A long-non-coding RNA, LINC00473, confers the human adipose tissue thermogenic phenotype through enhanced cAMP responsiveness

Specialized adipocytes localized in distinct depots mediate the many physiological functions of adipose tissue. In humans, paucity of thermogenic adipocytes correlates with high metabolic disease risk, raising much interest in the mechanisms by which these cells arise. Here we report molecular signatures associated with adipocyte development in different human depots and identify a long non-coding RNA, LINC00473, as the transcript most closely associated with enrichment of thermogenic adipocytes. LINC00473 expression is low in subjects with obesity or type-2 diabetes and is highly correlated with cAMP signaling and mitochondrial oxidative phosphorylation pathways. LINC00473 is localized in the nucleus and the cytoplasm, and its knockdown impairs induction of UCP1 and mitochondrial respiration. These results reveal that depot-enriched genes that modulate responsiveness to external stimuli, specifically LINC00473, are important determinants of the adipose tissue thermogenic phenotype, and potential targets for metabolic disease therapy.

[1]  S. Kuang,et al.  A novel brown adipocyte-enriched long non-coding RNA that is required for brown adipocyte differentiation and sufficient to drive thermogenic gene program in white adipocytes. , 2018, Biochimica et biophysica acta. Molecular and cell biology of lipids.

[2]  Yaqun Guan,et al.  Effect of lncRNA HOXA11-AS1 on adipocyte differentiation in human adipose-derived stem cells. , 2018, Biochemical and biophysical research communications.

[3]  Weihua Liu,et al.  LncRNA Gm15290 sponges miR-27b to promote PPARγ-induced fat deposition and contribute to body weight gain in mice. , 2017, Biochemical and biophysical research communications.

[4]  Kinyui A. Lo,et al.  Dynamic transcriptome changes during adipose tissue energy expenditure reveal critical roles for long noncoding RNA regulators , 2017, PLoS biology.

[5]  Daniel R. Caffrey,et al.  Immunobiology of Long Noncoding RNAs. , 2017, Annual review of immunology.

[6]  C. Schéele,et al.  Metabolic regulation and the anti-obesity perspectives of human brown fat , 2017, Redox biology.

[7]  Allison J. Richard,et al.  Transcriptional Regulation of Adipogenesis. , 2017, Comprehensive Physiology.

[8]  P. Scherer,et al.  The ominous triad of adipose tissue dysfunction: inflammation, fibrosis, and impaired angiogenesis. , 2017, The Journal of clinical investigation.

[9]  H. Bading,et al.  Networks of Cultured iPSC-Derived Neurons Reveal the Human Synaptic Activity-Regulated Adaptive Gene Program , 2017, Cell reports.

[10]  Ryan Berry,et al.  The Adipose Tissue Microenvironment Regulates Depot-Specific Adipogenesis in Obesity. , 2016, Cell metabolism.

[11]  Hong Chen,et al.  Long non-coding RNA ADNCR suppresses adipogenic differentiation by targeting miR-204. , 2016, Biochimica et biophysica acta.

[12]  F. Kaye,et al.  cAMP/CREB-regulated LINC00473 marks LKB1-inactivated lung cancer and mediates tumor growth. , 2016, The Journal of clinical investigation.

[13]  D. Guertin,et al.  Emerging Complexities in Adipocyte Origins and Identity. , 2016, Trends in cell biology.

[14]  Ji-Long Liu,et al.  Non-coding RNA LINC00473 mediates decidualization of human endometrial stromal cells in response to cAMP signaling , 2016, Scientific Reports.

[15]  Jong Hun Kim,et al.  Human ‘brite / beige’ adipocytes develop from capillary networks and their implantation improves metabolic homeostasis in mice , 2015, Nature Medicine.

[16]  Lihui Liu,et al.  Long Noncoding RNA ADINR Regulates Adipogenesis by Transcriptionally Activating C/EBPα , 2015, Stem cell reports.

[17]  D. Bartel,et al.  Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species. , 2015, Cell reports.

[18]  Yen Ching Lim,et al.  De Novo Reconstruction of Adipose Tissue Transcriptomes Reveals Long Non-coding RNA Regulators of Brown Adipocyte Development. , 2015, Cell metabolism.

[19]  J. D. Mills,et al.  Conservation and tissue-specific transcription patterns of long noncoding RNAs , 2015, Journal of human transcriptome.

[20]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[21]  Jiandie D. Lin,et al.  A long noncoding RNA transcriptional regulatory circuit drives thermogenic adipocyte differentiation. , 2014, Molecular cell.

[22]  P. Seale,et al.  Brown and beige fat: development, function and therapeutic potential , 2013, Nature Medicine.

[23]  B. Pedersen,et al.  A classical brown adipose tissue mRNA signature partly overlaps with brite in the supraclavicular region of adult humans. , 2013, Cell metabolism.

[24]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[25]  M. Mori,et al.  Anatomical Localization, Gene Expression Profiling, and Functional Characterization of Adult Human Neck Brown Fat , 2013, Nature Medicine.

[26]  Ryan Berry,et al.  Characterization of the adipocyte cellular lineage in vivo , 2013, Nature Cell Biology.

[27]  David R. Kelley,et al.  Long noncoding RNAs regulate adipogenesis , 2013, Proceedings of the National Academy of Sciences.

[28]  Sven Diederichs,et al.  The hallmarks of cancer , 2012, RNA biology.

[29]  A. Sbarbati,et al.  The vascular endothelium of the adipose tissue gives rise to both white and brown fat cells. , 2012, Cell metabolism.

[30]  Brad A Chapman,et al.  The genomic binding sites of a noncoding RNA , 2011, Proceedings of the National Academy of Sciences.

[31]  Cole Trapnell,et al.  Improving RNA-Seq expression estimates by correcting for fragment bias , 2011, Genome Biology.

[32]  Robert A. Edwards,et al.  Quality control and preprocessing of metagenomic datasets , 2011, Bioinform..

[33]  G. Muscat,et al.  Minireview: Nuclear hormone receptor 4A signaling: implications for metabolic disease. , 2010, Molecular endocrinology.

[34]  Howard Y. Chang,et al.  Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes , 2010, Science.

[35]  J. Rinn,et al.  A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response , 2010, Cell.

[36]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[37]  B. Cannon,et al.  The changed metabolic world with human brown adipose tissue: therapeutic visions. , 2010, Cell metabolism.

[38]  Howard Y. Chang,et al.  Long noncoding RNA HOTAIR reprograms chromatin state to promote cancer metastasis , 2010, Nature.

[39]  J. Orava,et al.  Functional brown adipose tissue in healthy adults. , 2009, The New England journal of medicine.

[40]  G. Muscat,et al.  β-Adrenergic signaling regulates NR4A nuclear receptor and metabolic gene expression in multiple tissues , 2009, Molecular and Cellular Endocrinology.

[41]  M. Miyagawa,et al.  High Incidence of Metabolically Active Brown Adipose Tissue in Healthy Adult Humans , 2009, Diabetes.

[42]  J. Mattick,et al.  Long non-coding RNAs: insights into functions , 2009, Nature Reviews Genetics.

[43]  T. Morgan,et al.  Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of β-secretase , 2008, Nature Medicine.

[44]  C. Glass,et al.  Induced ncRNAs Allosterically Modify RNA Binding Proteins in cis to Inhibit Transcription , 2008, Nature.

[45]  Naresh Kumar,et al.  Orphan nuclear receptor NOR-1 enhances 3',5'-cyclic adenosine 5'-monophosphate-dependent uncoupling protein-1 gene transcription. , 2008, Molecular endocrinology.

[46]  Bruce M. Spiegelman,et al.  Adipocytes as regulators of energy balance and glucose homeostasis , 2006, Nature.

[47]  J. Gorodkin,et al.  Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure. , 2006, Genome research.

[48]  S. Cinti The adipose organ: morphological perspectives of adipose tissues , 2001, Proceedings of the Nutrition Society.

[49]  P. Puigserver,et al.  Transcriptional regulation of adipogenesis. , 2000, Genes & development.

[50]  F. Villarroya,et al.  Dominant negative regulation by c-Jun of transcription of the uncoupling protein-1 gene through a proximal cAMP-regulatory element: a mechanism for repressing basal and norepinephrine-induced expression of the gene before brown adipocyte differentiation. , 1998, Molecular endocrinology.

[51]  F. Villarroya,et al.  CCAAT/enhancer binding proteins α and β are transcriptional activators of the brown fat uncoupling protein gene promoter , 1994 .

[52]  S. Enerbäck,et al.  An upstream enhancer regulating brown-fat-specific expression of the mitochondrial uncoupling protein gene , 1994, Molecular and cellular biology.

[53]  J. Freedman,et al.  Challenges and Opportunities in Linking Long Noncoding RNAs to Cardiovascular, Lung, and Blood Diseases. , 2017, Arteriosclerosis, thrombosis, and vascular biology.

[54]  Lawrence M. Lifshitz,et al.  Adipose tissue angiogenesis assay. , 2014, Methods in enzymology.

[55]  Jan Nedergaard,et al.  Brown adipose tissue: function and physiological significance. , 2004, Physiological reviews.

[56]  J. Bergstrom Percutaneous needle biopsy of skeletal muscle in physiological and clinical research. , 1975, Scandinavian journal of clinical and laboratory investigation.