Recent studies have shown that various neural and embryonic stem cells cultured in 1-8% oxygen (O 2 ), levels lower than those typically used in cell culture (20.9%), displayed increased rates of proliferation; however, the molecular mechanisms underlying these changes are largely undefined. In this study, using rigorously controlled O 2 levels, we found that neural stem cells (NSCs) from embryonic day 15 rat cortex increased their rate of proliferation and migration in 1% O 2 relative to 20% O 2 without changes in viability. We sought to identify molecular changes in NSCs grown in 1% O 2 that might account for these increases. In 1% O 2 , levels of the hypoxia-inducible transcription factor HIF-1␣ were transiently increased. Reduced adherence of NSCs in 1% O 2 to basement membrane-coated plates was observed, and quantitative RT-PCR analysis confirmed that the levels of mRNA for an assortment of cell adhesion and extracellular matrix molecules were altered. Most notable was a 5-fold increase in matrix metalloproteinase (MMP)-9 mRNA. Specific inhibition of MMP-9 activity, verified using a fluorescent substrate assay, prevented the increase in proliferation and migration in 1% O 2 . The canonical Wnt pathway was recently shown to be activated in stem cells in low O 2 via HIF-1␣. Inhibition of Wnt signaling by DKK-1 also prevented the increase in proliferation, migration, and MMP-9 expression. Thus, MMP-9 is a key molecular effector, downstream of HIF-1␣ and Wnt activation, responsible for increased rates of NSC proliferation and migration in 1% O 2 .A frequently overlooked variable for the in vitro expansion of stem/progenitor cells is the level of O 2 in cell culture (1-3). In fact, the level of O 2 (20.9% O 2 ) used for in vitro culture is hyperoxic for cells in vivo. The lung alveoli and bloodstream typically hold ϳ14% (4, 5) and 11.5% (6 -8) O 2 , respectively, and O 2 levels in various areas of the brain range from 0.1 to 9% (5, 7, 9 -12). Recent studies have shown that the use of lower O 2 levels in culture results in increased rates of proliferation of neural stem/progenitor cells (NSCs) 2 from various embryonic or adult brain regions (12-23), virally immortalized human NSCs (23), and embryonic stem (ES) cells (3,24,25) and that these O 2 levels can also influence the differentiation of NSCs (9 -16).A large body of work has described hypoxia-inducible transcription factors as key components of the O 2 -sensing machinery that responds to lowered O 2 in cells and organisms (5,10,26,27). It has been shown that levels of HIF-1␣ protein can vary significantly over physiological ranges of O 2 (28). Although HIF-1␣ is constitutively expressed, when O 2 levels are high, the protein is hydroxylated by a family of prolyl hydroxylase enzymes, catalyzing a modification that targets HIF-1␣ for proteasomal degradation. At lower O 2 levels, the HIF-1␣ protein undergoes less hydroxylation, is stabilized, and can then translocate to the nucleus where it activates several genes that modulate the cellular response to decreas...