Biomic study of human myeloid leukemia cells differentiation to macrophages using DNA array, proteomic, and bioinformatic analytical methods.
A biomic approach by integrating three independent methods, DNA microarray, proteomics and bioinformatics, is used to study the differentiation of human myeloid leukemia cell line HL-60 into macrophages when induced by 12-O-tetradecanoyl-phorbol-13-acetate (TPA). Analysis of gene expression changes at the RNA level using cDNA against an array of 6033 human genes showed that 5950 (98.6%) of the genes were expressed in the HL-60 cells. A total of 624 genes (10.5%) were found to be regulated during HL-60 cell differentiation. Most of these genes have not been previously associated with HL-60 cells and include genes encoded for secreted proteins as well as genes involved in cell adhesion, signaling transduction, and metabolism. Protein analysis using two-dimensional gel electrophoresis showed a total of 682 distinct protein spots; 136 spots (19.9%) exhibited quantitative changes between HL-60 control and macrophages. These differentially expressed proteins were identified by mass spectrometry. We developed a bioinformatics program, the Bulk Gene Search System (BGSS, http://www.sinica.edu.tw:8900/perl/genequery.pl) to search for the functions of genes and proteins identified by cDNA microarrays and proteomics. The identified regulated proteins and genes were classified into seven groups according to subcellular locations and functions. This powerful holistic biomic approach using cDNA microarray, proteomics coupled to bioinformatics can provide in-depth information on the impact and importance of the regulated genes and proteins for HL-60 differentiation.
Juan
Hsueh-Fen
HF
Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
Lin
John Yi-Chung
JY
Chang
Wen-Hwei
WH
Wu
Chi-Yue
CY
Pan
Tai-Long
TL
Tseng
Min-Jen
MJ
Khoo
Kay-Hooi
KH
Chen
Shui-Tein
ST
D002454:Cell Differentiation / Q000187:drug effects; D019295:Computational Biology; D015180:Electrophoresis, Gel, Two-Dimensional; D020869:Gene Expression Profiling; D023281:Genomics; D018922:HL-60 Cells; D006801:Humans; D007091:Image Processing, Computer-Assisted; D015470:Leukemia, Myeloid, Acute / Q000235:genetics* / Q000473:pathology*; D008264:Macrophages / Q000473:pathology*; D020411:Oligonucleotide Array Sequence Analysis; D040901:Proteomics; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D013755:Tetradecanoylphorbol Acetate / Q000494:pharmacology
D013755:Tetradecanoylphorbol Acetate