Bioinformatics Analysis Of Differential MicroRNAs Comprehensive Regulatory Network In B-cell Acute Lymphoblastic Leukemia

Caused by malignant blood diseases, B-cell acute lymphoblastic leukemia (B-ALL), is the most common type in acute lymphoblastic leukemia, is an abnormal proliferation of B lymphocytes in the blood or bone marrow. B acute lymphoblastic leukemia is the most common tumor in children and occurs relatively rare in adults. In recent years, based on the risk stratification treatment guidance, more than 85% children with B-ALL has been cured, but aslo have some children, not be considered as high-risk still relapse after treatment. Compared with the child, the survival rate of dult with B-ALL is clearly less than 40%. With the development of the whole genome genetic analysis technology and other technology, we know about the pathogenesis of B-ALL was mainly in chromosome aberration and gene expression abnormalities. Chromosome aberration is including numberical aberration and structural aberration in chromosome. Numberical aberration of chromosomes is aneuploidy such as hyperdiploidy and hypodiploidy etc. The chromosome structural aberration consist of gene loss, such as ATM、IKZF1 and CDKN2A gene, and chromosomal rearrangement, which was resulting in the translocation such as t (9; 22) (q34; q11.2) BCRABL1, t (12; 21) (p13; q22) ETV6-RUNX1, t (1; 19) (q23; p13) TCF3-PBX1 and MLL gene rearrangements. Gene expression abnormalities are including abnormal expression of BCL2, FLT3 and HOXA and other genes. Many of these genes have been elucidated it function and biological processes, but how them take participate in malignant transformation and multistep pathogenesis of regulatory mechanisms still little know. So far, the pathogenesis of B-ALL is still not completely clear, and for in-depth study of the pathogenesis is conducive to the development of more advanced diagnosis and treatment methods.Regulation of gene expression is very necessary for the stability and maintenance of all cells; otherwise, abnormal regulation of gene expression is associated with pathogenesis of many cancers. The regulation of growth, differentiation and maturation in hematopoietic cell is reated to in multi-factor, multi-level complex regulation, including gene regulation. To maintain balancing in normal hematopoiesis, regulation of blood was achieved by different regulating ways of hematopoietic cell proliferation, differentiation, migration, homing and apoptosis. The all aspects of cell proliferation and differentiation in hematopoietic stem cells and progenitor cells are subject to complex multi-gene regulation. Currently, a complex network interaction with multiple genes have been discovered a relation with B-cell acute lymphoblastic leukemia. MicroRNA (miRNA), long non-coding RNA (incRNA) and transcription factor (TF) for regulation of gene expression is an important part in the complex network.With the human genome project pecforming, gene chip has developed rapidly. It is the high-tech molecular biology including high through put, high integration, miniaturization, parallelization, automation and diversification features. As more development of chip technology, different types of chips have emerged. Commercial development more and more microRNA chips and more widely used. For example, miRNA expression chip has became a powerful tool for research miRNA because its features of high-throughput, specificity, high sensitivity, and also gradually become the most universal and effective detection method in research the expression of miRNA. With the rapid growth of chip data, it is need to collection, storage and management of those datas. There are Gene Expression Omnibus (GEO), Stanford Microarray Database (SMD), ArrayEpress gene expression data and other relevant public database; and these public databases provided chip data query, retrieval and downloading. The growth of chip data led to the development of microarray data analysis software. Currently microarray data analysis softwares are subdivided into the free open software and commercialized of microarray data analysis software. The application of microarray data analysis software provides a very important help in the entire data analysis. Recently, more and more people are deeply undergoing miRNA study, prompting the related miRNA bioinformatics rapid development, and formation of many related miRNA databases and software, such as the target gene of miRNA database, the interaction between miRNA with non-coding RNA database and the database of transcription factor regulation miRNA. These developments of miRNA-related bioinformatics tools are beneficial to our study which we used biological information to build a miRNA-centric of comprehensive regulation networks.First, the miRNA microarray data GSE51908 which is related B-cell acute lymphoblastic leukemia was download from the GEO public databases of National Center for Biotechnology formation (NCBI). Then GSE51908 dataset as analysis materials was to differentical expression analysis by the bioinformatics software of Qlucore Omics Explorer 3.0. Next, these differences miRNAs were bioinformatics analysis of the miRNAs target gene, LncRNA-miRNAs internation and transcription factor regulation miRNAs relationships. The analysis of differentially expressed miRNA target genes, we used the StarBase database which contains a plurality of prediction softwares and integrated the data of crosslinking immunoprecipitation sequencing (CLIP-Seq) and mRNA degradation sequencing (Degradome-Seq) experiment to support the miRNA target, and MiRNATarBas databases that specialized combination of integration verification data and inclusion other similar databases. The combination analysis is accurate and comprehensive analysisfor these differences miRNAs target genes, and the results received a total of 631 miRNAs regulated target genes. Then bioinformatics analysis the relationship betwent long non-coding RNA with miRNA by StarBase v2.0 software, which systematically identify the interaction between the long non-coding RNA and miRNA from 108 high-throughput sequencing data of CLIP-Seq experiments, and we obtein 161 the differentially miRNAs-long non-coding RNA interactions. Then we used ChlPBase database to analysis the regulation of transcription factor (TF) and differentially miRNAs. The ChIPBase database is a novel database that researchers developed and discovery the regulatory relationship between transcription factor with miRNA from high-throughput sequencing data of chromatin immunoprecipitation finishing with the second-generation sequencing (ChIP-seq) which detected tens of thousands of transcription factor binding sites (TFBS), and we got 301 regulation between difference miRNAs and transcription factors. Finally, the regulatory data including these target genes of differentially expressed miRNAs, the miRNAs-LncRNA and the TF-miRNAs by a variety of bioinformatics tools of comprehensive analysis, were used to build the differentially expressed miRNA-centered comprehensive regulatiory network by the visualization software of cytoscape. The further analysis was to identify the hub target in the miRNA-centered comprehensive regulatiory network. In addition, the target gene of some differences miRNAs in were analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis by the database for annotation, visualization and integrated discovery (DAVID)database.And then the hub target literature mining analysis, and then to find the core miRNAs in this comprehensive regulatory network.Through the above comprehensive analysis of a variety of bioinformatics tools, we got a total of 16 differences miRNAs form GSE51908 data related B-cell acute lymphoblastic leukemia, which of seven miRNAs upregulated and 8 miRNAs downregulated. According to the comprehensive regulatory network hub target analysis, found 20 hub targets in the comprehensive regulatory networks, only one is a long non-coding RNA XIST, the remaining 19 are all transcription factors.There is no hub target belong to the node of target gene. In the hub target of transcription factor PU.1 palys an important role in the selection process of hematopoietic stem cell lineage developmented the lymphatic system. The deletion of PU.1 cause disorder differentiation of hematopoietic stem cell into lymphoid.The PU.1 expression disorder impaired development of blood cells and caused human actue leukemia.All of PU.l study are compatible with that we believe hub targets played an important role in the development of B-ALL.By constructing difference miRNA-centric comprehensiv regulatory network, we can clear know that Hsa-miR-29a, hsa-miR-130a and hsa-miR-181c regulated of many long non-coding RNA, including XIST. Hub target XIST literature search showed that the XIST lost results in X reactivation and induces significantly higher abundance of X-linked genes including hematopoiesis regulators were downregulted such as Flt3. Transcription factor Yin Yang-1 (YY1) is capable of binding the XIST by specific sequences binding sites, prompting the X chromosome inactivation. The hsa-miR-29a inhibited the expression of YY1, and high expression of YY1 and NF-kB can inhibit the expression of hsa-miR-29a. Therefore, we believe that hsa-miR-29a by the interaction with NF κ B and YY1 negative regulation that lncR XIST regulated the inactive X chromosome, andpaticipate in the development of B-ALL.Accoding to the comprehensive regulatory network, Hsa-miR-181a-2, hsa-miR-181b-2 and hsa-miR-663 regulated a large number of transcription factors, including CDX2, YY1. The node of homeobox gene caudal-related homeobox transcription fact 2 (CDX2), in hub target, is connected to the 11 differentially expressed miRNA and is the most central of hub targets. We found that the transcription factor CDX2 regulated hsa-miR-181 famliy, and CDX2 gene is target gene of hsa-miR-181 c. There is feedback control in internation between hsa-miR-181 famliy and CDX2. The CDX2 was to further analysis including literature mining, found that the CDX2 is related the prognosis of acute leukemia, and also reltaed the Wnt signaling pathway. In addition, NLK gene is a target of hsa-miR-181 famliy and an inhibitor of Wnt signaling pathway. So we think that hsa-miR-181 famliy through feedback control CDX2 regulated the Wnt signaling pathway, impact on the B-cell proliferation and apoptosis.From the miRNA-centric comprehensiv regulatory network, hsa-miR-126 and hsa-miR-486-3p regulated a lots of target gene.Since no gene in the hub target, the target genes of hsa-miR-126 and hsa-miR-486-3p were analysis in pathway.The results of hsa-miR-126 target genes showed that enriched to 3 path comprises Wnt signaling pathway which The p value was less than 0.05 and the four gens were enrichmented to including DVL3 gene.wherein the target gene of hsa-miR 126 include DVL3 gene. In literature, the DVL3 gene transcribed into Dishevelled protein that is important protein in Wnt pathway and can carry Wnt signal from receptor to downstream effector molecules. Consequetly, we hold that hsa-miR-126 by DVL3 gene negative regulted the Wnt pathway and hsa-miR-181 famliy by CDX2 regulated the hsa-miR-126 control the Wnt pathway, ultimately affect the B-cell proliferation and apoptosis.Through the above comprehensive analysis, we have come to the conclusion that: The hsa-miR-29a by YY1 negative regulation the XIST control in X chromosome inactivation, involved in B-ALL development. The hsa-miR-181 family by CDX2 regulated hsa-miR-126 and NLK gene control Wnt pathway, affect the B-cell proliferation of apoptosis.The hsa-miR-29a, hsa-miR-126 and hsa-miR-181 family were the core differentially expressed miRNA in B-cell acute lymphoblastic leukemia, play an important role in the development of B-cell acute lymphoblastic leukemia. Hence, its may serve as a potential therapeutic targets and diagnostic indicators in B-cell acute lymphoblastic leukemia.