignancy, and a deeper understanding of malignant hematopoiesis will provide deeper insights into diagnosis and prognosis for patients with hematological malignancies. Here, we aim to review the recent technical progress and future prospects for scRNA-seq, as applied in physiological and malignant hematopoiesis, in efforts to further understand the hematopoietic hierarchy and to illuminate personalized therapy and precision medicine approaches used in the clinical treatment of hematological malignancies.
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Affiliation(s)
- Xiang-Tao Huang
- Center of Haematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xi Li
- Center of Haematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Pei-Zhong Qin
- Center of Haematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yao Zhu
- Center of Haematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Shuang-Nian Xu
- Center of Haematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Jie-Ping Chen
- Center of Haematology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
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26
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Byrnes LE, Wong DM, Subramaniam M, Meyer NP, Gilchrist CL, Knox SM, Tward AD, Ye CJ, Sneddon JB. Lineage dynamics of murine pancreatic development at single-cell resolution. Nat Commun 2018; 9:3922. [PMID: 30254276 PMCID: PMC6156586 DOI: 10.1038/s41467-018-06176-3] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 08/16/2018] [Indexed: 01/07/2023] Open
Abstract
Organogenesis requires the complex interactions of multiple cell lineages that coordinate their expansion, differentiation, and maturation over time. Here, we profile the cell types within the epithelial and mesenchymal compartments of the murine pancreas across developmental time using a combination of single-cell RNA sequencing, immunofluorescence, in situ hybridization, and genetic lineage tracing. We identify previously underappreciated cellular heterogeneity of the developing mesenchyme and reconstruct potential lineage relationships among the pancreatic mesothelium and mesenchymal cell types. Within the epithelium, we find a previously undescribed endocrine progenitor population, as well as an analogous population in both human fetal tissue and human embryonic stem cells differentiating toward a pancreatic beta cell fate. Further, we identify candidate transcriptional regulators along the differentiation trajectory of this population toward the alpha or beta cell lineages. This work establishes a roadmap of pancreatic development and demonstrates the broad utility of this approach for understanding lineage dynamics in developing organs. Coordinated proliferation and differentiation of diverse cell populations drive pancreatic epithelial and mesenchymal development. Here, the authors profile cell type dynamics in the developing mouse pancreas using single-cell RNA sequencing, identifying mesenchymal subtypes and undescribed endocrine progenitors.
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Affiliation(s)
- Lauren E Byrnes
- Diabetes Center, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA, 94143, USA
| | - Daniel M Wong
- Diabetes Center, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA, 94143, USA
| | - Meena Subramaniam
- Institute for Human Genetics, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA, 94143, USA
| | - Nathaniel P Meyer
- Diabetes Center, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA, 94143, USA
| | - Caroline L Gilchrist
- Diabetes Center, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA, 94143, USA
| | - Sarah M Knox
- Department of Cell and Tissue Biology, University of California, San Francisco, 513 Parnassus Avenue, CA, 94143, USA
| | - Aaron D Tward
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Francisco, 513 Parnassus Avenue, CA, 94143, USA
| | - Chun J Ye
- Institute for Human Genetics, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA, 94143, USA
| | - Julie B Sneddon
- Diabetes Center, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA, 94143, USA.
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27
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Davie K, Janssens J, Koldere D, De Waegeneer M, Pech U, Kreft Ł, Aibar S, Makhzami S, Christiaens V, Bravo González-Blas C, Poovathingal S, Hulselmans G, Spanier KI, Moerman T, Vanspauwen B, Geurs S, Voet T, Lammertyn J, Thienpont B, Liu S, Konstantinides N, Fiers M, Verstreken P, Aerts S. A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain. Cell 2018; 174:982-998.e20. [PMID: 29909982 PMCID: PMC6086935 DOI: 10.1016/j.cell.2018.05.057] [Citation(s) in RCA: 422] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/30/2018] [Accepted: 05/25/2018] [Indexed: 02/06/2023]
Abstract
The diversity of cell types and regulatory states in the brain, and how these change during aging, remains largely unknown. We present a single-cell transcriptome atlas of the entire adult Drosophila melanogaster brain sampled across its lifespan. Cell clustering identified 87 initial cell clusters that are further subclustered and validated by targeted cell-sorting. Our data show high granularity and identify a wide range of cell types. Gene network analyses using SCENIC revealed regulatory heterogeneity linked to energy consumption. During aging, RNA content declines exponentially without affecting neuronal identity in old brains. This single-cell brain atlas covers nearly all cells in the normal brain and provides the tools to study cellular diversity alongside other Drosophila and mammalian single-cell datasets in our unique single-cell analysis platform: SCope (http://scope.aertslab.org). These results, together with SCope, allow comprehensive exploration of all transcriptional states of an entire aging brain. A single-cell atlas of the adult fly brain during aging Network inference reveals regulatory states related to oxidative phosphorylation Cell identity is retained during aging despite exponential decline of gene expression SCope: An online tool to explore and compare single-cell datasets across species
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Affiliation(s)
- Kristofer Davie
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Jasper Janssens
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Duygu Koldere
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Maxime De Waegeneer
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Uli Pech
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Neurosciences, KU Leuven, Leuven 3000, Belgium
| | - Łukasz Kreft
- VIB Bioinformatics Core, VIB, Ghent 9052, Belgium
| | - Sara Aibar
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Samira Makhzami
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | | | - Gert Hulselmans
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Katina I Spanier
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Thomas Moerman
- ESAT, KU Leuven, Leuven 3001, Belgium; Smart Applications and Innovation Services, IMEC, Leuven 3001, Belgium
| | | | - Sarah Geurs
- Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Thierry Voet
- Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | | | | | - Sha Liu
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Neurosciences, KU Leuven, Leuven 3000, Belgium
| | | | - Mark Fiers
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Neurosciences, KU Leuven, Leuven 3000, Belgium
| | - Patrik Verstreken
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Neurosciences, KU Leuven, Leuven 3000, Belgium
| | - Stein Aerts
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium.
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28
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Tošić - Golubović S, Slavković V, Sibinović V, Guglet D, Nikolić G. D EPRESSION AMONG MEDCALLY ILL PATIENTS. ACTA MEDICA MEDIANAE 2017. [DOI: 10.5633/amm.2017.0307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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29
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Kim J, Okamoto H, Huang Z, Anguiano G, Chen S, Liu Q, Cavino K, Xin Y, Na E, Hamid R, Lee J, Zambrowicz B, Unger R, Murphy AJ, Xu Y, Yancopoulos GD, Li WH, Gromada J. Amino Acid Transporter Slc38a5 Controls Glucagon Receptor Inhibition-Induced Pancreatic α Cell Hyperplasia in Mice. Cell Metab 2017; 25:1348-1361.e8. [PMID: 28591637 PMCID: PMC8206958 DOI: 10.1016/j.cmet.2017.05.006] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 03/09/2017] [Accepted: 05/21/2017] [Indexed: 12/22/2022]
Abstract
Glucagon supports glucose homeostasis by stimulating hepatic gluconeogenesis, in part by promoting the uptake and conversion of amino acids into gluconeogenic precursors. Genetic disruption or pharmacologic inhibition of glucagon signaling results in elevated plasma amino acids and compensatory glucagon hypersecretion involving expansion of pancreatic α cell mass. Recent findings indicate that hyperaminoacidemia triggers pancreatic α cell proliferation via an mTOR-dependent pathway. We confirm and extend these findings by demonstrating that glucagon pathway blockade selectively increases expression of the sodium-coupled neutral amino acid transporter Slc38a5 in a subset of highly proliferative α cells and that Slc38a5 controls the pancreatic response to glucagon pathway blockade; most notably, mice deficient in Slc38a5 exhibit markedly decreased α cell hyperplasia to glucagon pathway blockade-induced hyperaminoacidemia. These results show that Slc38a5 is a key component of the feedback circuit between glucagon receptor signaling in the liver and amino-acid-dependent regulation of pancreatic α cell mass in mice.
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Affiliation(s)
- Jinrang Kim
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Haruka Okamoto
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - ZhiJiang Huang
- Departments of Cell Biology and of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Guillermo Anguiano
- Departments of Cell Biology and of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Shiuhwei Chen
- Departments of Cell Biology and of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Qing Liu
- Departments of Cell Biology and of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Katie Cavino
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Yurong Xin
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Erqian Na
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Rachid Hamid
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Joseph Lee
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | | | - Roger Unger
- Touchstone Center for Diabetes Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | | | - Yan Xu
- Departments of Cell Biology and of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | | | - Wen-Hong Li
- Departments of Cell Biology and of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA.
| | - Jesper Gromada
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA.
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30
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Dean ED, Li M, Prasad N, Wisniewski SN, Von Deylen A, Spaeth J, Maddison L, Botros A, Sedgeman LR, Bozadjieva N, Ilkayeva O, Coldren A, Poffenberger G, Shostak A, Semich MC, Aamodt KI, Phillips N, Yan H, Bernal-Mizrachi E, Corbin JD, Vickers KC, Levy SE, Dai C, Newgard C, Gu W, Stein R, Chen W, Powers AC. Interrupted Glucagon Signaling Reveals Hepatic α Cell Axis and Role for L-Glutamine in α Cell Proliferation. Cell Metab 2017; 25:1362-1373.e5. [PMID: 28591638 PMCID: PMC5572896 DOI: 10.1016/j.cmet.2017.05.011] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 03/15/2017] [Accepted: 05/23/2017] [Indexed: 02/06/2023]
Abstract
Decreasing glucagon action lowers the blood glucose and may be useful therapeutically for diabetes. However, interrupted glucagon signaling leads to α cell proliferation. To identify postulated hepatic-derived circulating factor(s) responsible for α cell proliferation, we used transcriptomics/proteomics/metabolomics in three models of interrupted glucagon signaling and found that proliferation of mouse, zebrafish, and human α cells was mTOR and FoxP transcription factor dependent. Changes in hepatic amino acid (AA) catabolism gene expression predicted the observed increase in circulating AAs. Mimicking these AA levels stimulated α cell proliferation in a newly developed in vitro assay with L-glutamine being a critical AA. α cell expression of the AA transporter Slc38a5 was markedly increased in mice with interrupted glucagon signaling and played a role in α cell proliferation. These results indicate a hepatic α islet cell axis where glucagon regulates serum AA availability and AAs, especially L-glutamine, regulate α cell proliferation and mass via mTOR-dependent nutrient sensing.
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Affiliation(s)
- E Danielle Dean
- Division of Diabetes, Endocrinology, and Metabolism, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Mingyu Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; School of Pharmaceutical Sciences, Xiamen University, Xiamen 361005, China
| | - Nripesh Prasad
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Scott N Wisniewski
- Division of Diabetes, Endocrinology, and Metabolism, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Alison Von Deylen
- Division of Diabetes, Endocrinology, and Metabolism, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jason Spaeth
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Lisette Maddison
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Anthony Botros
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Leslie R Sedgeman
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nadejda Bozadjieva
- Division of Metabolism, Endocrinology, and Diabetes, University of Michigan Health System, Ann Arbor, MI 48103, USA
| | - Olga Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University, Durham, NC 27701, USA
| | - Anastasia Coldren
- Division of Diabetes, Endocrinology, and Metabolism, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Greg Poffenberger
- Division of Diabetes, Endocrinology, and Metabolism, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Alena Shostak
- Division of Diabetes, Endocrinology, and Metabolism, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Michael C Semich
- Division of Diabetes, Endocrinology, and Metabolism, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kristie I Aamodt
- Division of Diabetes, Endocrinology, and Metabolism, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Neil Phillips
- Division of Diabetes, Endocrinology, and Metabolism, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Hai Yan
- REMD Biotherapeutics, Camarillo, CA 93012, USA
| | - Ernesto Bernal-Mizrachi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, University of Miami, Miami, FL 33146, USA
| | - Jackie D Corbin
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kasey C Vickers
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Shawn E Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Chunhua Dai
- Division of Diabetes, Endocrinology, and Metabolism, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Christopher Newgard
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University, Durham, NC 27701, USA
| | - Wei Gu
- Amgen, Thousand Oaks, CA 91320, USA
| | - Roland Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Wenbiao Chen
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Alvin C Powers
- Division of Diabetes, Endocrinology, and Metabolism, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; VA Tennessee Valley Healthcare, Nashville, TN 37212, USA.
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