1
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Zhang X, Ding X, Wang C, Le Q, Wu D, Song A, Huang G, Luo L, Luo Y, Yang X, Goins AE, Desai SP, Qiu C, Silva FD, Feldman LE, Zhou J, Spafford MF, Boyd NH, Prossnitz ER, Yang XO, Wang QA, Liu M. Depletion of JunB increases adipocyte thermogenic capacity and ameliorates diet-induced insulin resistance. Nat Metab 2024; 6:78-93. [PMID: 38191667 PMCID: PMC10954369 DOI: 10.1038/s42255-023-00945-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 11/10/2023] [Indexed: 01/10/2024]
Abstract
The coexistence of brown adipocytes with low and high thermogenic activity is a fundamental feature of brown adipose tissue heterogeneity and plasticity. However, the mechanisms that govern thermogenic adipocyte heterogeneity and its significance in obesity and metabolic disease remain poorly understood. Here we show that in male mice, a population of transcription factor jun-B (JunB)-enriched (JunB+) adipocytes within the brown adipose tissue exhibits lower thermogenic capacity compared to high-thermogenic adipocytes. The JunB+ adipocyte population expands in obesity. Depletion of JunB in adipocytes increases the fraction of adipocytes exhibiting high thermogenic capacity, leading to enhanced basal and cold-induced energy expenditure and protection against diet-induced obesity and insulin resistance. Mechanistically, JunB antagonizes the stimulatory effects of PPARγ coactivator-1α on high-thermogenic adipocyte formation by directly binding to the promoter of oestrogen-related receptor alpha, a PPARγ coactivator-1α downstream effector. Taken together, our study uncovers that JunB shapes thermogenic adipocyte heterogeneity, serving a critical role in maintaining systemic metabolic health.
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Affiliation(s)
- Xing Zhang
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Xiaofeng Ding
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Chunqing Wang
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Que Le
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Dandan Wu
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Anying Song
- Department of Molecular & Cellular Endocrinology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Guixiang Huang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, People's Republic of China
| | - Liping Luo
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Yan Luo
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Xin Yang
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Aleyah E Goins
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Sharina P Desai
- Autophagy Inflammation and Metabolism Center for Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Chengrui Qiu
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Floyd D Silva
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Lily Elizabeth Feldman
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Jianlin Zhou
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha, People's Republic of China
| | - Michael F Spafford
- Department of Surgery, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Nathan H Boyd
- Department of Surgery, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Eric R Prossnitz
- Autophagy Inflammation and Metabolism Center for Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
- UNM Comprehensive Cancer Center (UNMCCC), University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Xuexian O Yang
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
- Autophagy Inflammation and Metabolism Center for Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Qiong A Wang
- Department of Molecular & Cellular Endocrinology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Meilian Liu
- Department of Biochemistry and Molecular Biology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.
- Autophagy Inflammation and Metabolism Center for Biomedical Research Excellence, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.
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2
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You W, Xu Z, Chen W, Yang X, Liu S, Wang L, Tu Y, Zhou Y, Valencak TG, Wang Y, Kuang S, Shan T. Cellular and Transcriptional Dynamics during Brown Adipose Tissue Regeneration under Acute Injury. RESEARCH (WASHINGTON, D.C.) 2023; 6:0268. [PMID: 38434240 PMCID: PMC10907023 DOI: 10.34133/research.0268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/18/2023] [Indexed: 03/05/2024]
Abstract
Brown adipose tissue (BAT) is the major site of non-shivering thermogenesis and crucial for systemic metabolism. Under chronic cold exposures and high-fat diet challenges, BAT undergoes robust remodeling to adapt to physiological demands. However, whether and how BAT regenerates after acute injuries are poorly understood. Here, we established a novel BAT injury and regeneration model (BAT-IR) in mice and performed single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq to determine cellular and transcriptomic dynamics during BAT-IR. We further defined distinct fibro-adipogenic and myeloid progenitor populations contributing to BAT regeneration. Cell trajectory and gene expression analyses uncovered the involvement of MAPK, Wnt, and Hedgehog (Hh) signaling pathways in BAT regeneration. We confirmed the role of Hh signaling in BAT development through Myf5Cre-mediated conditional knockout (cKO) of the Sufu gene to activate Hh signaling in BAT and muscle progenitors. Our BAT-IR model therefore provides a paradigm to identify conserved cellular and molecular mechanisms underlying BAT development and remodeling.
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Affiliation(s)
- Wenjing You
- College of Animal Sciences,
Zhejiang University, Hangzhou, China
- The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
- Zhejiang Provincial Laboratory of Feed and Animal Nutrition, Hangzhou, China
| | - Ziye Xu
- College of Animal Sciences,
Zhejiang University, Hangzhou, China
- Department of Laboratory Medicine, the First Affiliated Hospital, College of Medicine,
Zhejiang University, Hangzhou, China
| | - Wentao Chen
- College of Animal Sciences,
Zhejiang University, Hangzhou, China
- The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
- Zhejiang Provincial Laboratory of Feed and Animal Nutrition, Hangzhou, China
| | - Xin Yang
- Department of Animal Sciences,
Purdue University, West Lafayette, IN, USA
| | - Shiqi Liu
- College of Animal Sciences,
Zhejiang University, Hangzhou, China
- The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
- Zhejiang Provincial Laboratory of Feed and Animal Nutrition, Hangzhou, China
| | - Liyi Wang
- College of Animal Sciences,
Zhejiang University, Hangzhou, China
- The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
- Zhejiang Provincial Laboratory of Feed and Animal Nutrition, Hangzhou, China
| | - Yuang Tu
- College of Animal Sciences,
Zhejiang University, Hangzhou, China
- The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
- Zhejiang Provincial Laboratory of Feed and Animal Nutrition, Hangzhou, China
| | - Yanbing Zhou
- College of Animal Sciences,
Zhejiang University, Hangzhou, China
- The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
- Zhejiang Provincial Laboratory of Feed and Animal Nutrition, Hangzhou, China
| | | | - Yizhen Wang
- College of Animal Sciences,
Zhejiang University, Hangzhou, China
- The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
- Zhejiang Provincial Laboratory of Feed and Animal Nutrition, Hangzhou, China
| | - Shihuan Kuang
- Department of Animal Sciences,
Purdue University, West Lafayette, IN, USA
| | - Tizhong Shan
- College of Animal Sciences,
Zhejiang University, Hangzhou, China
- The Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
- Zhejiang Provincial Laboratory of Feed and Animal Nutrition, Hangzhou, China
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3
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Ye M, Shan Y, Lu B, Luo H, Li B, Zhang Y, Wang Z, Guo Y, Ouyang L, Gu J, Xiong Z, Zhang T. Creating a semi-opened micro-cavity ovary through sacrificial microspheres as an in vitro model for discovering the potential effect of ovarian toxic agents. Bioact Mater 2023; 26:216-230. [PMID: 36936809 PMCID: PMC10017366 DOI: 10.1016/j.bioactmat.2023.02.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/26/2023] [Accepted: 02/26/2023] [Indexed: 03/09/2023] Open
Abstract
The bio-engineered ovary is an essential technology for treating female infertility. Especially the development of relevant in vitro models could be a critical step in a drug study. Herein, we develop a semi-opened culturing system (SOCS) strategy that maintains a 3D structure of follicles during the culture. Based on the SOCS, we further developed micro-cavity ovary (MCO) with mouse follicles by the microsphere-templated technique, where sacrificial gelatin microspheres were mixed with photo-crosslinkable gelatin methacryloyl (GelMA) to engineer a micro-cavity niche for follicle growth. The semi-opened MCO could support the follicle growing to the antral stage, secreting hormones, and ovulating cumulus-oocyte complex out of the MCO without extra manipulation. The MCO-ovulated oocyte exhibits a highly similar transcriptome to the in vivo counterpart (correlation of 0.97) and can be fertilized. Moreover, we found that a high ROS level could affect the cumulus expansion, which may result in anovulation disorder. The damage could be rescued by melatonin, but the end of cumulus expansion was 3h earlier than anticipation, validating that MCO has the potential for investigating ovarian toxic agents in vitro. We provide a novel approach for building an in vitro ovarian model to recapitulate ovarian functions and test chemical toxicity, suggesting it has the potential for clinical research in the future.
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Affiliation(s)
- Min Ye
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
- Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Beijing, 100084, China
- Biomanufacturing and Engineering Living Systems, Innovation International Talents Base (111 Base), Beijing, 100084, China
| | - Yiran Shan
- MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Bingchuan Lu
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
- Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Beijing, 100084, China
- Biomanufacturing and Engineering Living Systems, Innovation International Talents Base (111 Base), Beijing, 100084, China
| | - Hao Luo
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
- Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Beijing, 100084, China
- Biomanufacturing and Engineering Living Systems, Innovation International Talents Base (111 Base), Beijing, 100084, China
| | - Binhan Li
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
- Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Beijing, 100084, China
- Biomanufacturing and Engineering Living Systems, Innovation International Talents Base (111 Base), Beijing, 100084, China
| | - Yanmei Zhang
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
- Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Beijing, 100084, China
- Biomanufacturing and Engineering Living Systems, Innovation International Talents Base (111 Base), Beijing, 100084, China
| | - Zixuan Wang
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
- Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Beijing, 100084, China
- Biomanufacturing and Engineering Living Systems, Innovation International Talents Base (111 Base), Beijing, 100084, China
| | - Yuzhi Guo
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
- Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Beijing, 100084, China
- Biomanufacturing and Engineering Living Systems, Innovation International Talents Base (111 Base), Beijing, 100084, China
| | - Liliang Ouyang
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
- Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Beijing, 100084, China
- Biomanufacturing and Engineering Living Systems, Innovation International Talents Base (111 Base), Beijing, 100084, China
| | - Jin Gu
- MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Zhuo Xiong
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
- Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Beijing, 100084, China
- Biomanufacturing and Engineering Living Systems, Innovation International Talents Base (111 Base), Beijing, 100084, China
- Corresponding author. Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China.
| | - Ting Zhang
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
- Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Beijing, 100084, China
- Biomanufacturing and Engineering Living Systems, Innovation International Talents Base (111 Base), Beijing, 100084, China
- Corresponding author. Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China.
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4
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Maniyadath B, Zhang Q, Gupta RK, Mandrup S. Adipose tissue at single-cell resolution. Cell Metab 2023; 35:386-413. [PMID: 36889280 PMCID: PMC10027403 DOI: 10.1016/j.cmet.2023.02.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/22/2023] [Accepted: 02/03/2023] [Indexed: 03/09/2023]
Abstract
Adipose tissue exhibits remarkable plasticity with capacity to change in size and cellular composition under physiological and pathophysiological conditions. The emergence of single-cell transcriptomics has rapidly transformed our understanding of the diverse array of cell types and cell states residing in adipose tissues and has provided insight into how transcriptional changes in individual cell types contribute to tissue plasticity. Here, we present a comprehensive overview of the cellular atlas of adipose tissues focusing on the biological insight gained from single-cell and single-nuclei transcriptomics of murine and human adipose tissues. We also offer our perspective on the exciting opportunities for mapping cellular transitions and crosstalk, which have been made possible by single-cell technologies.
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Affiliation(s)
- Babukrishna Maniyadath
- Center for Functional Genomics and Tissue Plasticity, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Qianbin Zhang
- Department of Internal Medicine, Touchstone Diabetes Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Rana K Gupta
- Department of Internal Medicine, Touchstone Diabetes Center, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Susanne Mandrup
- Center for Functional Genomics and Tissue Plasticity, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark.
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5
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Roy A. Advances in the molecular level understanding of G-protein coupled receptor. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 196:1-13. [PMID: 36813353 DOI: 10.1016/bs.pmbts.2022.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
G-protein coupled receptors (GPCRs) represent largest family of plasma membrane-bound receptor proteins that are involved in numerous cellular and physiological functions. Many extracellular stimuli such as hormones, lipids and chemokines activate these receptors. Aberrant expression and genetic alteration in GPCR are associated with many human diseases including cancer and cardiovascular disease. GPCRs have emerged as potential therapeutic target and numerous drugs are either approved by FDA or under clinical trial. This chapter provides an update on GPCR research and its significance as a promising therapeutic target.
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Affiliation(s)
- Adhiraj Roy
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Noida, Uttar Pradesh, India.
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6
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Chang JS. Recent insights into the molecular mechanisms of simultaneous fatty acid oxidation and synthesis in brown adipocytes. Front Endocrinol (Lausanne) 2023; 14:1106544. [PMID: 36896177 PMCID: PMC9989468 DOI: 10.3389/fendo.2023.1106544] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
Brown adipocytes is a specialized fat cell that dissipates nutrient-derived chemical energy in the form of heat, instead of ATP synthesis. This unique feature provides a marked capacity for brown adipocyte mitochondria to oxidize substrates independent of ADP availability. Upon cold exposure, brown adipocytes preferentially oxidize free fatty acids (FFA) liberated from triacylglycerol (TAG) in lipid droplets to support thermogenesis. In addition, brown adipocytes take up large amounts of circulating glucose, concurrently increasing glycolysis and de novo FA synthesis from glucose. Given that FA oxidation and glucose-derived FA synthesis are two antagonistic mitochondrial processes in the same cell, it has long been questioned how brown adipocytes run FA oxidation and FA synthesis simultaneously. In this review, I summarize mechanisms regulating mitochondrial substrate selection and describe recent findings of two distinct populations of brown adipocyte mitochondria with different substrate preferences. I further discuss how these mechanisms may permit a concurrent increase in glycolysis, FA synthesis, and FA oxidation in brown adipocytes.
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7
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Qi Y, Hui XH. The Single-Cell Revelation of Thermogenic Adipose Tissue. Mol Cells 2022; 45:673-684. [PMID: 36254709 PMCID: PMC9589375 DOI: 10.14348/molcells.2022.0092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 11/07/2022] Open
Abstract
The past two decades have witnessed an upsurge in the appreciation of adipose tissue (AT) as an immuno-metabolic hub harbouring heterogeneous cell populations that collectively fine-tune systemic metabolic homeostasis. Technological advancements, especially single-cell transcriptomics, have offered an unprecedented opportunity for dissecting the sophisticated cellular networks and compositional dynamics underpinning AT remodelling. The "re-discovery" of functional brown adipose tissue dissipating heat energy in human adults has aroused tremendous interest in exploiting the mechanisms underpinning the engagement of AT thermogenesis for combating human obesity. In this review, we aim to summarise and evaluate the use of single-cell transcriptomics that contribute to a better appreciation of the cellular plasticity and intercellular crosstalk in thermogenic AT.
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Affiliation(s)
- Yue Qi
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaoyan Hannah Hui
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
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8
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Wang G, Song A, Bae M, Wang QA. Adipose Tissue Plasticity in Aging. Compr Physiol 2022; 12:4119-4132. [PMID: 36214190 DOI: 10.1002/cphy.c220005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
As a dynamic endocrine organ, white adipose tissue (WAT) stores lipids and plays a critical role in maintaining whole-body energy homeostasis and insulin sensitivity. A large group of the population over 65 years old suffer from increased WAT mass, especially in the visceral location. Visceral adiposity accelerates aging through promoting age-associated chronic conditions, significantly shortening life expectancy. Unlike WAT, brown adipose tissue (BAT) functions as an effective energy sink that burns and disposes of excess lipids and glucose upon activation of thermogenesis. Unfortunately, the thermogenic activity of BAT declines during aging. New appreciation of cellular and functional remodeling of WAT and BAT during aging has emerged in recent years. Efforts are underway to explore the potential underlying mechanisms behind these age-associated alterations in WAT and BAT and the impact of these alterations on whole-body metabolism. Lastly, it is intriguing to translate our knowledge obtained from animal models to the clinic to prevent and treat age-associated metabolic disorders. © 2022 American Physiological Society. Compr Physiol 12: 4119-4132, 2022.
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Affiliation(s)
- Guan Wang
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope Medical Center, Duarte, California, USA
| | - Anying Song
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope Medical Center, Duarte, California, USA
| | - Marie Bae
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope Medical Center, Duarte, California, USA
| | - Qiong A Wang
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope Medical Center, Duarte, California, USA.,Comprehensive Cancer Center, Beckman Research Institute, City of Hope Medical Center, Duarte, California, USA
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9
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Duerre DJ, Galmozzi A. Deconstructing Adipose Tissue Heterogeneity One Cell at a Time. Front Endocrinol (Lausanne) 2022; 13:847291. [PMID: 35399946 PMCID: PMC8990929 DOI: 10.3389/fendo.2022.847291] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 02/28/2022] [Indexed: 12/26/2022] Open
Abstract
As a central coordinator of physiologic metabolism, adipose tissue has long been appreciated as a highly plastic organ that dynamically responds to environmental cues. Once thought of as a homogenous storage depot, recent advances have enabled deep characterizations of the underlying structure and composition of adipose tissue depots. As the obesity and metabolic disease epidemics continue to accelerate due to modern lifestyles and an aging population, elucidation of the underlying mechanisms that control adipose and systemic homeostasis are of critical importance. Within the past decade, the emergence of deep cell profiling at tissue- and, recently, single-cell level has furthered our understanding of the complex dynamics that contribute to tissue function and their implications in disease development. Although many paradigm-shifting findings may lie ahead, profound advances have been made to forward our understanding of the adipose tissue niche in both health and disease. Now widely accepted as a highly heterogenous organ with major roles in metabolic homeostasis, endocrine signaling, and immune function, the study of adipose tissue dynamics has reached a new frontier. In this review, we will provide a synthesis of the latest advances in adipose tissue biology made possible by the use of single-cell technologies, the impact of epigenetic mechanisms on adipose function, and suggest what next steps will further our understanding of the role that adipose tissue plays in systemic physiology.
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Affiliation(s)
- Dylan J. Duerre
- Department of Medicine, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, United States
| | - Andrea Galmozzi
- Department of Medicine, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, United States
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, United States
- University of Wisconsin Carbone Cancer Center, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, United States
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10
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Gupta A, Shamsi F, Altemose N, Dorlhiac GF, Cypess AM, White AP, Yosef N, Patti ME, Tseng YH, Streets A. Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages. Genome Res 2022; 32:242-257. [PMID: 35042723 PMCID: PMC8805720 DOI: 10.1101/gr.275509.121] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 12/10/2021] [Indexed: 02/02/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) enables molecular characterization of complex biological tissues at high resolution. The requirement of single-cell extraction, however, makes it challenging for profiling tissues such as adipose tissue, for which collection of intact single adipocytes is complicated by their fragile nature. For such tissues, single-nucleus extraction is often much more efficient and therefore single-nucleus RNA sequencing (snRNA-seq) presents an alternative to scRNA-seq. However, nuclear transcripts represent only a fraction of the transcriptome in a single cell, with snRNA-seq marked with inherent transcript enrichment and detection biases. Therefore, snRNA-seq may be inadequate for mapping important transcriptional signatures in adipose tissue. In this study, we compare the transcriptomic landscape of single nuclei isolated from preadipocytes and mature adipocytes across human white and brown adipocyte lineages, with whole-cell transcriptome. We show that snRNA-seq is capable of identifying the broad cell types present in scRNA-seq at all states of adipogenesis. However, we also explore how and why the nuclear transcriptome is biased and limited, as well as how it can be advantageous. We robustly characterize the enrichment of nuclear-localized transcripts and adipogenic regulatory lncRNAs in snRNA-seq, while also providing a detailed understanding for the preferential detection of long genes upon using this technique. To remove such technical detection biases, we propose a normalization strategy for a more accurate comparison of nuclear and cellular data. Finally, we show successful integration of scRNA-seq and snRNA-seq data sets with existing bioinformatic tools. Overall, our results illustrate the applicability of snRNA-seq for the characterization of cellular diversity in the adipose tissue.
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Affiliation(s)
- Anushka Gupta
- University of California at Berkeley-University of California at San Francisco Graduate Program in Bioengineering, Berkeley, California 94720, USA
| | - Farnaz Shamsi
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nicolas Altemose
- University of California at Berkeley-University of California at San Francisco Graduate Program in Bioengineering, Berkeley, California 94720, USA
| | - Gabriel F Dorlhiac
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California 94720, USA
| | - Aaron M Cypess
- Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Andrew P White
- Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nir Yosef
- Center for Computational Biology, University of California, Berkeley, Berkeley, California 94720, USA
- Department of Electrical Engineering and Computer Sciences, University of California at Berkeley, Berkeley, California 94720, USA
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts 02139, USA
| | | | - Yu-Hua Tseng
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts 02115, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Aaron Streets
- University of California at Berkeley-University of California at San Francisco Graduate Program in Bioengineering, Berkeley, California 94720, USA
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California 94720, USA
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
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11
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Mejhert N, Rydén M. Insights from Studies of White Adipose Tissue Using Single-Cell Approaches. Handb Exp Pharmacol 2022; 274:131-144. [PMID: 35318510 DOI: 10.1007/164_2021_578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Technologies allowing studies at single-cell resolution have provided important insights into how different cell populations contribute to tissue function. Application of these methods to white adipose tissue (WAT) has revealed how various metabolic aspects of this organ, such as insulin response, inflammation and tissue expansion, are regulated by specific WAT resident cells, including different subtypes of adipocytes, adipocyte progenitors as well as immune and endothelial cells. In this chapter, we provide an overview of the different technical approaches, their strengths and weaknesses, and summarize how these studies have improved our understanding of WAT function in health and disease.
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Affiliation(s)
- Niklas Mejhert
- Department of Medicine (H7), Karolinska Institute, Stockholm, Sweden.
| | - Mikael Rydén
- Department of Medicine (H7), Karolinska Institute, Stockholm, Sweden.
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12
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Systematic Profiling of mRNA Splicing Reveals the Prognostic Predictor and Potential Therapeutic Target for Glioblastoma Multiforme. JOURNAL OF ONCOLOGY 2021; 2021:4664955. [PMID: 34326872 PMCID: PMC8277521 DOI: 10.1155/2021/4664955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/17/2021] [Accepted: 06/22/2021] [Indexed: 11/17/2022]
Abstract
Despite many changes in alternative splicing events (ASEs) are frequently involved in various cancers, prognosis-related ASEs and drug treatment targets in glioblastoma multiforme (GBM) have not been well explored. ASEs participate in many biological behaviors in the initiation and progression of tumors, the aberrant ASE has been considered another hallmark of cancer, and the systematic study of alternative splicing may provide potential biomarkers for malignancies. In this study, we carried out a systematic analysis to characterize the ASE signatures in GBM cohort. Through comparing GBM tissues and nontumor tissues, a total of 48,191 differently expressed ASEs from 10,727 genes were obtained, and these aberrant ASEs play an important role in the oncogenic process. Then, we identified 514 ASEs independently associated with patient survival in GBM by univariate and multivariate Cox regression, including exon skip in CD3D, alternate acceptor site in POLD2, and exon skip in DCN. Those prognostic models built on ASEs of each splice type can accurately predict the outcome of GBM patients, and values for the area under curve were 0.97 in the predictive model based on alternate acceptor site. In addition, the splicing-regulatory network revealed an interesting correlation between survival-associated splicing factors and prognostic ASE corresponding genes. Moreover, these three hub splicing factors in splicing regulation network are the potential targets of some drugs. In conclusion, a systematic analysis of ASE signatures in GBM could serve as an indicator for identifying novel prognostic biomarkers and guiding clinical treatment.
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13
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Zhao J, Tao C, Chen C, Wang Y, Liu T. Formation of thermogenic adipocytes: What we have learned from pigs. FUNDAMENTAL RESEARCH 2021. [DOI: 10.1016/j.fmre.2021.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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14
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Sun W, Modica S, Dong H, Wolfrum C. Plasticity and heterogeneity of thermogenic adipose tissue. Nat Metab 2021; 3:751-761. [PMID: 34158657 DOI: 10.1038/s42255-021-00417-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/19/2021] [Indexed: 12/13/2022]
Abstract
The perception of adipose tissue, both in the scientific community and in the general population, has changed dramatically in the past 20 years. While adipose tissue was thought for a long time to be a rather simple lipid storage entity, it is now recognized as a highly heterogeneous organ and a critical regulator of systemic metabolism, composed of many different subtypes of cells, with important endocrine functions. Additionally, adipose tissue is nowadays recognized to contribute to energy turnover, due to the presence of specialized thermogenic adipocytes, which can be found in many adipose depots. This review discusses the unprecedented insights that we have gained into the heterogeneity of thermogenic adipocytes and their respective precursors due to the technical developments in single-cell and nucleus technologies. These methodological advances have increased our understanding of how adipose tissue catabolic function is influenced by developmental and intercellular communication events.
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Affiliation(s)
- Wenfei Sun
- Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland
| | - Salvatore Modica
- Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland
| | - Hua Dong
- Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland
| | - Christian Wolfrum
- Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland.
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15
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Development of alternative splicing signature in lung squamous cell carcinoma. Med Oncol 2021; 38:49. [PMID: 33772655 PMCID: PMC8004499 DOI: 10.1007/s12032-021-01490-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/01/2021] [Indexed: 12/21/2022]
Abstract
Increasing evidence demonstrated that alternative splicing (AS) plays a vital role in tumorigenesis and clinical outcome of patient. However, systematical analysis of AS in lung squamous cell carcinoma (LUSC) is lacking and greatly necessary. Thus, this study was to systematically estimate the function of AS events served as prognostic indicators in LUSC. Among 31,345 mRNA AS events in 9633 genes, we detected 1996 AS in 1409 genes which have significant connection with overall survival (OS) of LUSC patients. Then, prognostic model based on seven types of AS events was established and we further constructed a combined prognostic model. The Kaplan–Meier curve results suggested that seven types of AS signatures and the combined prognostic model could exhibit robust performance in predicting prognosis. Patients in the high-risk group had significantly shorter OS than those in the low-risk group. The ROC showed all prognostic models had high accuracy and powerful predictive performance with different AUC ranging from 0.837 to 0.978. Moreover, the combined prognostic model had highest performance in risk stratification and predictive accuracy than single prognostic models and had higher accuracy than other mRNA model. Finally, a significant correlation network between survival-related AS genes and prognostic splicing factors (SFs) was established. In conclusion, our study provided several potential prognostic AS models and constructed splicing network between AS and SFs in LUSC, which could be used as potential indicators and treatment targets for LUSC patients.
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16
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Abstract
Adipose tissue depots in distinct anatomical locations mediate key aspects of metabolism, including energy storage, nutrient release, and thermogenesis. Although adipocytes make up more than 90% of adipose tissue volume, they represent less than 50% of its cellular content. Here, I review recent advances in genetic lineage tracing and transcriptomics that reveal the identities of the heterogeneous cell populations constituting mouse and human adipose tissues. In addition to mature adipocytes and their progenitors, these include endothelial and various immune cell types that together orchestrate adipose tissue development and functions. One salient finding is the identification of progenitor subtypes that can modulate adipogenic capacity through paracrine mechanisms. Another is the description of fate trajectories of monocyte/macrophages, which can respond maladaptively to nutritional and thermogenic stimuli, leading to metabolic disease. These studies have generated an extraordinary source of publicly available data that can be leveraged to explore commonalities and differences among experimental models, providing new insights into adipose tissues and their role in metabolic disease.
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Affiliation(s)
- Silvia Corvera
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA;
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17
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Zhang B, Li H, Zhu L, He X, Luo H, Huang K, Xu W. Single-cell transcriptomics uncovers potential marker genes of ochratoxin A-sensitive renal cells in an acute toxicity rat model. Cell Biol Toxicol 2021; 37:7-13. [PMID: 32468156 DOI: 10.1007/s10565-020-09531-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/28/2020] [Indexed: 01/10/2023]
Affiliation(s)
- Boyang Zhang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Hongyu Li
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Liye Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
| | - Xiaoyun He
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture and Rural Affairs, Beijing, 100083, China
| | - Haoshu Luo
- Department of Animal Physiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Kunlun Huang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture and Rural Affairs, Beijing, 100083, China
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100083, China.
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), Ministry of Agriculture and Rural Affairs, Beijing, 100083, China.
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18
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Shinde AB, Song A, Wang QA. Brown Adipose Tissue Heterogeneity, Energy Metabolism, and Beyond. Front Endocrinol (Lausanne) 2021; 12:651763. [PMID: 33953697 PMCID: PMC8092391 DOI: 10.3389/fendo.2021.651763] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/18/2021] [Indexed: 01/19/2023] Open
Abstract
Brown adipocyte in brown adipose tissue (BAT) specializes in expending energy through non-shivering thermogenesis, a process that produces heat either by uncoupling protein 1 (UCP1) dependent uncoupling of mitochondrial respiration or by UCP1 independent mechanisms. Apart from this, there is ample evidence suggesting that BAT has an endocrine function. Studies in rodents point toward its vital roles in glucose and lipid homeostasis, making it an important therapeutic target for treating metabolic disorders related to morbidities such as obesity and type 2 diabetes. The rediscovery of thermogenically active BAT depots in humans by several independent research groups in the last decade has revitalized interest in BAT as an even more promising therapeutic intervention. Over the last few years, there has been overwhelming interest in understanding brown adipocyte's developmental lineages and how brown adipocyte uniquely utilizes energy beyond UCP1 mediated uncoupling respiration. These new discoveries would be leveraged for designing novel therapeutic interventions for metabolic disorders.
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Affiliation(s)
- Abhijit Babaji Shinde
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, United States
| | - Anying Song
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, United States
| | - Qiong A. Wang
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, United States
- Comprehensive Cancer Center, Beckman Research Institute, City of Hope Medical Center, Duarte, CA, United States
- *Correspondence: Qiong A. Wang,
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19
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Thermogenic adipocytes: lineage, function and therapeutic potential. Biochem J 2020; 477:2071-2093. [PMID: 32539124 PMCID: PMC7293110 DOI: 10.1042/bcj20200298] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/13/2020] [Accepted: 05/15/2020] [Indexed: 12/12/2022]
Abstract
Metabolic inflexibility, defined as the inability to respond or adapt to metabolic demand, is now recognised as a driving factor behind many pathologies associated with obesity and the metabolic syndrome. Adipose tissue plays a pivotal role in the ability of an organism to sense, adapt to and counteract environmental changes. It provides a buffer in times of nutrient excess, a fuel reserve during starvation and the ability to resist cold-stress through non-shivering thermogenesis. Recent advances in single-cell RNA sequencing combined with lineage tracing, transcriptomic and proteomic analyses have identified novel adipocyte progenitors that give rise to specialised adipocytes with diverse functions, some of which have the potential to be exploited therapeutically. This review will highlight the common and distinct functions of well-known adipocyte populations with respect to their lineage and plasticity, as well as introducing the most recent members of the adipocyte family and their roles in whole organism energy homeostasis. Finally, this article will outline some of the more preliminary findings from large data sets generated by single-cell transcriptomics of mouse and human adipose tissue and their implications for the field, both for discovery and for therapy.
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20
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Kuryłowicz A, Puzianowska-Kuźnicka M. Induction of Adipose Tissue Browning as a Strategy to Combat Obesity. Int J Mol Sci 2020; 21:ijms21176241. [PMID: 32872317 PMCID: PMC7504355 DOI: 10.3390/ijms21176241] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 12/25/2022] Open
Abstract
The ongoing obesity pandemic generates a constant need to develop new therapeutic strategies to restore the energy balance. Therefore, the concept of activating brown adipose tissue (BAT) in order to increase energy expenditure has been revived. In mammals, two developmentally distinct types of brown adipocytes exist; the classical or constitutive BAT that arises during embryogenesis, and the beige adipose tissue that is recruited postnatally within white adipose tissue (WAT) in the process called browning. Research of recent years has significantly increased our understanding of the mechanisms involved in BAT activation and WAT browning. They also allowed for the identification of critical molecules and critical steps of both processes and, therefore, many new therapeutic targets. Several non-pharmacological approaches, as well as chemical compounds aiming at the induction of WAT browning and BAT activation, have been tested in vitro as well as in animal models of genetically determined and/or diet-induced obesity. The therapeutic potential of some of these strategies has also been tested in humans. In this review, we summarize present concepts regarding potential therapeutic targets in the process of BAT activation and WAT browning and available strategies aiming at them.
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Affiliation(s)
- Alina Kuryłowicz
- Department of Human Epigenetics, Mossakowski Medical Research Centre PAS, 02-106 Warsaw, Poland;
- Correspondence: ; Tel.: +48-226086591; Fax: +48-226086410
| | - Monika Puzianowska-Kuźnicka
- Department of Human Epigenetics, Mossakowski Medical Research Centre PAS, 02-106 Warsaw, Poland;
- Department of Geriatrics and Gerontology, Medical Centre of Postgraduate Education, 01-826 Warsaw, Poland
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21
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The Impact of Single-Cell Genomics on Adipose Tissue Research. Int J Mol Sci 2020; 21:ijms21134773. [PMID: 32635651 PMCID: PMC7369959 DOI: 10.3390/ijms21134773] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/30/2020] [Accepted: 07/03/2020] [Indexed: 01/05/2023] Open
Abstract
Adipose tissue is an important regulator of whole-body metabolism and energy homeostasis. The unprecedented growth of obesity and metabolic disease worldwide has required paralleled advancements in research on this dynamic endocrine organ system. Single-cell RNA sequencing (scRNA-seq), a highly meticulous methodology used to dissect tissue heterogeneity through the transcriptional characterization of individual cells, is responsible for facilitating critical advancements in this area. The unique investigative capabilities achieved by the combination of nanotechnology, molecular biology, and informatics are expanding our understanding of adipose tissue's composition and compartmentalized functional specialization, which underlie physiologic and pathogenic states, including adaptive thermogenesis, adipose tissue aging, and obesity. In this review, we will summarize the use of scRNA-seq and single-nuclei RNA-seq (snRNA-seq) in adipocyte biology and their applications to obesity and diabetes research in the hopes of increasing awareness of the capabilities of this technology and acting as a catalyst for its expanded use in further investigation.
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22
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Song A, Dai W, Jang MJ, Medrano L, Li Z, Zhao H, Shao M, Tan J, Li A, Ning T, Miller MM, Armstrong B, Huss JM, Zhu Y, Liu Y, Gradinaru V, Wu X, Jiang L, Scherer PE, Wang QA. Low- and high-thermogenic brown adipocyte subpopulations coexist in murine adipose tissue. J Clin Invest 2020; 130:247-257. [PMID: 31573981 PMCID: PMC6934193 DOI: 10.1172/jci129167] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 09/25/2019] [Indexed: 12/29/2022] Open
Abstract
Brown adipose tissue (BAT), as the main site of adaptive thermogenesis, exerts beneficial metabolic effects on obesity and insulin resistance. BAT has been previously assumed to contain a homogeneous population of brown adipocytes. Utilizing multiple mouse models capable of genetically labeling different cellular populations, as well as single-cell RNA sequencing and 3D tissue profiling, we discovered a brown adipocyte subpopulation with low thermogenic activity coexisting with the classical high-thermogenic brown adipocytes within the BAT. Compared with the high-thermogenic brown adipocytes, these low-thermogenic brown adipocytes had substantially lower Ucp1 and Adipoq expression, larger lipid droplets, and lower mitochondrial content. Functional analyses showed that, unlike the high-thermogenic brown adipocytes, the low-thermogenic brown adipocytes have markedly lower basal mitochondrial respiration, and they are specialized in fatty acid uptake. Upon changes in environmental temperature, the 2 brown adipocyte subpopulations underwent dynamic interconversions. Cold exposure converted low-thermogenic brown adipocytes into high-thermogenic cells. A thermoneutral environment had the opposite effect. The recruitment of high-thermogenic brown adipocytes by cold stimulation is not affected by high-fat diet feeding, but it does substantially decline with age. Our results revealed a high degree of functional heterogeneity of brown adipocytes.
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Affiliation(s)
- Anying Song
- Department of Molecular & Cellular Endocrinology, Diabetes & Metabolism Research Institute, City of Hope Medical Center, Duarte, California, USA
| | - Wenting Dai
- Department of Molecular & Cellular Endocrinology, Diabetes & Metabolism Research Institute, City of Hope Medical Center, Duarte, California, USA
| | - Min Jee Jang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Leonard Medrano
- Department of Translational Research & Cellular Therapeutics, Diabetes & Metabolism Research Institute, and
| | - Zhuo Li
- Electron Microscopy and Atomic Force Microscopy Core, Beckman Research Institute, City of Hope Medical Center, Duarte, California, USA
| | - Hu Zhao
- Department of Restorative Sciences, School of Dentistry, Texas A&M University, Dallas, Texas, USA
| | - Mengle Shao
- Touchstone Diabetes Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jiayi Tan
- Department of Molecular & Cellular Endocrinology, Diabetes & Metabolism Research Institute, City of Hope Medical Center, Duarte, California, USA
| | - Aimin Li
- Pathology Core of Shared Resources and
| | - Tinglu Ning
- Department of Molecular & Cellular Endocrinology, Diabetes & Metabolism Research Institute, City of Hope Medical Center, Duarte, California, USA
| | - Marcia M. Miller
- Electron Microscopy and Atomic Force Microscopy Core, Beckman Research Institute, City of Hope Medical Center, Duarte, California, USA
| | - Brian Armstrong
- Light Microscopy Digital Imaging Core, Beckman Research Institute, City of Hope Medical Center, Duarte, California, USA
| | - Janice M. Huss
- Department of Molecular & Cellular Endocrinology, Diabetes & Metabolism Research Institute, City of Hope Medical Center, Duarte, California, USA
| | - Yi Zhu
- Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Yong Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | | | - Lei Jiang
- Department of Molecular & Cellular Endocrinology, Diabetes & Metabolism Research Institute, City of Hope Medical Center, Duarte, California, USA
- Comprehensive Cancer Center, Beckman Research Institute, City of Hope Medical Center, Duarte, California, USA
| | - Philipp E. Scherer
- Touchstone Diabetes Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Qiong A. Wang
- Department of Molecular & Cellular Endocrinology, Diabetes & Metabolism Research Institute, City of Hope Medical Center, Duarte, California, USA
- Comprehensive Cancer Center, Beckman Research Institute, City of Hope Medical Center, Duarte, California, USA
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23
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Yang L, He Y, Zhang Z, Wang W. Systematic analysis and prediction model construction of alternative splicing events in hepatocellular carcinoma: a study on the basis of large-scale spliceseq data from The Cancer Genome Atlas. PeerJ 2019; 7:e8245. [PMID: 31844595 PMCID: PMC6907093 DOI: 10.7717/peerj.8245] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/19/2019] [Indexed: 02/05/2023] Open
Abstract
Growing evidence showed that alternative splicing (AS) event is significantly related to tumor occurrence and progress. This study was performed to make a systematic analysis of AS events and constructed a robust prediction model of hepatocellular carcinoma (HCC). The clinical information and the genes expression profile data of 335 HCC patients were collected from The Cancer Genome Atlas (TCGA). Information of seven types AS events were collected from the TCGA SpliceSeq database. Overall survival (OS) related AS events and splicing factors (SFs) were identified using univariate Cox regression analysis. The corresponding genes of OS-related AS events were sent for gene network analysis and functional enrichment analysis. Optimal OS-related AS events were selected by LASSO regression to construct prediction model using multivariate Cox regression analysis. Prognostic value of the prediction models were assessed by receiver operating characteristic (ROC) curve and KaplanMeir survival analysis. The relationship between the Percent Spliced In (PSI) value of OS-related AS events and SFs expression were analyzed using Spearman correlation analysis. And the regulation network was generated by Cytoscape. A total of 34,163 AS events were identified, which consist of 3,482 OS-related AS events. UBB, UBE2D3, SF3A1 were the hub genes in the gene network of the top 800 OS-related AS events. The area under the curve (AUC) of the final prediction model based on seven types OS-related AS events was 0.878, 0.843, 0.821 in 1, 3, 5 years, respectively. Upon multivariate analysis, risk score (All) served as the risk factor to independently predict OS for HCC patients. SFs HNRNPH3 and HNRNPL were overexpressed in tumor samples and were signifcantly associated with the OS of HCC patients. The regulation network showed prominent correlation between the expression of SFs and OS-related AS events in HCC patients. The final prediction model performs well in predicting the prognosis of HCC patients. And the findings in this study improve our understanding of the association between AS events and HCC.
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Affiliation(s)
- Lingpeng Yang
- Department of Liver Surgery & Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Yang He
- Department of Liver Surgery & Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Zifei Zhang
- Department of Liver Surgery & Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Wentao Wang
- Department of Liver Surgery & Liver Transplantation Center, West China Hospital of Sichuan University, Chengdu, Sichuan, China
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24
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Al Hasan M, Roy P, Dolan S, Martin PE, Patterson S, Bartholomew C. Adhesion G-protein coupled receptor 56 is required for 3T3-L1 adipogenesis. J Cell Physiol 2019; 235:1601-1614. [PMID: 31304602 DOI: 10.1002/jcp.29079] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/14/2019] [Indexed: 12/13/2022]
Abstract
Obesity-associated conditions represent major global health and financial burdens and understanding processes regulating adipogenesis could lead to novel intervention strategies. This study shows that adhesion G-protein coupled receptor 56 (GPR56) gene transcripts are reduced in abdominal visceral white adipose tissue derived from obese Zucker rats versus lean controls. Immunostaining in 3T3-L1 preadipocytes reveals both mitotic cell restricted surface and low level general expression patterns of Gpr56. Gpr56 transcripts are differentially expressed in 3T3-L1 cells during adipogenesis. Transient knockdown (KD) of Gpr56 in 3T3-L1 cells dramatically inhibits differentiation through reducing the accumulation of both neutral cellular lipids (56%) and production of established adipogenesis Pparγ 2 (60-80%), C/ebpα (40-78%) mediator, and Ap2 (56-80%) marker proteins. Furthermore, genome editing of Gpr56 in 3T3-L1 cells created CW2.2.4 and RM4.2.5.5 clones (Gpr56 -/- cells) with compound heterozygous deletion frameshift mutations which abolish adipogenesis. Genome edited cells have sustained levels of the adipogenesis inhibitor β-catenin, reduced proliferation, reduced adhesion, altered profiles, and or abundance of extracellular matrix component gene transcripts for fibronectin, types I, III, and IV collagens and loss of actin stress fibers. β-catenin KD alone is insufficient to restore adipogenesis in Gpr56 -/- cells. Together these data show that Gpr56 is required for adipogenesis in 3T3-L1 cells. This report is the first demonstration that Gpr56 participates in regulation of the adipogenesis developmental program. Modulation of the levels of this protein and/or its biological activity may represent a novel target for development of therapeutic agents for the treatment of obesity.
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Affiliation(s)
- Mohammad Al Hasan
- Department of Biological & Biomedical Sciences, School of Health & Life Sciences, Glasgow Caledonian University, Glasgow, Scotland
| | - Poornima Roy
- Department of Biological & Biomedical Sciences, School of Health & Life Sciences, Glasgow Caledonian University, Glasgow, Scotland
| | - Sharron Dolan
- Department of Biological & Biomedical Sciences, School of Health & Life Sciences, Glasgow Caledonian University, Glasgow, Scotland
| | - Patricia E Martin
- Department of Biological & Biomedical Sciences, School of Health & Life Sciences, Glasgow Caledonian University, Glasgow, Scotland
| | - Steven Patterson
- Department of Biological & Biomedical Sciences, School of Health & Life Sciences, Glasgow Caledonian University, Glasgow, Scotland
| | - Chris Bartholomew
- Department of Biological & Biomedical Sciences, School of Health & Life Sciences, Glasgow Caledonian University, Glasgow, Scotland
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25
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Insel PA, Sriram K, Gorr MW, Wiley SZ, Michkov A, Salmerón C, Chinn AM. GPCRomics: An Approach to Discover GPCR Drug Targets. Trends Pharmacol Sci 2019; 40:378-387. [PMID: 31078319 PMCID: PMC6604616 DOI: 10.1016/j.tips.2019.04.001] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/17/2019] [Accepted: 04/03/2019] [Indexed: 01/14/2023]
Abstract
G protein-coupled receptors (GPCRs) are targets for ∼35% of approved drugs but only ∼15% of the ∼800 human GPCRs are currently such targets. GPCRomics, the use of unbiased, hypothesis-generating methods [e.g., RNA-sequencing (RNA-seq)], with tissues and cell types to identify and quantify GPCR expression, has led to the discovery of previously unrecognized GPCRs that contribute to functional responses and pathophysiology and that may be therapeutic targets. The combination of GPCR expression data with validation studies (e.g., signaling and functional activities) provides opportunities for the discovery of disease-relevant GPCR targets and therapeutics. Here, we review insights from GPCRomic approaches, gaps in knowledge, and future directions by which GPCRomics can advance GPCR biology and the discovery of new GPCR-targeted drugs.
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Affiliation(s)
- Paul A Insel
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Krishna Sriram
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Matthew W Gorr
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Shu Z Wiley
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexander Michkov
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Cristina Salmerón
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Amy M Chinn
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
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26
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Evans BA, Merlin J, Bengtsson T, Hutchinson DS. Adrenoceptors in white, brown, and brite adipocytes. Br J Pharmacol 2019; 176:2416-2432. [PMID: 30801689 DOI: 10.1111/bph.14631] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 01/28/2019] [Accepted: 02/11/2019] [Indexed: 01/01/2023] Open
Abstract
Adrenoceptors play an important role in adipose tissue biology and physiology that includes regulating the synthesis and storage of triglycerides (lipogenesis), the breakdown of stored triglycerides (lipolysis), thermogenesis (heat production), glucose metabolism, and the secretion of adipocyte-derived hormones that can control whole-body energy homeostasis. These processes are regulated by the sympathetic nervous system through actions at different adrenoceptor subtypes expressed in adipose tissue depots. In this review, we have highlighted the role of adrenoceptor subtypes in white, brown, and brite adipocytes in both rodents and humans and have included detailed analysis of adrenoceptor expression in human adipose tissue and clonally derived adipocytes. We discuss important considerations when investigating adrenoceptor function in adipose tissue or adipocytes. LINKED ARTICLES: This article is part of a themed section on Adrenoceptors-New Roles for Old Players. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v176.14/issuetoc.
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Affiliation(s)
- Bronwyn A Evans
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Jon Merlin
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Tore Bengtsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Laboratories F3, Stockholm University, Stockholm, Sweden
| | - Dana S Hutchinson
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
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27
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Song Y, Xu X, Wang W, Tian T, Zhu Z, Yang C. Single cell transcriptomics: moving towards multi-omics. Analyst 2019; 144:3172-3189. [DOI: 10.1039/c8an01852a] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Single-cell multi-omics analysis helps characterize multiple layers of molecular features at a single-cell scale to provide insights into cellular processes and functions.
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Affiliation(s)
- Yanling Song
- Institute of Molecular Medicine
- Renji Hospital
- Shanghai Jiao Tong University
- School of Medicine
- Shanghai
| | - Xing Xu
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Key Laboratory for Chemical Biology of Fujian Province
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation
- Department of Chemical Biology
- College of Chemistry and Chemical Engineering
| | - Wei Wang
- Institute of Molecular Medicine
- Renji Hospital
- Shanghai Jiao Tong University
- School of Medicine
- Shanghai
| | - Tian Tian
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Key Laboratory for Chemical Biology of Fujian Province
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation
- Department of Chemical Biology
- College of Chemistry and Chemical Engineering
| | - Zhi Zhu
- State Key Laboratory of Physical Chemistry of Solid Surfaces
- Key Laboratory for Chemical Biology of Fujian Province
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation
- Department of Chemical Biology
- College of Chemistry and Chemical Engineering
| | - Chaoyong Yang
- Institute of Molecular Medicine
- Renji Hospital
- Shanghai Jiao Tong University
- School of Medicine
- Shanghai
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28
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Cook D, Achanta S, Hoek JB, Ogunnaike BA, Vadigepalli R. Cellular network modeling and single cell gene expression analysis reveals novel hepatic stellate cell phenotypes controlling liver regeneration dynamics. BMC SYSTEMS BIOLOGY 2018; 12:86. [PMID: 30285726 PMCID: PMC6171157 DOI: 10.1186/s12918-018-0605-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 08/21/2018] [Indexed: 12/26/2022]
Abstract
Background Recent results from single cell gene and protein regulation studies are starting to uncover the previously underappreciated fact that individual cells within a population exhibit high variability in the expression of mRNA and proteins (i.e., molecular variability). By combining cellular network modeling, and high-throughput gene expression measurements in single cells, we seek to reconcile the high molecular variability in single cells with the relatively low variability in tissue-scale gene and protein expression and the highly coordinated functional responses of tissues to physiological challenges. In this study, we focus on relating the dynamic changes in distributions of hepatic stellate cell (HSC) functional phenotypes to the tightly regulated physiological response of liver regeneration. Results We develop a mathematical model describing contributions of HSC functional phenotype populations to liver regeneration and test model predictions through isolation and transcriptional characterization of single HSCs. We identify and characterize four HSC transcriptional states contributing to liver regeneration, two of which are described for the first time in this work. We show that HSC state populations change in vivo in response to acute challenges (in this case, 70% partial hepatectomy) and chronic challenges (chronic ethanol consumption). Our results indicate that HSCs influence the dynamics of liver regeneration through steady-state tissue preconditioning prior to an acute insult and through dynamic control of cell state balances. Furthermore, our modeling approach provides a framework to understand how balances among cell states influence tissue dynamics. Conclusions Taken together, our combined modeling and experimental studies reveal novel HSC transcriptional states and indicate that baseline differences in HSC phenotypes as well as a dynamic balance of transitions between these phenotypes control liver regeneration responses. Electronic supplementary material The online version of this article (10.1186/s12918-018-0605-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel Cook
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.,Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Sirisha Achanta
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jan B Hoek
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Babatunde A Ogunnaike
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | - Rajanikanth Vadigepalli
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA. .,Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA.
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29
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Ji Q, Zheng Y, Zhang G, Hu Y, Fan X, Hou Y, Wen L, Li L, Xu Y, Wang Y, Tang F. Single-cell RNA-seq analysis reveals the progression of human osteoarthritis. Ann Rheum Dis 2018; 78:100-110. [PMID: 30026257 PMCID: PMC6317448 DOI: 10.1136/annrheumdis-2017-212863] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 05/21/2018] [Accepted: 05/28/2018] [Indexed: 12/19/2022]
Abstract
Objectives Understanding the molecular mechanisms underlying human cartilage degeneration and regeneration is helpful for improving therapeutic strategies for treating osteoarthritis (OA). Here, we report the molecular programmes and lineage progression patterns controlling human OA pathogenesis using single-cell RNA sequencing (scRNA-seq). Methods We performed unbiased transcriptome-wide scRNA-seq analysis, computational analysis and histological assays on 1464 chondrocytes from 10 patients with OA undergoing knee arthroplasty surgery. We investigated the relationship between transcriptional programmes of the OA landscape and clinical outcome using severity index and correspondence analysis. Results We identified seven molecularly defined populations of chondrocytes in the human OA cartilage, including three novel phenotypes with distinct functions. We presented gene expression profiles at different OA stages at single-cell resolution. We found a potential transition among proliferative chondrocytes, prehypertrophic chondrocytes and hypertrophic chondrocytes (HTCs) and defined a new subdivision within HTCs. We revealed novel markers for cartilage progenitor cells (CPCs) and demonstrated a relationship between CPCs and fibrocartilage chondrocytes using computational analysis. Notably, we derived predictive targets with respect to clinical outcomes and clarified the role of different cell types for the early diagnosis and treatment of OA. Conclusions Our results provide new insights into chondrocyte taxonomy and present potential clues for effective and functional manipulation of human OA cartilage regeneration that could lead to improved health.
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Affiliation(s)
- Quanbo Ji
- Department of Orthopaedics, General Hospital of Chinese People's Liberation Army, Beijing, China.,Biomedical Institute for Pioneering Investigation via Convergence and Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Yuxuan Zheng
- Biomedical Institute for Pioneering Investigation via Convergence and Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China.,Beijing Advanced Innovation Center for Genomics (ICG), College of Life Science, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Guoqiang Zhang
- Department of Orthopaedics, General Hospital of Chinese People's Liberation Army, Beijing, China
| | - Yuqiong Hu
- Biomedical Institute for Pioneering Investigation via Convergence and Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China.,Beijing Advanced Innovation Center for Genomics (ICG), College of Life Science, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xiaoying Fan
- Biomedical Institute for Pioneering Investigation via Convergence and Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China.,Beijing Advanced Innovation Center for Genomics (ICG), College of Life Science, Peking University, Beijing, China
| | - Yu Hou
- Biomedical Institute for Pioneering Investigation via Convergence and Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China.,Beijing Advanced Innovation Center for Genomics (ICG), College of Life Science, Peking University, Beijing, China
| | - Lu Wen
- Biomedical Institute for Pioneering Investigation via Convergence and Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China.,Beijing Advanced Innovation Center for Genomics (ICG), College of Life Science, Peking University, Beijing, China
| | - Li Li
- Biomedical Institute for Pioneering Investigation via Convergence and Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China.,Beijing Advanced Innovation Center for Genomics (ICG), College of Life Science, Peking University, Beijing, China
| | - Yameng Xu
- Department of Traditional Chinese Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Wang
- Department of Orthopaedics, General Hospital of Chinese People's Liberation Army, Beijing, China
| | - Fuchou Tang
- Biomedical Institute for Pioneering Investigation via Convergence and Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China.,Beijing Advanced Innovation Center for Genomics (ICG), College of Life Science, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
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30
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Application of Multiplex Biomarker Approaches to Accelerate Drug Discovery and Development. Methods Mol Biol 2018; 1546:3-17. [PMID: 27896754 DOI: 10.1007/978-1-4939-6730-8_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Multiplex biomarker tests are becoming an essential part of the drug development process. This chapter explores the role of biomarker-based tests as effective tools in improving preclinical research and clinical development, and the challenges that this presents. The potential of incorporating biomarkers in the clinical pipeline to improve decision making, accelerate drug development, improve translation, and reduce development costs is discussed. This chapter also discusses the latest biomarker technologies in use to make this possible and details the next steps that must undertaken to keep driving this process forwards.
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31
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Cook DJ, Nielsen J. Genome-scale metabolic models applied to human health and disease. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017. [DOI: 10.1002/wsbm.1393] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Daniel J Cook
- Department of Biology and Biological Engineering; Chalmers University of Technology; Gothenburg Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering; Chalmers University of Technology; Gothenburg Sweden
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32
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Single-Cell RNA-Seq Analysis Maps Development of Human Germline Cells and Gonadal Niche Interactions. Cell Stem Cell 2017; 20:858-873.e4. [DOI: 10.1016/j.stem.2017.03.007] [Citation(s) in RCA: 237] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/30/2016] [Accepted: 03/15/2017] [Indexed: 11/15/2022]
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33
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Li Y, Sun N, Lu Z, Sun S, Huang J, Chen Z, He J. Prognostic alternative mRNA splicing signature in non-small cell lung cancer. Cancer Lett 2017; 393:40-51. [PMID: 28223168 DOI: 10.1016/j.canlet.2017.02.016] [Citation(s) in RCA: 144] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/04/2017] [Accepted: 02/12/2017] [Indexed: 12/20/2022]
Abstract
Alternative splicing provides a major mechanism to generate protein diversity. Increasing evidence suggests a link of dysregulation of splicing associated with cancer. Genome-wide alternative splicing profiling in lung cancer remains largely unstudied. We generated alternative splicing profiles in 491 lung adenocarcinoma (LUAD) and 471 lung squamous cell carcinoma (LUSC) patients in TCGA using RNA-seq data, prognostic models and splicing networks were built by integrated bioinformatics analysis. A total of 3691 and 2403 alternative splicing events were significantly associated with patient survival in LUAD and LUSC, respectively, including EGFR, CD44, PIK3C3, RRAS2, MAPKAP1 and FGFR2. The area under the curve of the receiver-operator characteristic curve for prognostic predictor in NSCLC was 0.817 at 2000 days of overall survival which were also over 0.8 in LUAD and LUSC, separately. Interestingly, splicing correlation networks uncovered opposite roles of splicing factors in LUAD and LUSC. We created prognostic predictors based on alternative splicing events with high performances for risk stratification in NSCLC patients and uncovered interesting splicing networks in LUAD and LUSC which could be underlying mechanisms.
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MESH Headings
- Adenocarcinoma/genetics
- Adenocarcinoma/metabolism
- Adenocarcinoma/mortality
- Adenocarcinoma/pathology
- Adenocarcinoma of Lung
- Alternative Splicing
- Area Under Curve
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- Carcinoma, Non-Small-Cell Lung/mortality
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/mortality
- Carcinoma, Squamous Cell/pathology
- Computational Biology
- Databases, Genetic
- Gene Expression Profiling/methods
- Gene Expression Regulation, Neoplastic
- Gene Regulatory Networks
- Genome-Wide Association Study
- Humans
- Kaplan-Meier Estimate
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/mortality
- Lung Neoplasms/pathology
- Prognosis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- ROC Curve
- Signal Transduction
- Time Factors
- Transcriptome
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Affiliation(s)
- Yuan Li
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Nan Sun
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Zhiliang Lu
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Shouguo Sun
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jianbing Huang
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zhaoli Chen
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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34
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Loft A, Forss I, Mandrup S. Genome-Wide Insights into the Development and Function of Thermogenic Adipocytes. Trends Endocrinol Metab 2017; 28:104-120. [PMID: 27979331 DOI: 10.1016/j.tem.2016.11.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 11/01/2016] [Accepted: 11/07/2016] [Indexed: 12/31/2022]
Abstract
Brown and brown-like adipocytes are specialized adipocytes with a high capacity to convert metabolic energy to heat. This function is not only eminent in supporting organismal thermogenesis, but may also have potential in the fight against obesity. The latter has spurred a massive interest in understanding the development and regulation of these thermogenic adipocytes. Here, we review how genome-wide studies based on next-generation sequencing have provided insight into how the chromatin and transcriptional landscapes are established in thermogenic adipocytes and how thermogenic signals can change the genomic programming of white adipocytes. Furthermore, we discuss how the integration of genomic data can be used to discover novel transcriptional pathways that may be modulated as part of therapeutic strategies for the treatment of obesity.
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Affiliation(s)
- Anne Loft
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark; Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich, 85764 Neuherberg, Germany; Joint Heidelberg-IDC Translational Diabetes Program, Inner Medicine 1, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Isabel Forss
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.
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35
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Abstract
Single-cell RNA-sequencing methods are now robust and economically practical and are becoming a powerful tool for high-throughput, high-resolution transcriptomic analysis of cell states and dynamics. Single-cell approaches circumvent the averaging artifacts associated with traditional bulk population data, yielding new insights into the cellular diversity underlying superficially homogeneous populations. Thus far, single-cell RNA-sequencing has already shown great effectiveness in unraveling complex cell populations, reconstructing developmental trajectories, and modeling transcriptional dynamics. Ongoing technical improvements to single-cell RNA-sequencing throughput and sensitivity, the development of more sophisticated analytical frameworks for single-cell data, and an increasing array of complementary single-cell assays all promise to expand the usefulness and potential applications of single-cell transcriptomic profiling.
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Affiliation(s)
- Serena Liu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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36
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Khaladkar M, Buckley PT, Lee MT, Francis C, Eghbal MM, Chuong T, Suresh S, Kuhn B, Eberwine J, Kim J. Subcellular RNA sequencing reveals broad presence of cytoplasmic intron-sequence retaining transcripts in mouse and rat neurons. PLoS One 2013; 8:e76194. [PMID: 24098440 PMCID: PMC3789819 DOI: 10.1371/journal.pone.0076194] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/20/2013] [Indexed: 12/03/2022] Open
Abstract
Recent findings have revealed the complexity of the transcriptional landscape in mammalian cells. One recently described class of novel transcripts are the Cytoplasmic Intron-sequence Retaining Transcripts (CIRTs), hypothesized to confer post-transcriptional regulatory function. For instance, the neuronal CIRT KCNMA1i16 contributes to the firing properties of hippocampal neurons. Intronic sub-sequence retention within IL1-β mRNA in anucleate platelets has been implicated in activity-dependent splicing and translation. In a recent study, we showed CIRTs harbor functional SINE ID elements which are hypothesized to mediate dendritic localization in neurons. Based on these studies and others, we hypothesized that CIRTs may be present in a broad set of transcripts and comprise novel signals for post-transcriptional regulation. We carried out a transcriptome-wide survey of CIRTs by sequencing micro-dissected subcellular RNA fractions. We sequenced two batches of 150-300 individually dissected dendrites from primary cultures of hippocampal neurons in rat and three batches from mouse hippocampal neurons. After statistical processing to minimize artifacts, we found a broad prevalence of CIRTs in the neurons in both species (44-60% of the expressed transcripts). The sequence patterns, including stereotypical length, biased inclusion of specific introns, and intron-intron junctions, suggested CIRT-specific nuclear processing. Our analysis also suggested that these cytoplasmic intron-sequence retaining transcripts may serve as a primary transcript for ncRNAs. Our results show that retaining intronic sequences is not isolated to a few loci but may be a genome-wide phenomenon for embedding functional signals within certain mRNA. The results hypothesize a novel source of cis-sequences for post-transcriptional regulation. Our results hypothesize two potentially novel splicing pathways: one, within the nucleus for CIRT biogenesis; and another, within the cytoplasm for removing CIRT sequences before translation. We also speculate that release of CIRT sequences prior to translation may form RNA-based signals within the cell potentially comprising a novel class of signaling pathways.
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Affiliation(s)
- Mugdha Khaladkar
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Peter T. Buckley
- Penn Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Pharmacology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Miler T. Lee
- Department of Genetics, Yale University, New Haven, Connecticut, United States of America
| | - Chantal Francis
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mitra M. Eghbal
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Tina Chuong
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sangita Suresh
- Department of Pediatrics, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Bernhard Kuhn
- Department of Pediatrics, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - James Eberwine
- Penn Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Pharmacology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Genomics and Computational Biology Program, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Penn Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Genomics and Computational Biology Program, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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