RNA-seq methods for identifying differentially expressed gene in human pancreatic islet cells treated with pro-inflammatory cytokines

Molecular Biology Reports

Volumn 41, Issue 4, 2014, Pages 1917-1925

  Li, Bo ^a   Bi, Chang Long ^a   Lang, Ning ^a   Li, Yu Ze ^b   Xu, Chao ^a   Zhang, Ying Qi ^a   Zhai, Ai Xia ^a   Cheng, Zhi Feng ^a  

^a HARBIN MEDICAL UNIVERSITY   (China)

^b Tuberculosis Control Center of Heilongjiang Province   (China)

Author keywords

Cytokine; lncRNA; RNA seq; Transcript; Type 1 diabetes

Indexed keywords

CXCL9 CHEMOKINE; CYTOKINE; GUANINE NUCLEOTIDE BINDING PROTEIN; LONG UNTRANSLATED RNA; PROTEIN GBP5; TRANSCRIPTOME; UNCLASSIFIED DRUG; AUTACOID;

ARTICLE; COMPUTER PROGRAM; DOWN REGULATION; GENE EXPRESSION; GENETIC IDENTIFICATION; GENETIC SCREENING; HUMAN; HUMAN CELL; MARKER GENE; PANCREAS ISLET CELL; PROTEIN FOLDING; PROTEIN FUNCTION; PTF1A GENE; REG3G GENE; RNA ANALYSIS; RNA SEQUENCE; RNA TRANSCRIPTION; SEQUENCE ALIGNMENT; SEQUENCE DATABASE; TRANSCRIPTION REGULATION; UPREGULATION; BIOLOGY; CYTOLOGY; DRUG EFFECTS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HIGH THROUGHPUT SEQUENCING; METABOLISM; NUCLEIC ACID DATABASE; PANCREAS ISLET; PANCREAS ISLET BETA CELL; PROCEDURES; SEQUENCE ANALYSIS;

COMPUTATIONAL BIOLOGY; CYTOKINES; DATABASES, NUCLEIC ACID; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INFLAMMATION MEDIATORS; INSULIN-SECRETING CELLS; ISLETS OF LANGERHANS; RNA, LONG NONCODING; SEQUENCE ANALYSIS, RNA;

EID: 84897547220     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-013-3016-2     Document Type: Article

References (58)

1. Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G (2008) Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods 5:613-619 (Pubitemid 351911866)
2. Mortazavi A, Williams BA, Mccue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621-628 (Pubitemid 351911867)
3. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: A revolutionary tool for transcriptomics. Nat Rev Genet 10:57-63
4. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644-652
5. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 28:503-510
6. 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
7. Mitchell Guttman IA, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458:223-227
8. Pauli A, Valen E, Lin MF, Garber M, Vastenhouw NL, Levin JZ, Fan L, Sandelin A, Rinn JL, Regev A (2012) Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res 22:577-591
9. Kukreja A, Cost G, Marker J, Zhang C, Sun Z, Lin-Su K, Ten S, Sanz M, Exley M, Wilson B (2002) Multiple immuno-regulatory defects in type-1 diabetes. J Clin Investig 109:131-140 (Pubitemid 34052549)
10. Todd JA (2010) Etiology of type 1 diabetes. Immunity 32:457-467
11. Durinovic-Bello I, Schlosser M, Riedl M, Maisel N, Rosinger S, Kalbacher H, Deeg M, Ziegler M, Elliott J, Roep B (2004) Pro-and anti-inflammatory cytokine production by autoimmune T cells against preproinsulin in HLA-DRB104, DQ8 Type 1 diabetes. Diabetologia 47:439-450 (Pubitemid 38491240)
12. Dandona P, Aljada A, Bandyopadhyay A (2004) Inflammation: the link between insulin resistance, obesity and diabetes. Trends Immunol 25:4-7 (Pubitemid 38032801)
13. Epstein FH, Ross R (1999) Atherosclerosis - an inflammatory disease. N Engl J Med 340:115-126 (Pubitemid 29054847)
14. Hultcrantz M, Hühn MH, Wolf M, Olsson A, Jacobson S, Williams BR, Korsgren O, Flodström-Tullberg M (2007) Interferons induce an antiviral state in human pancreatic islet cells. Virology 367:92-101 (Pubitemid 47418925)
15. Ylipaasto P, Kutlu B, Rasilainen S, Rasschaert J, Salmela K, Teerijoki H, Korsgren O, Lahesmaa R, Hovi T, Eizirik DL (2005) Global profiling of coxsackievirus-and cytokine-induced gene expression in human pancreatic islets. Diabetologia 48:1510-1522 (Pubitemid 41175504)
16. Rasschaert J, Ladrière L, Urbain M, Dogusan Z, Katabua B, Sato S, Akira S, Gysemans C, Mathieu C, Eizirik DL (2005) Toll-like receptor 3 and STAT-1 contribute to double-stranded RNA+ interferon-γ-induced apoptosis in primary pancreatic β-cells. J Biol Chem 280:33984-33991 (Pubitemid 41443119)
17. Liu D, Darville M, Eizirik DL (2001) Double-stranded ribonucleic acid (RNA) induces β-cell Fas messenger RNA expression and increases cytokine-induced β-cell apoptosis. Endocrinology 142:2593-2599 (Pubitemid 32473115)
18. Foulis A, Farquharson M, Meager A (1987) Immunoreactive α-interferon in insulin-secreting β cells in type 1 diabetes mellitus. Lancet 330:1423-1427 (Pubitemid 18010318)
19. Shimada A, Morimoto J, Kodama K, Suzuki R, Oikawa Y, Funae O, Kasuga A, Saruta T, Narumi S (2001) Elevated serum IP-10 levels observed in type 1 diabetes. Diabetes Care 24:510-515 (Pubitemid 32198422)
20. Nicoletti F, Conget I, Di Mauro M, Di Marco R, Mazzarino M, Bendtzen K, Messina A, Gomis R (2002) Serum concentrations of the interferon-γ- inducible chemokine IP-10/CXCL10 are augmented in both newly diagnosed type I diabetes mellitus patients and subjects at risk of developing the disease. Diabetologia 45:1107-1110 (Pubitemid 34985286)
21. Hanifi-Moghaddam P, Kappler S, Seissler J, Müller-Scholze S, Martin S, Roep B, Strassburger K, Kolb H, Schloot N (2006) Altered chemokine levels in individuals at risk of Type 1 diabetes mellitus. Diabet Med 23:156-163
22. Wang X, Jia S, Geoffrey R, Alemzadeh R, Ghosh S, Hessner MJ (2008) Identification of a molecular signature in human type 1 diabetes mellitus using serum and functional genomics. J Immunol 180:1929-1937
23. Martin AP, Rankin S, Pitchford S, Charo IF, Furtado GC, Lira SA (2008) Increased expression of CCL2 in insulin-producing cells of transgenic mice promotes mobilization of myeloid cells from the bone marrow, marked insulitis, and diabetes. Diabetes 57:3025-3033
24. Christen U, Mcgavern DB, Luster AD, Von Herrath MG, Oldstone MB (2003) Among CXCR3 chemokines, IFN-γ-inducible protein of 10 kDa (CXC chemokine ligand (CXCL) 10) but not monokine induced by IFN-γ (CXCL9) imprints a pattern for the subsequent development of autoimmune disease. J Immunol 171:6838-6845 (Pubitemid 37532119)
25. Eizirik DL, Colli ML, Ortis F (2009) The role of inflammation in insulitis and β-cell loss in type 1 diabetes. Nat Rev Endocrinol 5:219-226
26. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105-1111
27. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, Van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511-515
28. Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci 100:9440-9445 (Pubitemid 37033947)
29. Wang L, Park HJ, Dasari S, Wang S, Kocher J-P, Li W (2013) CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res 41:e74
30. Haas BJ, Zody MC (2010) Advancing RNA-seq analysis. Nat Biotechnol 28:421
31. Yassour M, Kaplan T, Fraser HB, Levin JZ, Pfiffner J, Adiconis X, Schroth G, Luo S, Khrebtukova I, Gnirke A (2009) Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci 106:3264-3269
32. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, Van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nat Biotechnol 28:511
33. Eizirik DL, Sammeth M, Bouckenooghe T, Bottu G, Sisino G, Igoillo-Esteve M, Ortis F, Santin I, Colli ML, Barthson J (2012) The human pancreatic islet transcriptome: expression of candidate genes for type 1 diabetes and the impact of pro-inflammatory cytokines. PLoS Genet 8:e1002552
34. Rose SD, Swift GH, Peyton MJ, Hammer RE, Macdonald RJ (2001) The role of PTF1-P48 in pancreatic acinar gene expression. J Biol Chem 276:44018-44026
35. Sellick GS, Barker KT, Stolte-Dijkstra I, Fleischmann C, Coleman RJ, Garrett C, Gloyn AL, Edghill EL, Hattersley AT, Wellauer PK (2004) Mutations in PTF1A cause pancreatic and cerebellar agenesis. Nat Genet 36:1301-1305 (Pubitemid 39577939)
36. Obata J, Yano M, Mimura H, Goto T, Nakayama R, Mibu Y, Oka C, Kawaichi M (2001) p48 subunit of mouse PTF1 binds to RBP-Jκ/CBF-1, the intracellular mediator of Notch signalling, and is expressed in the neural tube of early stage embryos. Genes Cells 6:345-360 (Pubitemid 32401280)
37. Lin JW, Biankin AV, Horb ME, Ghosh B, Prasad NB, Yee NS, Pack MA, Leach SD (2004) Differential requirement for ptf1a in endocrine and exocrine lineages of developing zebrafish pancreas. Dev Biol 274:491-503
38. Fukuda A, Kawaguchi Y, Furuyama K, Kodama S, Horiguchi M, Kuhara T, Kawaguchi M, Terao M, Doi R, Wright CV (2008) Reduction of Ptf1a gene dosage causes pancreatic hypoplasia and diabetes in mice. Diabetes 57:2421-2431
39. Christa L, Felin M, Morali O, Simon M-T, Lasserre C, Brechot C, Sève A-P (1994) The human HIP gene, overexpressed in primary liver cancer encodes for a C-type carbohydrate binding protein with lactose binding activity. FEBS Lett 337:114-118 (Pubitemid 24039506)
40. Marselli L, Thorne J, Dahiya S, Sgroi DC, Sharma A, Bonner-Weir S, Marchetti P, Weir GC (2010) Gene expression profiles of Beta-cell enriched tissue obtained by laser capture microdissection from subjects with type 2 diabetes. PLoS One 5:e11499
41. Terazono K, Uchiyama Y, Ide M, Watanabe T, Yonekura H, Yamamoto H, Okamoto H (1990) Expression of reg protein in rat regenerating islets and its co-localization with insulin in the beta cell secretory granules. Diabetologia 33:250-252 (Pubitemid 20136243)
42. Miyaura C, Chen L, Appel M, Alam T, Inman L, Hughes SD, Milburn JL, Unger RH, Newgard CB (1991) Expression of reg/PSP, a pancreatic exocrine gene: relationship to changes in islet β-cell mass. Mol Endocrinol 5:226-234 (Pubitemid 21923686)
43. Akiyama T, Takasawa S, Nata K, Kobayashi S, Abe M, Shervani NJ, Ikeda T, Nakagawa K, Unno M, Matsuno S (2001) Activation of Reg gene, a gene for insulin-producing β-cell regeneration: poly (ADP-ribose) polymerase binds Reg promoter and regulates the transcription by autopoly (ADP-ribosyl) ation. Proc Natl Acad Sci 98:48-53 (Pubitemid 32095861)
44. Kobayashi S, Akiyama T, Nata K, Abe M, Tajima M, Shervani NJ, Unno M, Matsuno S, Sasaki H, Takasawa S (2000) Identification of a receptor for reg (regenerating gene) protein, a pancreatic β-cell regeneration factor. J Biol Chem 275:10723-10726 (Pubitemid 30212698)
45. Okamoto H (1999) The Reg gene family and Reg proteins: with special attention to the regeneration of pancreatic β-cells. J Hepatobiliary Pancreat Surg 6:254-262
46. Yip L, Su L, Sheng D, Chang P, Atkinson M, Czesak M, Albert PR, Collier A-R, Turley SJ, Fathman CG (2009) Deaf1 isoforms control the expression of genes encoding peripheral tissue antigens in the pancreatic lymph nodes during type 1 diabetes. Nat Immunol 10:1026-1033
47. Pugazhenthi U, Velmurugan K, Tran A, Mahaffey G, Pugazhenthi S (2010) Anti-inflammatory action of exendin-4 in human islets is enhanced by phosphodiesterase inhibitors: potential therapeutic benefits in diabetic patients. Diabetologia 53:2357-2368
48. Vukkadapu SS, Belli JM, Ishii K, Jegga AG, Hutton JJ, Aronow BJ, Katz JD (2005) Dynamic interaction between T cell-mediated β-cell damage and β-cell repair in the run up to autoimmune diabetes of the NOD mouse. Physiol Genomics 21:201-211 (Pubitemid 40898480)
49. Gerard C, Rollins BJ (2001) Chemokines and disease. Nat Immunol 2:108-115 (Pubitemid 33707927)
50. Jamali Z, Nazari M, Khoramdelazad H, Hakimizadeh E, Mahmoodi M, Karimabad MN, Hassanshahi G, Rezaeian M, Balaei P, Darakhshan S (2013) Expression of CC chemokines CCL2, CCL5, and CCL11 is associated with duration of disease and complications in type-1 diabetes: A study on Iranian diabetic patients. Clin. Lab 11:1
51. Wellen KE, Hotamisligil GS (2005) Inflammation, stress, and diabetes. J Clin Investig 115:1111-1119 (Pubitemid 40629025)
52. Navarro JF, Milena FJ, Mora C, Leon C, Garcia J (2007) Renal pro-inflammatory cytokine gene expression in diabetic nephropathy: effect of angiotensin-converting enzyme inhibition and pentoxifylline administration. Am J Nephrol 26:562-570 (Pubitemid 46143878)
53. Boehm U, Klamp T, Groot M, Howard J (1997) Cellular responses to interferon-γ. Annu Rev Immunol 15:749-795 (Pubitemid 27169298)
54. Shenoy AR, Wellington DA, Kumar P, Kassa H, Booth CJ, Cresswell P, Macmicking JD (2012) GBP5 promotes NLRP3 inflammasome assembly and immunity in mammals. Science 336:481-485
55. Haneklaus M, O'neill LA, Coll RC (2013) Modulatory mechanisms controlling the NLRP3 inflammasome in inflammation: recent developments. Curr Opin Immunol 25(1):40-45
56. Lehuen A, Diana J, Zaccone P, Cooke A (2010) Immune cell crosstalk in type 1 diabetes. Nat Rev Immunol 10:501-513
57. Yan B, Wang Z (2012) Long noncoding RNA: its physiological and pathological roles. DNA Cell Biol 31:S-34-S-41
58. Alvarez ML, Distefano JK (2012) The role of non-coding RNAs in diabetic nephropathy: potential applications as biomarkers for disease development and progression. Diabetes Res Clin Pract 99(1):1-11