Genome-wide small noncoding RNA profiling of pediatric high-grade gliomas reveals deregulation of several miRNAs, identifies downregulation of snoRNA cluster HBII-52 and delineates H3F3A and TP53 mutant-specific miRNAs and snoRNAs

International Journal of Cancer

Volumn 137, Issue 10, 2015, Pages 2343-2353

  Jha, Prerana ^a   Agrawal, Rahul ^a   Pathak, Pankaj ^b   Kumar, Anupam ^b   Purkait, Suvendu ^b   Mallik, Supriyo ^c   Suri, Vaishali ^b   Chand Sharma, Mehar ^b   Gupta, Deepak ^b   Suri, Ashish ^b   Sharma, B S ^b   Julka, P K ^c   Kulshreshtha, Ritu ^a   Sarkar, Chitra ^b  

^a INDIAN INSTITUTE OF TECHNOLOGY DELHI   (India)

^b ALL INDIA INSTITUTE OF MEDICAL SCIENCES   (India)

^c INSTITUTE ROTARY CANCER HOSPITAL   (India)

Author keywords

H3F3A; miRNA; pediatric GBM; small nucleolar RNA; TP53

Indexed keywords

HISTONE H3; MESSENGER RNA; MICRORNA; MICRORNA 106A; MICRORNA 106B; MICRORNA 17; MICRORNA 25; MICRORNA 363; MICRORNA 379; MICRORNA 656; MICRORNA 92; PROTEIN P53; SMAD2 PROTEIN; SMAD3 PROTEIN; SMALL NUCLEOLAR RNA; UNCLASSIFIED DRUG; HISTONE; TP53 PROTEIN, HUMAN;

ADOLESCENT; ADULT; ARTICLE; CANCER SURVIVAL; CHILD; CLINICAL ARTICLE; DOWN REGULATION; FEMALE; GENE EXPRESSION; GENE TARGETING; GENOME ANALYSIS; GLIOBLASTOMA; GLIOMA; H3F3A GENE; HUMAN; HUMAN TISSUE; MALE; METHYLATION; MICROARRAY ANALYSIS; OVERALL SURVIVAL; PREDICTION; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; RNA ANALYSIS; SIGNAL TRANSDUCTION; TUMOR GENE; TUMOR SUPPRESSOR GENE; UPREGULATION; BRAIN TUMOR; COMPARATIVE STUDY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; MUTATION; PATHOLOGY; PRESCHOOL CHILD; PROCEDURES; SURVIVAL;

ADOLESCENT; ADULT; BRAIN NEOPLASMS; CHILD; CHILD, PRESCHOOL; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GLIOMA; HISTONES; HUMANS; MICRORNAS; MUTATION; RNA, SMALL NUCLEOLAR; SURVIVAL ANALYSIS; TUMOR SUPPRESSOR PROTEIN P53;

EID: 84941943097     PISSN: 00207136     EISSN: 10970215     Source Type: Journal    
DOI: 10.1002/ijc.29610     Document Type: Article

References (51)

1. Kanu OO, Hughes B, Di C, et al., Glioblastoma multiforme oncogenomics and signaling pathways. Clin Med Oncol 2009; 3: 39-52.
2. Kaatsch P, Kaletsch U, Spix C, et al., Annual Report 1998 German Childhood Cancer Resigtry. Mainz: Lindner, 1999.
3. Packer RJ,. Primary central nervous system tumors in children. Curr Treat Options Neurol 1999; 1: 395-408.
4. Broniscer A, Gajjar A,. Supratentorial high-grade astrocytoma and diffuse brainstem glioma: two challenges for the pediatric oncologist. Oncologist 2004; 9: 197-206.
5. The Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 2008; 455: 1061.
6. Jha P, Suri V, Singh G, et al., Characterization of molecular genetic alterations in GBMs highlights a distinctive molecular profile in young adults. Diagn Mol Pathol 2011; 20: 225-32.
7. Schwartzentruber J, Korshunov A, Liu XY, et al., Driver mutations in histone h3.3 and chromatin remodelling genes in paediatric glioblastoma [published correction appears in nature.2012;484:130]. Nature 2012; 482: 226-31.
8. Jha P, Pia Patric IR, Shukla S, et al., Genome-wide methylation profiling identifies an essential role of reactive oxygen species in pediatric glioblastoma multiforme and validates a methylome specific for H3 histone family 3A with absence of G-CIMP/isocitrate dehydrogenase 1 mutation. Neuro Oncol 2014; 16: 1607-17.
9. Sturm D, Witt H, Hovestadt V, et al., Hotspot mutations in H3F3A and idh1 define distinct epigenetic and biological subgroups of glioblastoma. Cancer Cell 2012; 22: 425-37.
10. Drake LG, Min L,. MicroRNAs in glioblastoma multiforme: profiling studies and therapeutic Impacts. Mol Cell Pharmacol 2011; 3: 93-105.
11. Singh SK, Vartanian A, Burrell K, et al., A microRNA link to glioblastoma heterogeneity. Cancers 2012; 4: 846-72.
12. Karsy M, Arslan E, Moy F,. Current progress on understanding MicroRNAs in glioblastoma multiforme. Genes Cancer 2012; 3: 3-15.
13. Mizoguchi M, Guan Y, Yoshimoto K, et al., MicroRNAs in human malignant gliomas. J Oncol 2012; 2012: 732874. doi: 10.1155/2012/732874. Epub 2012 Jul 10.
14. Møller HG, Rasmussen AP, Andersen HH, et al., A systematic review of microRNA in glioblastoma multiforme: micro-modulators in the mesenchymal mode of migration and invasion. Mol Neurobiol 2013; 47: 131-44.
15. Skalsky RL, Cullen BR,. Reduced expression of brain-enriched micrornas in glioblastomas permits targeted regulation of a cell death gene. Plos One 2011; 6: e24248.
16. Srinivasan S, Patric IR, Somasundaram K,. A ten-microRNA expression signature predicts survival in glioblastoma. PLoS One 2011; 6: e17438.
17. Kim TM, Huang W, Park R, et al., A developmental taxonomy of glioblastoma defined and maintained by MicroRNAs. Cancer Res 2011; 71: 3387-99.
18. Birks DK, Barton VN, Donson AM, et al., Survey of MicroRNA expression in pediatric brain tumors. Pediatr Blood Cancer 2011; 56: 211-6.
19. Miele E, Buttarelli FR, Arcella A, et al., High-throughput microRNA profiling of pediatric high-grade gliomas. Neuro Oncol 2014; 16: 228-40.
20. Williams GT, Farzaneh F,. Are snoRNAs and snoRNA host genes new players in cancer? Nat Rev Cancer 2012; 12: 84-8.
21. Kiss T,. Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions. Cell 2002; 109: 145-8.
22. Chang LS, Lin SY, Lieu AS, et al., Differential expression of human 5S snoRNA genes. Biochem Biophys Res Commun 2002; 299: 196-200.
23. Liao J, Yu L, Mei Y, et al., Small nucleolar RNA signatures as biomarkers for non-small-cell lung cancer. Mol Cancer 2010; 9: 198.
24. Valleron W, Laprevotte E, Gautier EF, et al., Specific small nucleolar RNA expression profiles in acute leukemia. Leukemia 2012; 26: 2052-60.
25. Ronchetti D, Todoerti K, Tuana G, et al., The expression pattern of small nucleolar and small cajal body-specific RNAs characterizes distinct molecular subtypes of multiple myeloma. Blood Cancer J 2012; 2: e96.
26. Kleihues P, Louis DN, Wiestler OD, et al., WHO grading of tumours of the central nervous system. In:, Louis DN, Ohgaki H, Wiestler OD, Cavenee WK, eds. WHO classification of tumours of the central nervous system, 4th edn. Lyon: IARC, 2007. 10-49.
27. Lu M, Zhang Q, Deng M, et al., An analysis of human MicroRNA and disease associations. PLoS One 2008; 3: e3420.
28. Lu TP, Lee CY, Tsai MH, et al., miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets. PLoS One 2012; 7: e42390.
29. Vlachos IS, Kostoulas N, Vergoulis T, et al., DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways. Nucleic Acids Res 2012; 40: W498-504.
30. Li B, He H, Tao BB, et al., Knockdown of cdk6 enhances glioma sensitivity to chemotherapy. Oncol Rep 2012; 28: 909-14.
31. Verginelli F, Perin A, Dali R, et al., Transcription factors foxg1 and groucho/TLE promote glioblastoma growth. Nat Commun 2013; 4: 2956.
32. Halatsch ME, Löw S, Mursch K, et al., Candidate genes for sensitivity and resistance of human glioblastoma multiforme cell lines to erlotinib. Laboratory investigation. J Neurosurg 2009; 111: 211-8.
33. Chu SH, Ma YB, Feng DF, et al., Correlation between satb1 and Bcl-2 expression in human glioblastoma multiforme. Mol Med Rep 2013; 7: 139-43.
34. D'Urso PI, D'Urso OF, Storelli C, et al., miR-155 is up-regulated in primary and secondary glioblastoma and promotes tumour growth by inhibiting GABA receptors. Int J Oncol 2012; 41: 228-34.
35. Liu Z, Liu Y, Li L, et al., MiR-7-5p is frequently downregulated in glioblastoma microvasculature and inhibits vascular endothelial cell proliferation by targeting raf1. Tumour Biol 2014; 35: 10177-84.
36. Northcott PA, Fernandez LA, Hagan JP, et al., The miR-17/92 polycistron is up-regulated in sonic hedgehog-driven medulloblastomas and induced by N-myc in sonic hedgehog-treated cerebellar neural precursors. Cancer Res 2009; 69: 3249-55.
37. Fontana L, Fiori ME, Albini S, et al., Antagomir-17-5p abolishes the growth of therapy-resistant neuroblastoma through p21 and BIM. PLoS One 2008; 3: e2236.
38. Laddha SV, Nayak S, Paul D, et al., Genome-wide analysis reveals downregulation of miR-379/miR-656 cluster in human cancers. Biol Direct 2013; 8: 10.
39. Lucon DR, Rocha Cde S, Craveiro RB, et al., Downregulation of 14q32 microRNAs in primary human desmoplastic medulloblastoma. Front Oncol 2013; 3: 254.
40. Hu J, Jiang C, Ng HK, et al., Chromosome 14q may harbor multiple tumor suppressor genes in primary glioblastoma multiforme. Chin Med J 2002; 115: 1201-4.
41. Gattolliat CH, Thomas L, Ciafrè SA, et al., Expression of miR-487b and miR-410 encoded by 14q32.31 locus is a prognostic marker in neuroblastoma. Br J Cancer 2011; 105: 1352-61.
42. Kulshreshtha R, Davuluri RV, Calin GA, et al., A microRNA component of the hypoxic response. Cell Death Differ 2008; 15: 667-71.
43. Swarbrick A, Woods SL, Shaw A, et al., miR-380-5p represses p53 to control cellular survival and is associated with poor outcome in MYCN-amplified neuroblastoma. Nat Med 2010; 16: 1134-40.
44. Paugh BS, Qu C, Jones C, et al., Integrated molecular genetic profiling of pediatric high-grade gliomas reveals key differences with the adult disease. J Clin Oncol 2010; 28: 3061-8.
45. Bruna A, Darken RS, Rojo F, et al., High TGF beta-smad activity confers poor prognosis in glioma patients and promotes cell proliferation depending on the methylation of the PDGF-B gene. Cancer Cell 2007; 11: 147-60.
46. Ganci F, Sacconi A, Bossel Ben-Moshe N, et al., Expression of tp53 mutation-associated microRNAs predicts clinical outcome in head and neck squamous cell carcinoma patients. Ann Oncol 2013; 24: 3082-8.
47. Bueno MJ, Malumbres M,. MicroRNAs and the cell cycle. Biochim Biophys Acta 2011; 1812: 592-601.
48. Ronchetti D, Mosca L, Cutrona G, et al., Small nucleolar RNAs as new biomarkers in chronic lymphocytic leukemia. BMC Med Genomics 2013; 6: 27.
49. Kishore S, Stamm S,. The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science 2006; 311: 230-2.
50. Nahkuri S, Taft RJ, Korbie DJ, et al., Molecular evolution of the HBII-52 snoRNA cluster. J Mol Biol 2008; 381: 810-5.
51. Freed-Pastor WA, Prives C,. Mutant p53: one name, many proteins. Genes Dev 2012; 26: 1268-86.