Epigenetic regulation of the DLK1-MEG3 microRNA cluster in human type 2 diabetic islets.

Type 2 diabetes mellitus (T2DM) is a complex disease characterized by the inability of the insulin-producing β cells in the endocrine pancreas to overcome insulin resistance in peripheral tissues. To determine if microRNAs are involved in the pathogenesis of human T2DM, we sequenced the small RNAs of human islets from diabetic and nondiabetic organ donors. We identified a cluster of microRNAs in an imprinted locus on human chromosome 14q32 that is highly and specifically expressed in human β cells and dramatically downregulated in islets from T2DM organ donors. The downregulation of this locus strongly correlates with hypermethylation of its promoter. Using HITS-CLIP for the essential RISC-component Argonaute, we identified disease-relevant targets of the chromosome 14q32 microRNAs, such as IAPP and TP53INP1, that cause increased β cell apoptosis upon overexpression in human islets. Our results support a role for microRNAs and their epigenetic control by DNA methylation in the pathogenesis of T2DM.

[1]  C. Ricordi,et al.  MicroRNA miR-7 is preferentially expressed in endocrine cells of the developing and adult human pancreas. , 2009, Gene expression patterns : GEP.

[2]  Y Taya,et al.  p53DINP1, a p53-inducible gene, regulates p53-dependent apoptosis. , 2001, Molecular cell.

[3]  C. Lips,et al.  Role of islet amyloid in type 2 diabetes mellitus. , 2006, The international journal of biochemistry & cell biology.

[4]  Ayellet V. Segrè,et al.  Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis , 2010, Nature Genetics.

[5]  C. Gieger,et al.  Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis (vol 42, pg 579, 2010) , 2011 .

[6]  L. Groop,et al.  Epigenetic regulation of PPARGC1A in human type 2 diabetic islets and effect on insulin secretion , 2008, Diabetologia.

[7]  G. Dranitsaris,et al.  CpG methylation analysis of the MEG3 and SNRPN imprinted genes in acute myeloid leukemia and myelodysplastic syndromes. , 2010, Leukemia research.

[8]  J. Friedman,et al.  Circulating MicroRNA Is a Biomarker of Biliary Atresia , 2012, Journal of pediatric gastroenterology and nutrition.

[9]  Leif Groop,et al.  Survival of pancreatic beta cells is partly controlled by a TCF7L2-p53-p53INP1-dependent pathway. , 2012, Human molecular genetics.

[10]  P. Jacquemin,et al.  MiR-495 and miR-218 regulate the expression of the Onecut transcription factors HNF-6 and OC-2. , 2010, Biochemical and biophysical research communications.

[11]  Joshua J. Forman,et al.  A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence , 2008, Proceedings of the National Academy of Sciences.

[12]  J. Schug,et al.  Epigenomic plasticity enables human pancreatic α to β cell reprogramming. , 2013, The Journal of clinical investigation.

[13]  Kyle J. Gaulton,et al.  The miRNA Profile of Human Pancreatic Islets and Beta-Cells and Relationship to Type 2 Diabetes Pathogenesis , 2013, PloS one.

[14]  M. McCarthy,et al.  Human β cell transcriptome analysis uncovers lncRNAs that are tissue-specific, dynamically regulated, and abnormally expressed in type 2 diabetes. , 2012, Cell metabolism.

[15]  M. Zavolan,et al.  MicroRNAs 103 and 107 regulate insulin sensitivity , 2011, Nature.

[16]  J. Schug,et al.  Transcriptomes of the major human pancreatic cell types , 2011, Diabetologia.

[17]  Tatiana A. Tatusova,et al.  NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy , 2011, Nucleic Acids Res..

[18]  L. Shaffer,et al.  Epigenetic detection of human chromosome 14 uniparental disomy , 2003, Human mutation.

[19]  M. Kiebler,et al.  Faculty Opinions recommendation of Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. , 2009 .

[20]  M. Prentki,et al.  Type 2 diabetes across generations: from pathophysiology to prevention and management , 2011, The Lancet.

[21]  M. Grompe,et al.  Isolation of major pancreatic cell types and long-term culture-initiating cells using novel human surface markers. , 2008, Stem cell research.

[22]  G. Gyapay,et al.  Human-ovine comparative sequencing of a 250-kb imprinted domain encompassing the callipyge (clpg) locus and identification of six imprinted transcripts: DLK1, DAT, GTL2, PEG11, antiPEG11, and MEG8. , 2001, Genome research.

[23]  P. Allhoff,et al.  The Framingham Offspring Study , 1991 .

[24]  Per Westermark,et al.  Islet amyloid: a critical entity in the pathogenesis of type 2 diabetes. , 2004, The Journal of clinical endocrinology and metabolism.

[25]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[26]  P. Wilson,et al.  Parental transmission of type 2 diabetes: the Framingham Offspring Study. , 2000, Diabetes.

[27]  A. Green,et al.  The IG-DMR and the MEG3-DMR at Human Chromosome 14q32.2: Hierarchical Interaction and Distinct Functional Properties as Imprinting Control Centers , 2010, PLoS genetics.

[28]  Chengyang Liu,et al.  MicroRNA-7 Regulates the mTOR Pathway and Proliferation in Adult Pancreatic β-Cells , 2013, Diabetes.

[29]  Daniel F. Gudbjartsson,et al.  Parental origin of sequence variants associated with complex diseases , 2009, Nature.

[30]  Robert A. Rizza,et al.  β-Cell Deficit and Increased β-Cell Apoptosis in Humans With Type 2 Diabetes , 2003, Diabetes.

[31]  Robert A Rizza,et al.  Beta-cell deficit and increased beta-cell apoptosis in humans with type 2 diabetes. , 2003, Diabetes.

[32]  P. Ryvkin,et al.  Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis , 2010, PLoS genetics.

[33]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[34]  J. Mendell,et al.  MicroRNAs in Stress Signaling and Human Disease , 2012, Cell.

[35]  S. Murphy,et al.  Novel imprinted DLK1/GTL2 domain on human chromosome 14 contains motifs that mimic those implicated in IGF2/H19 regulation. , 2000, Genome research.

[36]  Martina Paulsen,et al.  Identification of tandemly-repeated C/D snoRNA genes at the imprinted human 14q32 domain reminiscent of those at the Prader-Willi/Angelman syndrome region. , 2002, Human molecular genetics.

[37]  Zhijie Jiang,et al.  MicroRNA Expression in Alpha and Beta Cells of Human Pancreatic Islets , 2013, PloS one.

[38]  C. Ricordi,et al.  Antisense miR-7 Impairs Insulin Expression in Developing Pancreas and in Cultured Pancreatic Buds , 2012, Cell transplantation.

[39]  J. Cavaille,et al.  A large imprinted microRNA gene cluster at the mouse Dlk1-Gtl2 domain. , 2004, Genome research.

[40]  B. Gregory,et al.  PRMD: an integrated database for plant RNA modifications , 2012, Plant Cell.

[41]  H. Iba,et al.  Vectors expressing efficient RNA decoys achieve the long-term suppression of specific microRNA activity in mammalian cells , 2009, Nucleic acids research.

[42]  I. Rigoutsos,et al.  The microRNAs within the DLK1-DIO3 genomic region: involvement in disease pathogenesis , 2012, Cellular and Molecular Life Sciences.

[43]  David Tollervey,et al.  Cross-linking, ligation, and sequencing of hybrids reveals RNA–RNA interactions in yeast , 2011, Proceedings of the National Academy of Sciences.

[44]  C. Nejjari,et al.  European genetic variants associated with type 2 diabetes in North African Arabs. , 2012, Diabetes & metabolism.

[45]  Anton J. Enright,et al.  Human MicroRNA Targets , 2004, PLoS biology.

[46]  M. McCarthy,et al.  The Genetic and Epigenetic Basis of Type 2 Diabetes and Obesity , 2012, Clinical pharmacology and therapeutics.

[47]  C. Burge,et al.  Most mammalian mRNAs are conserved targets of microRNAs. , 2008, Genome research.

[48]  M. McCarthy,et al.  Insights Into the Molecular Mechanism for Type 2 Diabetes Susceptibility at the KCNQ1 Locus From Temporal Changes in Imprinting Status in Human Islets , 2013, Diabetes.

[49]  Jonathan Schug,et al.  MicroRNAs control intestinal epithelial differentiation, architecture, and barrier function. , 2010, Gastroenterology.

[50]  M. Joglekar,et al.  Expression of islet-specific microRNAs during human pancreatic development. , 2009, Gene expression patterns : GEP.

[51]  Ana Kozomara,et al.  miRBase: integrating microRNA annotation and deep-sequencing data , 2010, Nucleic Acids Res..

[52]  L. Eliasson,et al.  Differences in islet-enriched miRNAs in healthy and glucose intolerant human subjects. , 2011, Biochemical and biophysical research communications.

[53]  C. Sander,et al.  A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing , 2007, Cell.

[54]  S. Murphy,et al.  Novel Imprinted DLK 1 / GTL 2 Domain on Human Chromosome 14 Contains Motifs that Mimic Those Implicated in IGF 2 / H 19 Regulation , 2000 .

[55]  J. Schug,et al.  Dynamic recruitment of microRNAs to their mRNA targets in the regenerating liver , 2013, BMC Genomics.