title: MicroRNA expression profiling and functional annotation analysis of their targets in patients with type 1 diabetes mellitus.
abstract: Type 1 diabetes mellitus (T1DM) results from an autoimmune attack against the insulin-producing pancreatic β-cells, leading to elimination of insulin production. The exact cause of this disorder is still unclear. Although the differential expression of microRNAs (miRNAs), small non-coding RNAs that control gene expression in a post-transcriptional manner, has been identified in many diseases, including T1DM, only scarce information exists concerning miRNA expression profile in T1DM. Thus, we employed the microarray technology to examine the miRNA expression profiles displayed by peripheral blood mononuclear cells (PBMCs) from T1DM patients compared with healthy subjects. Total RNA extracted from PBMCs from 11 T1DM patients and nine healthy subjects was hybridized onto Agilent human miRNA microarray slides (V3), 8x15K, and expression data were analyzed on R statistical environment. After applying the rank products statistical test, the receiver-operating characteristic (ROC) curves were generated and the areas under the ROC curves (AUC) were calculated. To examine the functions of the differentially expressed (p-value<0.01, percentage of false-positives <0.05) miRNAs that passed the AUC cutoff value ≥ 0.90, the database miRWalk was used to predict their potential targets, which were afterwards submitted to the functional annotation tool provided by the Database for Annotation, Visualization, and Integrated Discovery (DAVID), version 6.7, using annotations from the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. We found 57 probes, corresponding to 44 different miRNAs (35 up-regulated and 9 down-regulated), that were differentially expressed in T1DM and passed the AUC threshold of 0.90. The hierarchical clustering analysis indicated the discriminatory power of those miRNAs, since they were able to clearly distinguish T1DM patients from healthy individuals. Target prediction indicated that 47 candidate genes for T1DM are potentially regulated by the differentially expressed miRNAs. After performing functional annotation analysis of the predicted targets, we observed 22 and 12 annotated KEGG pathways for the induced and repressed miRNAs, respectively. Interestingly, many pathways were enriched for the targets of both up- and down-regulated miRNAs and the majority of those pathways have been previously associated with T1DM, including many cancer-related pathways. In conclusion, our study indicated miRNAs that may be potential biomarkers of T1DM as well as provided new insights into the molecular mechanisms involved in this disorder.
authors: Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo - USP, Av. Bandeirantes 3900, Monte Alegre 14049-900, Ribeirão Preto, SP, Brazil.
authors: Paula
authors: P
authors: Takahashi
authors: Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo - USP, Av. Bandeirantes 3900, Monte Alegre 14049-900, Ribeirão Preto, SP, Brazil.
authors: Danilo J
authors: DJ
authors: Xavier
authors: Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo - USP, Av. Bandeirantes 3900, Monte Alegre 14049-900, Ribeirão Preto, SP, Brazil.
authors: Adriane F
authors: AF
authors: Evangelista
authors: Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo - USP, Av. Bandeirantes 3900, Monte Alegre 14049-900, Ribeirão Preto, SP, Brazil; Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo - USP, Av. Bandeirantes 3900, Monte Alegre 14040-901, Ribeirão Preto, SP, Brazil.
authors: Fernanda S
authors: FS
authors: Manoel-Caetano
authors: Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo - USP, Av. Bandeirantes 3900, Monte Alegre 14049-900, Ribeirão Preto, SP, Brazil.
authors: Claudia
authors: C
authors: Macedo
authors: Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo - USP, Av. Bandeirantes 3900, Monte Alegre 14049-900, Ribeirão Preto, SP, Brazil; Division of Clinical Immunology, Department of Medicine, Faculty of Medicine of Ribeirão Preto, University of São Paulo - USP, Av. Bandeirantes 3900, Monte Alegre 14048-900, Ribeirão Preto, SP, Brazil.
authors: Cristhianna V A
authors: CV
authors: Collares
authors: Department of Internal Medicine, Faculty of Medicine of Ribeirão Preto, University of São Paulo - USP, Av. Bandeirantes 3900, Monte Alegre 14048-900, Ribeirão Preto, SP, Brazil.
authors: Maria C
authors: MC
authors: Foss-Freitas
authors: Department of Internal Medicine, Faculty of Medicine of Ribeirão Preto, University of São Paulo - USP, Av. Bandeirantes 3900, Monte Alegre 14048-900, Ribeirão Preto, SP, Brazil.
authors: Milton C
authors: MC
authors: Foss
authors: Division of Clinical Immunology, Department of Medicine, Faculty of Medicine of Ribeirão Preto, University of São Paulo - USP, Av. Bandeirantes 3900, Monte Alegre 14048-900, Ribeirão Preto, SP, Brazil.
authors: Diane M
authors: DM
authors: Rassi
authors: Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo - USP, Av. Bandeirantes 3900, Monte Alegre 14049-900, Ribeirão Preto, SP, Brazil; Division of Clinical Immunology, Department of Medicine, Faculty of Medicine of Ribeirão Preto, University of São Paulo - USP, Av. Bandeirantes 3900, Monte Alegre 14048-900, Ribeirão Preto, SP, Brazil.
authors: Eduardo A
authors: EA
authors: Donadi
authors: Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo - USP, Av. Bandeirantes 3900, Monte Alegre 14049-900, Ribeirão Preto, SP, Brazil; Disciplines of Genetics and Molecular Biology, Department of Morphology, Faculty of Dentistry of Ribeirão Preto, University of São Paulo - USP, Av. Do Café s/n, Monte Alegre 14040-904, Ribeirão Preto, SP, Brazil.
authors: Geraldo A
authors: GA
authors: Passos
authors: Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo - USP, Av. Bandeirantes 3900, Monte Alegre 14049-900, Ribeirão Preto, SP, Brazil; Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo - USP, Av. Bandeirantes 3900, Monte Alegre 14040-901, Ribeirão Preto, SP, Brazil. Electronic address: etshojo@usp.br.
authors: Elza T
authors: ET
authors: Sakamoto-Hojo
mesh_terms: D000293:Adolescent; D000328:Adult; D015415:Biomarkers / Q000378:metabolism*; D016022:Case-Control Studies; D016000:Cluster Analysis; D019295:Computational Biology; D003922:Diabetes Mellitus, Type 1 / Q000235:genetics*; D005260:Female; D005500:Follow-Up Studies; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000378:metabolism; D008297:Male; D035683:MicroRNAs / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D011379:Prognosis; D055815:Young Adult
chemical_list: D015415:Biomarkers; D035683:MicroRNAs
keywords: Expression profile; Functional annotation analysis; Microarray; T1DM candidate genes; Type 1 diabetes mellitus; microRNA