An integrated approach to mapping the proteome of the human bone marrow stromal cell

Bone marrow stromal cells, also known as mesenchymal stem or progenitor cells, are thought to play a critical role in hematopoiesis. Because hematopoiesis is dysregulated in leukemic individuals, expression profiling in leukemic stromal cells might yield valuable insights into mechanisms of normal and dysregulated hematopoiesis. Here, proteomics was used to identify expressed proteins in normal and leukemic bone marrow stromal cells. Isobaric tags for relative and absolute quantification (iTRAQ) technology and MS/MS were used to identify and quantify proteins in bone marrow stromal cells from two normal and two leukemic individuals. Approximately 900 distinct proteins were identified with >95% confidence, 73 of which were differentially expressed in leukemic stromal cells. cDNA microarray analysis on Affymetrix oligonucleotide gene chips showed that transcripts correlated with approximately 90% of the expressed proteins. A novel integrated approach for mining and visualization of iTRAQ data is presented. The results provide an initial assessment of the proteome in human bone marrow stromal cells, laying the groundwork for comprehensive analysis of the proteome in these cells, and ultimately, for improved understanding of normal and dysregulated hematopoiesis.