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Prepublished online as a Blood First Edition Paper on July 5, 2002; DOI 10.1182/blood-2002-03-0850.
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Blood, 1 November 2002, Vol. 100, No. 9, pp. 3209-3220
HEMATOPOIESIS
Genomic and proteomic analysis of the myeloid differentiation
program: global analysis of gene expression during induced
differentiation in the MPRO cell line
Zheng Lian,
Yuval Kluger,
Dov S. Greenbaum,
David Tuck,
Mark Gerstein,
Nancy Berliner,
Sherman M. Weissman, and
Peter E. Newburger
From the Department of Genetics, Boyer Center for
Molecular Medicine, Section of Hematology, Department of Internal
Medicine, and Center for Medical Informatics, Yale University School of
Medicine; Department of Molecular Biophysics and Biochemistry, Yale
University, New Haven, CT; and Department of Pediatrics, University of
Massachusetts Medical School, Worcester.
We have used an approach using 2-dimensional gel electrophoresis
with mass spectrometry analysis combined with oligonucleotide chip
hybridization for a comprehensive and quantitative study of the
temporal patterns of protein and mRNA expression during myeloid
development in the MPRO murine cell line. This global analysis detected
123 known proteins and 29 "new" proteins out of 220 protein spots
identified by tandem mass spectroscopy, including proteins in 12 functional categories such as transcription factors and cytokines.
Bioinformatic analysis of these proteins revealed clusters with
functional importance to myeloid differentiation. Previous analyses
have found that for a substantial number of genes the absolute amount
of protein in the cell is not strongly correlated to the amount of
mRNA. These conclusions were based on simultaneous measurement of mRNA
and protein at just a single time point. Here, however, we are able to
investigate the relationship between mRNA and protein in terms of
simultaneous changes in their levels over multiple time points. This is
the first time such a relationship has been studied, and we find that
it gives a much stronger correlation, consistent with the hypothesis
that a substantial proportion of protein change is a consequence of
changed mRNA levels, rather than posttranscriptional effects.
Cycloheximide inhibition also showed that most of the proteins detected
by gel electrophoresis were relatively stable. Specific investigation of transcription factor mRNA representation showed considerable similarity to those of mature human neutrophils and highlighted several
transcription factors and other functional nuclear proteins whose mRNA
levels change prominently during MPRO differentiation but which have
not been investigated previously in the context of myeloid development.
Data are available online at
http://bioinfo.mbb.yale.edu/expression/myelopoiesis.
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