Discovery of novel gene biomarker for Acute Myeloid Leukemia through differential gene expression analysis
Keywords:
Leukemia, Gene,
Abstract
Acute Myeloid Leukemia (AML) is the major cause of death in developing countries. It is more prevalent in males as compared to females. Various cytogenetic detection methods are currently available, but their results are varied due to chromosomal changes. To overcome this, multiple microarray studies have been conducted on transcriptional profiling of AML patients. In depth reanalysis of microarray studies was performed. It was found that 21 genes involved in the seven pathways. The most significant pathway is antigen presentation and processing and genes are CD4, CD8a, and CD8b. On the basis of this result, we suggested that genes CD4, Neuraminidase (NA), Androgen-dependent TFPI-regulating (ADTRP) are helpful in discovering novel biomarkers and also as a therapeutic target of AML.References
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[2] Boles, K. S., Barchet, W., Diacovo, T., Cella, M., & Colonna, M. (2005). Plenary paper The tumor suppressor TSLC1 / NECL-2 triggers NK-cell and CD8 ϩ T-cell responses through the cell-surface receptor CRTAM, 106(3), 779–786. doi:10.1182/blood-2005-02-0817.The
[3] Bonnet, D., & Dick, J. E. (1997). Human acute myeloid leukemia is organised as a hierarchy that originates from a primitive hematopoietic cell. Nature, 3, 730–737. doi:10.1038
[4] Botstein, D. (1998). Cluster analysis and display of genome-wide expression patterns, 95(December), 14863–14868.
[5] Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., … Vingron, M. (2001). Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nature genetics, 29(4), 365–371. doi:10.1038/ng1201-365
[6] Carbone, E., Neri, P., Mesuraca, M., Fulciniti, M. T., Otsuki, T., Pende, D., … Venuta, S. (2005). IMMUNOBIOLOGY HLA class I , NKG2D , and natural cytotoxicity receptors regulate multiple myeloma cell recognition by natural killer cells, 105(1), 251–258. doi:10.1182/blood-2004-04-1422.Supported
[7] Cheng, X., & Kao, H.-Y. (2012). Microarray analysis revealing common and distinct functions of promyelocytic leukemia protein (PML) and tumor necrosis factor (TNF alpha) signaling in endothelial cells. BMC Genomics. doi:10.1186/1471-2164-13-453
[8] Dalman, M. R., Deeter, A., Nimishakavi, G., & Duan, Z.-H. (2012). Fold change and p-value cutoffs significantly alter microarray interpretations. BMC bioinformatics, 13 Suppl 2(Suppl 2), S11. doi:10.1186/1471-2105-13-S2-S11
[9] Dudoit, S., & Yang, J. (2003). Bioconductor R packages for exploratory analysis and normalization of cDNA microarray data. The Analysis of Gene Expression Data, 1–35. Retrieved from http://link.springer.com/chapter/10.1007/0-387-21679-0_3
[10] Estey, E. H. (2009). Treatment of acute myeloid leukemia. Haematologica, 94(1), 10–6. doi:10.3324/haematol.2008.001263
[11]Gautier, L., Cope, L., Bolstad, B. M., & Irizarry, R. A. (2004). Affy - Analysis of Affymetrix GeneChip data at the probe level. Bioinformatics, 20(3), 307–315.
[12] Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., … Zhang, J. (2004). Bioconductor : open software development for computational biology and bioinformatics, (10).
[13] Gillespie, C. S., Lei, G., Boys, R. J., Greenall, A., & Wilkinson, D. J. (2010). Analysing time course microarray data using Bioconductor : a case study using yeast2 Affymetrix arrays.
[14] Glienke, J., Sobanov, Y., Brostjan, C., Steffens, C., Nguyen, C., Lehrach, H., … Francis, F. (1998). The genomic organization of NKG2C, E, F, and D receptor genes in the human natural killer gene complex. Immunogenetics, 48(3), 163–173.
[15] Goswami, R. S., Sukhai, M. A., Thomas, M., Reis, P. P., & Kamel-Reid, S. (2009). Applications of microarray technology to Acute Myelogenous Leukemia. Cancer informatics, 7, 13–28.
[16] Grimwade, B. D., Walker, H., Oliver, F., Wheatley, K., Harrison, C., Harrison, G., … Goldstone, A. (1998). The Importance of Diagnostic Cytogenetics on Outcome in AML: Analysis of 1,612 Patients Entered Into the MRC AML 10 Trial, 2322–2333.
[17] Harty, J. T., Tvinnereim, A. R., & White, D. W. (2000). CD8+ T cell effector mechanisms in resistance to infection. Annual review of immunology, 18, 275–308. doi:10.1146/annurev.immunol.18.1.275
[18] Heber, S., & Sick, B. (2006). Quality Assessment of Affymetrix GeneChip Data, 10(3), 358–368.
[19] Hehlmann, R., Berger, U., Aul, C., Büchner, T., Döhner, H., Ehninger, G., … Hasford, J. (2004). The German competence network “Acute and chronic leukemias”. Leukemia, 18(4), 665–9. doi:10.1038/sj.leu.2403317
[20] Hikami, K., Tsuchiya, N., Yabe, T., & Tokunaga, K. (2003). Variations of human killer cell lectin-like receptors: common occurrence of NKG2-C deletion in the general population. Genes and immunity, 4(2), 160–7. doi:10.1038/sj.gene.6363940
[21] Hua, Y. J., Tu, K., Tang, Z. Y., Li, Y. X., & Xiao, H. S. (2008). Comparison of normalization methods with microRNA microarray. Genomics, 92(2), 122–128.
[22] Huang, D. W., Sherman, B. T., Tan, Q., Kir, J., Liu, D., Bryant, D., … Lempicki, R. A. (2007). DAVID Bioinformatics Resources: Expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Research, 35(SUPPL.2).
[23] Kauffmann, A., Gentleman, R., & Huber, W. (2009). arrayQualityMetrics - A bioconductor package for quality assessment of microarray data. Bioinformatics, 25(3), 415–416.
[24] Le Dieu, R., Taussig, D. C., Ramsay, A. G., Mitter, R., Miraki-Moud, F., Fatah, R., … Gribben, J. G. (2009). Peripheral blood T cells in acute myeloid leukemia (AML) patients at diagnosis have abnormal phenotype and genotype and form defective immune synapses with AML blasts. Blood, 114(18), 3909–3916.
[25] Lung, H. L., Cheung, A. K. L., Xie, D., Cheng, Y., Kwong, F. M., Murakami, Y., … Lung, M. L. (2006). TSLC1 is a tumor suppressor gene associated with metastasis in nasopharyngeal carcinoma. Cancer research, 66(19), 9385–92. doi:10.1158/0008-5472.CAN-06-0590
[26] Lupu, C., Zhu, H., Popescu, N. I., Wren, J. D., & Lupu, F. (2011). Novel protein ADTRP regulates TFPI expression and function in human endothelial cells in normal conditions and in response to androgen. Blood, 118(16), 4463–4471.
[27] Miwa, H., Mizutani, M., Mahmud, N., Yamaguchi, M., Takahashi, T., Shikami, M., … Kita, K. (1998). Biphasic expression of CD4 in acute myelocytic leukemia (AML) cells: AML of monocyte origin and hematopoietic precursor cell origin. Leukemia: official journal of the Leukemia Society of America, Leukemia Research Fund, U.K, 12(1), 44–51. doi:10.1038/sj.leu.2400877
[28] Opin, C., Biol, C., Biol, M. C., & Trans, B. S. (1998). Tandem duplication of the FLT3 gene in acute lymphoblastic leukemia: a marker for, 522–524.
[29] Parkinson, H., Kapushesky, M., Shojatalab, M., Abeygunawardena, N., Coulson, R., Farne, a, … Brazma, a. (2007). ArrayExpress--a public database of microarray experiments and gene expression profiles. Nucleic acids research, 35(Database issue), D747–50. doi:10.1093/nar/gkl995
[30] Pradervand, S., Weber, J., Thomas, J., Bueno, M., Wirapati, P., Lefort, K., … Harshman, K. (2009). Impact of normalization on miRNA microarray expression profiling. RNA (New York, N.Y.), 15(3), 493–501.
[31] Rasi, S., Spina, V., Bruscaggin, A., Vaisitti, T., Tripodo, C., Forconi, F., … Rossi, D. (2011). A variant of the LRP4 gene affects the risk of chronic lymphocytic leukaemia transformation to Richter syndrome. British Journal of Haematology, 152(3), 284–294.
[32] Robinson, M. D., & Oshlack, A. (2010). A scaling normalization method for differential expression analysis of RNA-seq data. Genome biology, 11(3), R25.
[33] Smyth, G. K. (2005). limma: Linear Models for Microarray Data. In R. Gentleman, V. J. Carey, W. Huber, R. A. Irizarry, & S. Dudoit (Eds.), Bioinformatics and Computational Biology Solutions Using R and Bioconductor (pp. 397–420). Springer-Verlag. doi:10.1007/0-387-29362-0
[34] Vilchez, R. A., & Butel, J. S. (2003). SV40 in human brain cancers and non-Hodgkin’s lymphoma. Oncogene, 22(33), 5164–5172. doi:10.1038/sj.onc.1206547
[35] Wu, Z., LeBlanc, R., & Irizarry, R. (2003). Stochastic models based on molecular hybridization theory for short oligonucleotide microarrays. John Hopkins University, Department of Biostatistics Working Paper, 4. Retrieved from http://biostats.bepress.com/jhubiostat/paper4/
[36] Yu, M. W., Pai, C. I., Yang, S. Y., Hsiao, T. J., Chang, H. C., Lin, S. M., … Chen, C. J. (2000). Role of N-acetyltransferase polymorphisms in hepatitis B related hepatocellular carcinoma: impact of smoking on risk. Gut, 47(5), 703–709.
[37]Zhang, H., & Li, S. (2013). Dataset Paper DNA Microarray Assay Helps to Identify Functional Genes Specific for Leukemia Stem Cells, 2013.
[38]Gentleman R,Carey V,Huber W,Hahne F:Genefilter:method for filtering from microarray experiments. R package version1.44.0
Published
2016-03-07
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