Cell-type, allelic, and genetic signatures in the human pancreatic beta cell transcriptome

Genome Research

Volumn 23, Issue 9, 2013, Pages 1554-1562

  Nica, Alexandra C ^a,b,c   Ongen, Halit ^a,b,c   Irminger, Jean Claude ^a,b   Bosco, Domenico ^d   Berney, Thierry ^d   Antonarakis, Stylianos E ^a,b   Halban, Philippe A ^a,b   Dermitzakis, Emmanouil T ^a,b,c  

^a UNIVERSITY OF GENEVA MEDICAL SCHOOL   (Switzerland)

^b Institute of Genetics and Genomics of Geneva (iGE3)   (Switzerland)

^c SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^d GENEVA UNIVERSITY HOSPITALS   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE DIPHOSPHATE; ADENOSINE TRIPHOSPHATE; BONE MORPHOGENETIC PROTEIN 5; DITHIZONE; GLUCAGON; HYPOPHYSIS ADENYLATE CYCLASE ACTIVATING POLYPEPTIDE RECEPTOR 1; INSULIN; LONG UNTRANSLATED RNA; PREALBUMIN; PURINERGIC RECEPTOR; SECRETORY PROTEIN; SOMATOMEDIN BINDING PROTEIN 2; SOMATOSTATIN; TRANSCRIPTOME; UNTRANSLATED RNA;

ALLELE; ALLELIC IMBALANCE; ALTERNATIVE RNA SPLICING; ARTICLE; CADAVER; CELL POPULATION; CELL PROLIFERATION; CELL REGENERATION; CELL TYPE; CLINICAL ARTICLE; COMPARATIVE STUDY; DNA LIBRARY; EXTRACELLULAR MATRIX; FLUORESCENCE ACTIVATED CELL SORTING; GENE EXPRESSION; GENETIC REGULATION; GENETIC VARIABILITY; HUMAN; HUMAN CELL; HUMAN GENOME; IMMUNOFLUORESCENCE; INSULIN RELEASE; LYMPHOBLASTOID CELL LINE; MICROARRAY ANALYSIS; PANCREAS ISLET ALPHA CELL; PANCREAS ISLET BETA CELL; PANCREAS ISLET DELTA CELL; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; RNA SEQUENCE; STAINING;

ALLELES; GENE REGULATORY NETWORKS; HUMANS; INSULIN-SECRETING CELLS; ORGAN SPECIFICITY; QUANTITATIVE TRAIT LOCI; TRANSCRIPTOME;

EID: 84883706987     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.150706.112     Document Type: Article

References (44)

1. Ahren B. 2000. Autonomic regulation of islet hormone secretion - implications for health and disease. Diabetologia 43: 393-410.
2. Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biol 11: R106.
3. Barrett JC, Clayton DG, Concannon P, Akolkar B, Cooper JD, Erlich HA, Julier C, Morahan G, Nerup J, Nierras C, et al. 2009. Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nat Genet 41: 703-707.
4. Browning SR, Browning BL. 2007. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet 81: 1084-1097.
5. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. 2011. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25: 1915-1927.
6. Danzer C, Eckhardt K, Schmidt A, Fankhauser N, Ribrioux S, Wollscheid B, Muller L, Schiess R, Zullig R, Lehmann R, et al. 2012. Comprehensive description of the N-glycoproteome of mouse pancreatic b-cells and human islets. J Proteome Res 11: 1598-1608.
7. DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, et al. 2011. A framework for variation discovery and genotyping using nextgeneration DNA sequencing data. Nat Genet 43: 491-498.
8. Dimas AS, Deutsch S, Stranger BE, Montgomery SB, Borel C, Attar-Cohen H, Ingle C, Beazley C, Gutierrez Arcelus M, Sekowska M, et al. 2009. Common regulatory variation impacts gene expression in a cell typedependent manner. Science 325: 1246-1250.
9. Dorrell C, Grompe MT, Pan FC, Zhong Y, Canaday PS, Shultz LD, Greiner DL, Wright CV, Streeter PR, Grompe M. 2011a. Isolation of mouse pancreatic a, b, duct and acinar populations with cell surface markers. Mol Cell Endocrinol 339: 144-150.
10. Dorrell C, Schug J, Lin CF, Canaday PS, Fox AJ, Smirnova O, Bonnah R, Streeter PR, Stoeckert CJ Jr, Kaestner KH, et al. 2011b. Transcriptomes of the major human pancreatic cell types. Diabetologia 54: 2832-2844.
11. Emilsson V, Thorleifsson G, Zhang B, Leonardson AS, Zink F, Zhu J, Carlson S, Helgason A, Walters GB, Gunnarsdottir S, et al. 2008. Genetics of gene expression and its effect on disease. Nature 452: 423-428.
12. Fernandez-Alvarez J, Hillaire-Buys D, Loubatières-Mariani MM, Gomis R, Petit P. 2001. P2 receptor agonists stimulate insulin release from human pancreatic islets. Pancreas 22: 69-71.
13. Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, et al. 2013. Ensembl 2013. Nucl Acids Res 41: D48-D55.
14. Gaulton KJ, NammoT, Pasquali L, Simon JM, Giresi PG, Fogarty MP, Panhuis TM, Mieczkowski P, Secchi A, Bosco D, et al. 2010. A map of open chromatin in human pancreatic islets. Nat Genet 42: 255-259.
15. Grundberg E, Small KS, Hedman AK, Nica AC, Buil A, Keildson S, Bell JT, Yang TP, Meduri E, Barrett A, et al. 2012. Mapping cis- and transregulatory effects across multiple tissues in twins. Nat Genet 44: 1084-1089.
16. Hardy OT, Hohmeier HE, Becker TC, Manduchi E, Doliba NM, Gupta RK, White P, Stoeckert CJ Jr, Matschinsky FM, Newgard CB, et al. 2007. Functional genomics of the b-cell: short-chain 3-hydroxyacylcoenzyme A dehydrogenase regulates insulin secretion independent of K+ currents. Mol Endocrinol 21: 765-773.
17. Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D et al. 2006. GENCODE: Producing a reference annotation for ENCODE. Genome Biol 7 (Suppl 1): S4.
18. Huang Y, Sook-Kim M, Ratovitski E. 2008. Midkine promotes tetraspaninintegrin interaction and induces FAK-Stat1a pathway contributing to migration/invasiveness of human head and neck squamous cell carcinoma cells. Biochem Biophys Res Commun 377: 474-478.
19. Huang DW, Sherman BT, Lempicki RA. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
20. Jiang FX, Stanley EG, Gonez LJ, Harrison LC. 2002. Bone morphogenetic proteins promote development of fetal pancreas epithelial colonies containing insulin-positive cells. J Cell Sci 115: 753-760.
21. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics 25: 1754-1760.
22. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, et al. 2010. The Genome Analysis Toolkit: A MapReduce framework for analyzing nextgeneration DNA sequencing data. Genome Res 20: 1297-1303.
23. Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, Nisbett J, Guigo R, Dermitzakis ET. 2010. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464: 773-777.
24. Mora'n I, Akerman I, van de Bunt M, Xie R, Benazra M, Nammo T, Arnes L, Nakic N, Garcia-Hurtado J, Rodríguez-Seguí S, et al. 2012. Human b cell transcriptome analysis uncovers lncRNAs that are tissue-specific, dynamically regulated, and abnormally expressed in type 2 diabetes. Cell Metab 16: 435-448.
25. Morris AP, Voight BF, Teslovich TM, Ferreira T, Segre AV, Steinthorsdottir V, Strawbridge RJ, Khan H, Grallert H, Mahajan A, et al. 2012. Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes. Nat Genet 44: 981-990.
26. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628.
27. Nica AC, Montgomery SB, Dimas AS, Stranger BE, Beazley C, Barroso I, Dermitzakis ET. 2010. Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. PLoS Genet 6: e1000895.
28. Nica AC, Parts L, Glass D, Nisbet J, Barrett A, SekowskaM, Travers M, Potter S, Grundberg E, Small K, et al. 2011. The architecture of gene regulatory variation across multiple human tissues: The MuTHER study. PLoS Genet 7: e1002003.
29. Nicolls MR, D'Antonio JM, Hutton JC, Gill RG, Czwornog JL, Duncan MW. 2003. Proteomics as a tool for discovery: Proteins implicated in Alzheimer's disease are highly expressed in normal pancreatic islets. J Proteome Res 2: 199-205.
30. Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. 2008. Deep surveying of alternative splicing complexity in the human transcriptome by highthroughput sequencing. Nat Genet 40: 1413-1415.
31. Parnaud G, Bosco D, Berney T, Pattou F, Kerr-Conte J, Donath MY, Bruun C, Mandrup-Poulsen T, Billestrup N, Halban PA. 2008. Proliferation of sorted human and rat b cells. Diabetologia 51: 91-100.
32. Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK. 2010. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464: 768-772.
33. Pisania A, Weir GC, O'Neil JJ, Omer A, Tchipashvili V, Lei J, Colton CK, Bonner-Weir S. 2010. Quantitative analysis of cell composition and purity of human pancreatic islet preparations. Lab Invest 90: 1661-1675.
34. Price AL, Helgason A, Thorleifsson G, McCarroll SA, Kong A, Stefansson K. 2011. Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individuals. PLoS Genet 7: e1001317.
35. Rondas D, Tomas A, Halban PA. 2011. Focal adhesion remodeling is crucial for glucose-stimulated insulin secretion and involves activation of focal adhesion kinase and paxillin. Diabetes 60: 1146-1157.
36. Sakurai Y, Shintani N, Hayata A, Hashimoto H, Baba A. 2011. Trophic effects of PACAP on pancreatic islets: A mini-review. J Mol Neurosci 43: 3-7.
37. Saltiel AR, Kahn CR. 2001. Insulin signalling and the regulation of glucose and lipid metabolism. Nature 414: 799-806.
38. Schwartz MW, Woods SC, Porte D Jr, Seeley RJ, Baskin DG. 2000. Central nervous system control of food intake. Nature 404: 661-671.
39. Storey JD, Tibshirani R. 2003. Statistical significance for genomewide studies. Proc Natl Acad Sci 100: 9440-9445.
40. Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, Beazley C, Ingle CE, Dunning M, Flicek P, Koller D, et al. 2007. Population genomics of human gene expression. Nat Genet 39: 1217-1224.
41. Thomas MF, Ansel KM. 2010. Construction of small RNA cDNA libraries for deep sequencing. Methods Mol Biol 667: 93-111.
42. Tisch R, McDevitt H. 1996. Insulin-dependent diabetes mellitus. Cell 85: 291-297.
43. Villasenor A, Wang ZV, Rivera LB, Ocal O, Asterholm IW, Scherer PE, Brekken RA, Cleaver O, Wilkie TM. 2010. Rgs16 and Rgs8 in embryonic endocrine pancreas and mouse models of diabetes. Dis Model Mech 3: 567-580.
44. Zhang L, Gao J, Li Z, Gong Y. 2012. Neuronal pentraxin II (NPTX2) is frequently down-regulated by promoter hypermethylation in pancreatic cancers. Dig Dis Sci 57: 2608-2614.