Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer

BMC Genomics

Volumn 10, Issue , 2009, Pages 442-

  Avondo, Federica ^a   Roncaglia, Paola ^b   Crescenzio, Nicoletta ^c   Krmac, Helena ^b   Garelli, Emanuela ^c   Armiraglio, Marta ^a   Castagnoli, Carlotta ^d   Campagnoli, Maria F ^c   Ramenghi, Ugo ^c   Gustincich, Stefano ^b   Santoro, Claudio ^a   Dianzani, Irma ^a  

^a UNIVERSITY OF EASTERN PIEDMONT   (Italy)

^b SISSA   (Italy)

^c UNIVERSITY OF TURIN   (Italy)

^d CTO HOSPITAL   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; RIBOSOME PROTEIN; STEROID; RIBOSOMAL PROTEIN S19;

AMINO ACID METABOLISM; ARTICLE; BLACKFAN DIAMOND ANEMIA; BONE MARROW TRANSPLANTATION; CASE REPORT; CELL DEATH; CONTROLLED STUDY; FEMALE; FIBROBLAST; FRAMESHIFT MUTATION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE MUTATION; HUMAN; HUMAN CELL; MALE; MICROARRAY ANALYSIS; MISSENSE MUTATION; MUTATIONAL ANALYSIS; PROTEIN SYNTHESIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SPLICING; SOLID TUMOR; TISSUE GROWTH; CASE CONTROL STUDY; DNA MICROARRAY; GENETICS; METABOLISM; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE SEQUENCE;

ANEMIA, DIAMOND-BLACKFAN; BASE SEQUENCE; CASE-CONTROL STUDIES; DNA MUTATIONAL ANALYSIS; FEMALE; FIBROBLASTS; GENE EXPRESSION PROFILING; HUMANS; MALE; MOLECULAR SEQUENCE DATA; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN BIOSYNTHESIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RIBOSOMAL PROTEINS;

EID: 70350450581     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-442     Document Type: Article

References (46)

1. Lecompte O, Ripp R, Thierry JC, Moras D, Poch O. Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale. Nucleic Acids Res 2002, 30:5382-5390. 140077, 12490706, 10.1093/nar/gkf693.
2. Ebert BL, Pretz J, Bosco J, Chang CY, Tamayo P, Galili N, Raza A, Root DE, Attar E, Ellis SR, Golub TR. Identification of RPS14 as a 5q- syndrome gene by RNA interference screen. Nature 2008, 451:335-9. 10.1038/nature06494, 18202658.
3. Liu JM, Ellis SR. Ribosomes and marrow failure: coincidental association or molecular paradigm?. Blood 2006, 107:4583-4588. 10.1182/blood-2005-12-4831, 16507776.
4. Campagnoli MF, Ramenghi U, Armiraglio M, Quarello P, Garelli E, Carando A, Avondo F, Pavesi E, Fribourg S, Gleizes PE, Loreni F, Dianzani I. RPS19 mutations in patients with Diamond-Blackfan anemia. Hum Mutat 2008, 7:911-920.
5. Vlachos A, Ball S, Dahl N, Alter BP, Sheth S, Ramenghi U, Meerpohl J, Karlsson S, Liu JM, Leblanc T, Paley C, Kang EM, Leder EJ, Atsidaftos E, Shimamura A, Bessler M, Glader B, Lipton JM, . Participants of Sixth Annual Daniella Maria Arturi International Consensus Conference Diagnosing and treating Diamond Blackfan anaemia: results of an international clinical consensus conference. Br J Haematol 2008, 142:859-876. 2654478, 18671700, 10.1111/j.1365-2141.2008.07269.x.
6. Cmejla R, Cmejlova J, Handrkova H, Petrak J, Pospisilova D. Ribosomal protein S17 gene (RPS17) is mutated in Diamond-Blackfan anemia. Hum Mutat 2007, 28:1178-82. 10.1002/humu.20608, 17647292.
7. Draptchinskaia N, Gustavsson P, Andersson B, Pettersson M, Willig TN, Dianzani I, Ball S, Tchernia G, Klar J, Matsson H, Tentler D, Mohandas N, Carlsson B, Dahl N. The gene encoding ribosomal protein S19 is mutated in Diamond-Blackfan anaemia. Nat Genet 1999, 21:169-75. 10.1038/5951, 9988267.
8. Farrar JE, Nater M, Caywood E, McDevitt MA, Kowalski J, Takemoto CM, Talbot CC, Meltzer P, Esposito D, Beggs AH, Schneider HE, Grabowska A, Ball SE, Niewiadomska E, Sieff CA, Vlachos A, Atsidaftos E, Ellis SR, Lipton JM, Gazda HT, Arceci RJ. Abnormalities of the large ribosomal subunit protein, Rpl35a, in Diamond-Blackfan anemia. Blood 2008, 112:1582-1592. 2518874, 18535205, 10.1182/blood-2008-02-140012.
9. Gazda HT, Grabowska A, Merida-Long LB, Latawiec E, Schneider HE, Lipton JM, Vlachos A, Atsidaftos E, Ball SE, Orfali KA, Niewiadomska E, Da Costa L, Tchernia G, Niemeyer C, Meerpohl JJ, Stahl J, Schratt G, Glader B, Backer K, Wong C, Nathan DG, Beggs AH, Sieff CA. Ribosomal protein S24 gene is mutated in Diamond-Blackfan anemia. Am J Hum Genet 2006, 79:1110-1108. 1698708, 17186470, 10.1086/510020.
10. Gazda HT, Sheen MR, Vlachos A, Choesmel V, O'Donohue MF, Schneider H, Darras N, Hasman C, Sieff CA, Newburger PE, Ball SE, Niewiadomska E, Matysiak M, Zaucha JM, Glader B, Niemeyer C, Meerpohl JJ, Atsidaftos E, Lipton JM, Gleizes PE, Beggs AH. Ribosomal protein L5 and L11 mutations are associated with cleft palate and abnormal thumbs in diamond-blackfan anemia patients. Am J Hum Genet 2008, 83:769-780. 2668101, 19061985, 10.1016/j.ajhg.2008.11.004.
11. Choesmel V, Bacqueville D, Rouquette J, Noaillac-Depeyre J, Fribourg S, Cretien A, Leblanc T, Tchernia G, Da Costa L, Gleizes PE. Impaired ribosome biogenesis in Diamond-Blackfan anemia. Blood 2007, 109:1275-1283. 1785132, 17053056, 10.1182/blood-2006-07-038372.
12. Flygare J, Aspesi A, Bailey JC, Miyake K, Caffrey JM, Karlsson S, Ellis S. Human RPS19, the gene mutated in Diamond Blackfan anemia, encodes a ribosomal protein required for the maturation of 40S ribosomal subunits. Blood 2007, 109:980-986. 1785147, 16990592, 10.1182/blood-2006-07-038232.
13. Idol RA, Robledo S, Du HY, Crimmins DL, Wilson DB, Ladenson JH, Bessler M, Mason PJ. Cells depleted for RPS19, a protein associated with Diamond Blackfan Anemia, show defects in 18S ribosomal RNA synthesis and small ribosomal subunit production. Blood Cells Mol Dis 2007, 39:35-43. 10.1016/j.bcmd.2007.02.001, 17376718.
14. Léger-Silvestre I, Caffrey JM, Dawaliby R, Alvarez-Arias DA, Gas N, Bertolone SJ, Gleizes PE, Ellis SR. Specific Role for Yeast Homologs of the Diamond Blackfan Anemia-associated Rps19 Protein in Ribosome Synthesis. J Biol Chem 2005, 280:38177-38185. 10.1074/jbc.M506916200, 16159874.
15. Robledo S, Idol RA, Crimmins DL, Ladenson JH, Mason PJ, Bessler M. The role of human ribosomal proteins in the maturation of rRNA and ribosome production. RNA 2008, 14:1918-1929. 2525958, 18697920, 10.1261/rna.1132008.
16. Giri N, Kang E, Tisdale JF, Follman D, Rivera M, Schwartz GN, Kim S, Young NS, Rick ME, Dunbar CE. Clinical and laboratory evidence for a trilineage haematopoietic defect in patients with refractory Diamond-Blackfan anaemia. Br J Haematol 2000, 108:167-175. 10.1046/j.1365-2141.2000.01796.x, 10651740.
17. Chatr-Aryamontri A, Angelini M, Garelli E, Tchernia G, Ramenghi U, Dianzani I, Loreni F. Nonsense-mediated and nonstop decay of ribosomal protein S19 mRNA in Diamond-Blackfan anemia. Hum Mutat 2004, 24:526-533. 10.1002/humu.20117, 15523650.
18. Gazda HT, Zhong R, Long L, Niewiadomska E, Lipton JM, Ploszynska A, Zaucha JM, Vlachos A, Atsidaftos E, Viskochil DH, Niemeyer CM, Meerpohl JJ, Rokicka-Milewska R, Pospisilova D, Wiktor-Jedrzejczak W, Nathan DG, Beggs AH, Sieff CA. RNA and protein evidence for haplo-insufficiency in Diamond-Blackfan anaemia patients with RPS19 mutations. Br J Haematol 2004, 127:105-113. 10.1111/j.1365-2141.2004.05152.x, 15384984.
19. Ingenuity Pathway Analysis Software. , http://www.ingenuity.com/
20. Qin D, Wu H, Peng H, Yao Y, Ni Z, Li Z, Zhou C, Sun Q. Heat stress-responsive transcriptome analysis in heat susceptible and tolerant wheat (Triticum aestivum L.) by using Wheat Genome Array. BMC Genomics 2008,
21. Liu J, Huang Q, Higdon J, Liu W, Xie T, Yamashita T, Cheon K, Cheng C, Zuo J. Distinct gene expression profiles and reduced JNK signaling in retinitis pigmentosa caused by RP1 mutations. Hum Mol Genet 2005, 14:2945-2958. 10.1093/hmg/ddi325, 16126734.
22. Cmejlova J, Dolezalova L, Pospisilova D, Petrtylova K, Petrak J, Cmejla R. Translational efficiency in patients with Diamond-Blackfan anemia. Haematologica 2006, 91:1456-1464.
23. Gazda HT, Kho AT, Sanoudou D, Zaucha JM, Kohane IS, Sieff CA, Beggs AH. Defective ribosomal protein gene expression alters transcription, translation, apoptosis, and oncogenic pathways in Diamond-Blackfan anemia. Stem Cells 2006, 24:2034-2044. 10.1634/stemcells.2005-0554, 16741228.
24. Koga Y, Ohga S, Nomura A, Takada H, Hara T. Reduced gene expression of clustered ribosomal proteins in Diamond-Blackfan anemia patients without RPS19 gene mutations. J Pediatr Hematol Oncol 2006, 28:355-361. 10.1097/00043426-200606000-00007, 16794503.
25. Lee SW, Cho BH, Park SG, Kim S. Aminoacyl-tRNA synthetase complexes: beyond translation. J Cell Sci 2004, 117:3725-3734. 10.1242/jcs.01342, 15286174.
26. Shaw AC, Larsen MR, Roepstorff P, Justese J, Christiansen G, Birkelund S. Mapping and identification of interferon γ-regulates Hela cell proteins separated by immobilized pH gradient two-dimensional gel electrophoresis. Electrophoresis 1999, 20:984-993. 10.1002/(SICI)1522-2683(19990101)20:4/5<984::AID-ELPS984>3.0.CO;2-R, 10344276.
27. Yasui H, Takai K, Yoshida R, Hayaishi O. Interferon enhances tryptophan metabolism by inducing pulmunary indoleamine 2,3-dioxygenase: Its possible occurrence in cancer patients. Proc Natl Acad Sci USA 1986, 83:6622-6626. 386556, 2428037, 10.1073/pnas.83.17.6622.
28. Boasso A, Herbeuval JP, Hardy AW, Winkler C, Shearer GM. Regulation of indoleamine 2,3-dioxygenase and tryptophanyl-tRNA-synthetase by CTLA-4-Fc in human CD4+ T cells. Blood 2005, 105:1574-1581. 10.1182/blood-2004-06-2089, 15466932.
29. Wakasugi K. Human tryptophanyl-tRNA synthetase binds with heme to enhance its aminoacylation activity. Biochemistry 2007, 46:11291-11298. 10.1021/bi7012068, 17877375.
30. Thomas SR, Salahifar H, Mashima R, Hunt NH, Richardson DR, Stocker R. Antioxidants inhibit indoleamine 2,3-dioxygenase in IFN-gamma-activated human macrophages: posttranslational regulation by pyrrolidine dithiocarbamate. J Immunol 2001, 166:6332-6340.
31. Rey MA, Duffy SP, Brown JK, Kennedy JA, Dick JE, Dror Y, Tailor CS. Enhanced alternative splicing of the FLVCR1 gene in Diamond Blackfan anemia disrupts FLVCR1 expression and function that are critical for erythropoiesis. Haematologica 2008, 93:1617-26. 10.3324/haematol.13359, 18815190.
32. Sampath P, Mazumder B, Seshadri V, Gerber CA, Chavatte L, Kinter M, Ting SM, Dignam JD, Kim S, Driscoll DM, Fox PL. Noncanonical function of glutamyl-prolyl-tRNA synthetase: gene-specific silencing of translation. Cell 2004, 119:195-208. 10.1016/j.cell.2004.09.030, 15479637.
33. Hunsucker SA, Mitchell BS, Spychala J. The 5'-nucleotidases as regulators of nucleotide and drug metabolism. Pharmacol Ther 2005, 107:1-30. 10.1016/j.pharmthera.2005.01.003, 15963349.
34. Bianchi V, Spychala J. Mammalian 5'-nucleotidases. J Biol Chem 2003, 278:46195-46198. 10.1074/jbc.R300032200, 12947102.
35. MacInnes AW, Amsterdam A, Whittaker CA, Hopkins N, Lees JA. Loss of p53 synthesis in zebrafish tumors with ribosomal protein gene mutations. Proc Natl Acad Sci USA 2008, 105:10408-10413. 2492501, 18641120, 10.1073/pnas.0805036105.
36. Aruga J, Minowa O, Yaginuma H, Kuno J, Nagai T, Noda T, Mikoshiba K. Mouse Zic1 is involved in cerebellar development. J Neurosci 1998, 18:284-293.
37. Aruga J, Mizugishi K, Koseki H, Imai K, Balling R, Noda T, Mikoshiba K. Zic1 regulates the patterning of vertebral arches in cooperation with Gli3. Mech Dev 1999, 89:141-150. 10.1016/S0925-4773(99)00220-8, 10559489.
38. Boria I, Quarello P, Avondo F, Garelli E, Aspesi A, Carando A, Campagnoli MF, Dianzani I, Ramenghi U. A new database for ribosomal protein genes which are mutated in Diamond-Blackfan Anemia. Hum Mutat 2008, 29:E263-270. 10.1002/humu.20864, 18781615.
39. Diamond-Blackfan anemia Leiden Open Variation Database. , http://www.dbagenes.unito.it/home.php
40. The R Project for Statistical Computing. , http://www.r-project.org/
41. BioConductor open source software for bioinformatics. , http://www.bioconductor.org/
42. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP. ummaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003, 31:Se15.
43. McClintick JN, Edenberg HJ. Effects of filtering by Present call on analysis of microarray experiments. BMC Bioinformatics 2006, 7:49. 1409797, 16448562, 10.1186/1471-2105-7-49.
44. Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J. TM4: a free, open-source system for microarray data management and analysis. Biotechniques 2003, 34(2):374-378.
45. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 2001, 98:5116-5121. 33173, 11309499, 10.1073/pnas.091062498.
46. Chu G, Narasimhan B, Tibshirani R, Tusher V. SAM "Significance Analysis of Microarrays" Users Guide and Technical Document. , http://www-stat.stanford.edu/~tibs/SAM/