An anaerobic home for the stem cell proteome

Comment on Unwin et al, page 4687

The paper by Unwin and colleagues in this issue of Blood gives us a first glimpse into the stem cell proteome that points to a key role of anaerobic metabolism and oxidative protection in the maintenance of the stem cell state.

Extensive transcriptional profiling of hematopoietic stem cells (HSCs) has yielded a variety of molecular signatures that are as different as they are similar.¹  Despite all this transcriptional profiling, there have been relatively few insights into how a stem cell really maintains its stem cell nature. Unwin and colleagues used a sophisticated mass spectrometric method with isobaric covalent modification of peptides for relative quantification (iTRAQ) that allowed the relative quantification of hundreds of proteins in 4 samples simultaneously. Cell lysates were prepared from lineage-negative, Sca-1–positive, cKit-positive (LSK⁺), and LSK-negative (LSK^–) cells. LSK⁺ cells are substantially enriched for long-term repopulating stem cells compared with their LSK^– counterparts.²  Individual lysates were proteolytically digested, and the resulting peptides were labeled with one of 4 isobaric isotope-coded tags. After all 4 samples were mixed, the peptides were separated by extensive 2-dimensional liquid chromatography online to a mass spectrometer. These analyses were repeated 3 times using about 1 × 10⁶ LSK⁺ and LSK^– cells for each labeling. Microarray analyses were also performed in triplicate with similarly isolated cells. Careful statistical analyses yielded 145 differentially expressed proteins between LSK⁺ and LSK^– cells from a total of 668 relatively quantitated proteins. Comparative analyses of the differentially expressed proteins with the microarray data revealed that less than half (45.3%) showed the same trend in expression, while the remaining 55% showed no change at the transcriptome level. These data reveal that posttranslational controls are important regulators of stem cell properties. A coupling of the 2 methodologies is suggested in order to achieve a complete stem cell profile in systems biology.³  Of course, these benchmarks will be difficult to achieve with more highly purified, rare stem cell populations than with LSK⁺ cells, because the cell numbers are just too limiting. Nevertheless, given the rapid advances in these methodologies, it is highly likely that this goal will be achieved in the future. Perhaps the most interesting aspect of these data is that the HSC proteome is well adapted to the relatively hypoxic environment of the endosteum, the proposed stem cell niche. The most highly represented metabolic pathway was glycolysis; 8 out of 11 enzymes in the pathway were more highly expressed in LSK⁺ cells. In particular, anaerobic glycolysis was indicated, as LSK⁺ cells showed a greater production of lactate. Coupled with the preponderance of glycolytic enzymes were proteins involved in protection against DNA damage from oxidative stress. These data support the observation that stem cells lose their self-renewal ability if they cannot overcome oxidative damage.⁴  The emerging picture of the HSC proteome forces us to ponder a broader role of the metabolome in the maintenance of the stem cell state. It also suggests an additional feature of the stem cell niche, as a sheltering environment that provides protection from damaging systemic stimuli.⁵  ▪