Identification of dysregulated microRNAs in lymphocytes from children with Down syndrome

Gene

Volumn 530, Issue 2, 2013, Pages 278-286

  Xu, Yong ^a,b   Li, Wuxian ^b   Liu, Xueyan ^c   Chen, Hong ^c   Tan, Kuibi ^c   Chen, Yuyu ^c   Tu, Zhiguang ^b   Dai, Yong ^b,c  

^a Shenzhen   (China)

^b CHONGQING MEDICAL UNIVERSITY   (China)

^c SHENZHEN PEOPLE'S HOSPITAL   (China)

Author keywords

Deep sequencing technology; Down syndrome; Lymphocytes; MicroRNA

Indexed keywords

MICRORNA;

ARTICLE; B LYMPHOCYTE; CHILD; CHROMOSOME 21; CONTROLLED STUDY; DOWN SYNDROME; GENE CLUSTER; GENE FREQUENCY; GENE LIBRARY; GENE OVEREXPRESSION; GENE SEQUENCE; HIGH THROUGHPUT SEQUENCING; HUMAN; LYMPHOCYTE; LYMPHOCYTE DIFFERENTIATION; LYMPHOID ORGAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; T LYMPHOCYTE; THYMUS;

DCS; DEEP SEQUENCING TECHNOLOGY; DENDRITIC CELLS; DOWN SYNDROME; DS; GENE ONTOLOGY; GO; HEMATOPOIETIC STEM CELLS; HSA21; HSCS; HUMAN CHROMOSOME 21; LYMPHOCYTES; MICRORNA; MIRNA-INDUCED SILENCING COMPLEXES; NT; NUCLEOTIDES; PAGE; POLYACRYLAMIDE GEL ELECTROPHORESIS; REVERSE TRANSCRIPTASE-POLYMERASE CHAIN REACTION; RISC; RT-PCR; SMALL RNA; SRNA; TPM; TRANSCRIPTS PARTS PER MILLION;

B-LYMPHOCYTES; BASE SEQUENCE; CASE-CONTROL STUDIES; CELL DIFFERENTIATION; CHILD; CHILD, PRESCHOOL; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN, PAIR 21; DOWN SYNDROME; GENE EXPRESSION REGULATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; IMMUNITY, INNATE; MICRORNAS; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; T-LYMPHOCYTES;

EID: 84884532955     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2013.07.055     Document Type: Article

References (71)

1. Akao Y., Nakagawa Y., Kitade Y., Kinoshita T., Naoe T. Downregulation of microRNAs-143 and -145 in B-cell malignancies. Cancer Sci. 2007, 98:1914-1920.
2. Akao Y., Nakagawa Y., Iio A., Naoe T. Role of microRNA-143 in Fas-mediated apoptosis in human T-cell leukemia Jurkat cells. Leuk. Res. 2009, 33:1530-1538.
3. Altuvia Y., et al. Clustering and conservation patterns of human microRNAs. Nucleic Acids Res. 2005, 33:2697-2706.
4. Astier A., Trescol-Biemont M.C., Azocar O., Lamouille B., Rabourdin-Combe C. Cutting edge: CD46, a new costimulatory molecule for T cells, that induces p120CBL and LAT phosphorylation. J. Immunol. 2000, 164:6091-6095.
5. Audic S., Claverie J.M. The significance of digital gene expression profiles. Genome Res. 1997, 7:986-995.
6. Avanzini M.A., et al. Humoral immunodeficiencies in Down syndrome: serum IgG subclass and antibody response to hepatitis B vaccine. Am. J. Med. Genet. Suppl. 1990, 7:231-233.
7. Bandiera S., Hatem E., Lyonnet S., Henrion-Caude A. microRNAs in diseases: from candidate to modifier genes. Clin. Genet. 2010, 77:306-313.
8. Banerjee R., et al. Adaptive immune neuroprotection in G93A-SOD1 amyotrophic lateral sclerosis mice. PLoS One 2008, 3:e2740.
9. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297.
10. Bazzoni F., et al. Induction and regulatory function of miR-9 in human monocytes and neutrophils exposed to proinflammatory signals. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:5282-5287.
11. Bissels U., Bosio A., Wagner W. MicroRNAs are shaping the hematopoietic landscape. Haematologica 2011, 97:160-167.
12. Boldin M.P., Baltimore D. MicroRNAs, new effectors and regulators of NF-kappaB. Immunol. Rev. 2012, 246:205-220.
13. Burgio G.R., Ugazio A.G., Nespoli L., Marcioni A.F., Bottelli A.M., Pasquali F. Derangements of immunoglobulin levels, phytohemagglutinin responsiveness and T and B cell markers in Down's syndrome at different ages. Eur. J. Immunol. 1975, 5:600-603.
14. Burgio G.R., Lanzavecchia A., Maccario R., Vitiello A., Plebani A., Ugazio A.G. Immunodeficiency in Down's syndrome: T-lymphocyte subset imbalance in trisomic children. Clin. Exp. Immunol. 1978, 33:298-301.
15. Castillo-Davis C.I., Hartl D.L. GeneMerge-post-genomic analysis, data mining, and hypothesis testing. Bioinformatics 2003, 19:891-892.
16. Chen C.Z., Li L., Lodish H.F., Bartel D.P. MicroRNAs modulate hematopoietic lineage differentiation. Science 2004, 303:83-86.
17. Chen X., et al. Identification and characterization of novel amphioxus microRNAs by Solexa sequencing. Genome Biol. 2009, 10:R78.
18. Dai R., Ahmed S.A. MicroRNA, a new paradigm for understanding immunoregulation, inflammation, and autoimmune diseases. Transl. Res. 2011, 157:163-179.
19. Dehingh Y., et al. Intrinsic abnormalities of lymphocyte counts in children with Down syndrome. J. Pediatr. 2005, 147:744-747.
20. Egawa T., Tillman R.E., Naoe Y., Taniuchi I., Littman D.R. The role of the Runx transcription factors in thymocyte differentiation and in homeostasis of naive T cells. J. Exp. Med. 2007, 204:1945-1957.
21. Elton T.S., Sansom S.E., Martin M.M. Trisomy-21 gene dosage over-expression of miRNAs results in the haploinsufficiency of specific target proteins. RNA Biol. 2010, 7:540-547.
22. Garrison M.M., Jeffries H., Christakis D.A. Risk of death for children with down syndrome and sepsis. J. Pediatr. 2005, 147:748-752.
23. Gaziel-Sovran A., et al. miR-30b/30d regulation of GalNAc transferases enhances invasion and immunosuppression during metastasis. Cancer Cell 2011, 20:104-118.
24. Gerrits A., et al. Genetic screen identifies microRNA cluster 99b/let-7e/125a as a regulator of primitive hematopoietic cells. Blood 2012, 119:377-387.
25. Giannone S., et al. Gene expression profile analysis in human T lymphocytes from patients with Down syndrome. Ann. Hum. Genet. 2004, 68:546-554.
26. Gracias D.T., Katsikis P.D. MicroRNAs: key components of immune regulation. Adv. Exp. Med. Biol. 2011, 780:15-26.
27. Growney J.D., et al. Loss of Runx1 perturbs adult hematopoiesis and is associated with a myeloproliferative phenotype. Blood 2005, 106:494-504.
28. Guo L., Sun B., Wu Q., Yang S., Chen F. miRNA-miRNA interaction implicates for potential mutual regulatory pattern. Gene 2012, 511:187-194.
29. Gururajan M., et al. MicroRNA 125b inhibition of B cell differentiation in germinal centers. Int. Immunol. 2010, 22:583-592.
30. Hassold T.J., Jacobs P.A. Trisomy in man. Annu. Rev. Genet. 1984, 18:69-97.
31. Havelange V., Garzon R. MicroRNAs: emerging key regulators of hematopoiesis. Am. J. Hematol. 2010, 85:935-942.
32. Huang da W., Sherman B.T., Lempicki R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2009, 4:44-57.
33. Jain J., McCaffrey P.G., Valge-Archer V.E., Rao A. Nuclear factor of activated T cells contains Fos and Jun. Nature 1992, 356:801-804.
34. Jiang P., Wu H., Wang W., Ma W., Sun X., Lu Z. MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res. 2007, 35:W339-W344.
35. Keck-Wherley J., et al. Abnormal MicroRNA expression in Ts65Dn hippocampus and whole blood: contributions to down syndrome phenotypes. Dev Neurosci. 2011, 33:451-467.
36. Kozomara A., Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 2011, 39:D152-D157.
37. Kuhn D.E., et al. Human chromosome 21-derived miRNAs are overexpressed in Down syndrome brains and hearts. Biochem. Biophys. Res. Commun. 2008, 370:473-477.
38. Kuhn D.E., et al. Chromosome 21-derived microRNAs provide an etiological basis for aberrant protein expression in human Down syndrome brains. J. Biol. Chem. 2010, 285:1529-1543.
39. Kusters M.A., Verstegen R.H., Gemen E.F., de Vries E. Intrinsic defect of the immune system in children with Down syndrome: a review. Clin. Exp. Immunol. 2009, 156:189-193.
40. Levin S., et al. Thymic deficiency in Down's syndrome. Pediatrics 1979, 63:80-87.
41. Li C.M., et al. Cell type-specific over-expression of chromosome 21 genes in fibroblasts and fetal hearts with trisomy 21. BMC Med. Genet. 2006, 7:24.
42. Li G., Luna C., Qiu J., Epstein D.L., Gonzalez P. Alterations in microRNA expression in stress-induced cellular senescence. Mech. Ageing Dev. 2009, 130:731-741.
43. Li R., et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009, 25:1966-1967.
44. Li X., Sanda T., Look A.T., Novina C.D., von Boehmer H. Repression of tumor suppressor miR-451 is essential for NOTCH1-induced oncogenesis in T-ALL. J. Exp. Med. 2011, 208:663-675.
45. Li Y.Y., Alexandrov P.N., Pogue A.I., Zhao Y., Bhattacharjee S., Lukiw W.J. miRNA-155 upregulation and complement factor H deficits in Down's syndrome. Neuroreport 2012, 23:168-173.
46. Liu X., et al. MicroRNA-148/152 impair innate response and antigen presentation of TLR-triggered dendritic cells by targeting CaMKIIalpha. J. Immunol. 2010, 185:7244-7251.
47. Livak K.J., Schmittgen T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001, 25:402-408.
48. Lu L.F., Liston A. MicroRNA in the immune system, microRNA as an immune system. Immunology 2009, 127:291-298.
49. Malago W., et al. Gene expression profile of human Down syndrome leukocytes. Croat. Med. J. 2005, 46:647-656.
50. Mattes J., Collison A., Plank M., Phipps S., Foster P.S. Antagonism of microRNA-126 suppresses the effector function of TH2 cells and the development of allergic airways disease. Proc. Natl. Acad. Sci. U. S. A. 2009, 106:18704-18709.
51. Mayoral R.J., Pipkin M.E., Pachkov M., van Nimwegen E., Rao A., Monticelli S. MicroRNA-221-222 regulate the cell cycle in mast cells. J. Immunol. 2009, 182:433-445.
52. Morin R.D., et al. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res. 2008, 18:610-621.
53. Murphy M., Insoft R.M., Pike-Nobile L., Epstein L.B. A hypothesis to explain the immune defects in Down syndrome. Prog. Clin. Biol. Res. 1995, 393:147-167.
54. O'Connell R.M., et al. Sustained expression of microRNA-155 in hematopoietic stem cells causes a myeloproliferative disorder. J. Exp. Med. 2008, 205:585-594.
55. Ooi A.G., Sahoo D., Adorno M., Wang Y., Weissman I.L., Park C.Y. MicroRNA-125b expands hematopoietic stem cells and enriches for the lymphoid-balanced and lymphoid-biased subsets. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:21505-21510.
56. Patterson D. Molecular genetic analysis of Down syndrome. Hum. Genet. 2009, 126:195-214.
57. Philip R., Berger A.C., McManus N.H., Warner N.H., Peacock M.A., Epstein L.B. Abnormalities of the in vitro cellular and humoral responses to tetanus and influenza antigens with concomitant numerical alterations in lymphocyte subsets in Down syndrome (trisomy 21). J. Immunol. 1986, 136:1661-1667.
58. Ram G., Chinen J. Infections and immunodeficiency in Down syndrome. Clin. Exp. Immunol. 2011, 164:9-16.
59. Rodriguez A., et al. Requirement of bic/microRNA-155 for normal immune function. Science 2007, 316:608-611.
60. Sethupathy P., et al. Human microRNA-155 on chromosome 21 differentially interacts with its polymorphic target in the AGTR1 3' untranslated region: a mechanism for functional single-nucleotide polymorphisms related to phenotypes. Am. J. Hum. Genet. 2007, 81:405-413.
61. Shen W.F., Hu Y.L., Uttarwar L., Passegue E., Largman C. MicroRNA-126 regulates HOXA9 by binding to the homeobox. Mol. Cell. Biol. 2008, 28:4609-4619.
62. Sommer C.A., Pavarino-Bertelli E.C., Goloni-Bertollo E.M., Henrique-Silva F. Identification of dysregulated genes in lymphocytes from children with Down syndrome. Genome 2008, 51:19-29.
63. Stittrich A.B., et al. The microRNA miR-182 is induced by IL-2 and promotes clonal expansion of activated helper T lymphocytes. Nat. Immunol. 2010, 11:1057-1062.
64. Szulwach K.E., Jin P., Alisch R.S. Noncoding RNAs in mental retardation. Clin. Genet. 2009, 75:209-219.
65. Vaz C., et al. Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood. BMC Genomics 2010, 11:288.
66. Ventura A., et al. Targeted deletion reveals essential and overlapping functions of the miR-17 through 92 family of miRNA clusters. Cell 2008, 132:875-886.
67. Vigorito E., et al. microRNA-155 regulates the generation of immunoglobulin class-switched plasma cells. Immunity 2007, 27:847-859.
68. Wong W.F., Kohu K., Chiba T., Sato T., Satake M. Interplay of transcription factors in T-cell differentiation and function: the role of Runx. Immunology 2011, 132:157-164.
69. Zhang H., et al. Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach. PLoS One 2009, 4:e6849.
70. Zhao S., et al. MicroRNA-126 regulates DNA methylation in CD4+ T cells and contributes to systemic lupus erythematosus by targeting DNA methyltransferase 1. Arthritis Rheum. 2011, 63:1376-1386.
71. Zhou B., Wang S., Mayr C., Bartel D.P., Lodish H.F. miR-150, a microRNA expressed in mature B and T cells, blocks early B cell development when expressed prematurely. Proc. Natl. Acad. Sci. U. S. A. 2007, 104:7080-7085.