COMPREHENSIVE REVIEW Autophagy in Stem Cell Maintenance and Differentiation Alexandre Teixeira Vessoni, 1 Alysson Renato Muotri, 2 and Oswaldo Keith Okamoto 3 Autophagy is a lysosome-dependent degradation pathway that allows cells to recycle damaged or superfluous cytoplasmic content, such as proteins, organelles, and lipids. As a consequence of autophagy, the cells generate metabolic precursors for macromolecular biosynthesis or ATP generation. Deficiencies in this pathway were associated to several pathological conditions, such as neurodegenerative and cardiac diseases, cancer, and aging. The aim of this review is to summarize recent discoveries showing that autophagy also plays a critical role in stem cell maintenance and in a variety of cell differentiation processes. We also discuss a possible role for autophagy during cellular reprogramming and induced pluripotent stem (iPS) cell generation by taking ad- vantage of ATP generation for chromatin remodeling enzyme activity and mitophagy. Finally, the significance of autophagy modulation is discussed in terms of augmenting efficiency of iPS cell generation and differentiation processes. Introduction P luripotent stem cells are defined by their self-renewal capacity and their ability to develop into cells of all 3 germ layers. Theoretically, those cells hold great promise for re- generative medicine, where they could be used to replace damaged cells of a tissue, thus constituting a powerful tool to treat several diseases [1–5]. The advent of induced pluripotent stem (iPS) cells [6] opened new avenues to model complex diseases in vitro [7–10]. Moreover, resultant iPS cells are iso- genic to the donor, thereby allowing transplantation of the reprogrammed cells with theoretically lower risks of immune rejection [11–14]. Mechanisms of cellular homeostasis are important for preventing cellular injuries that could lead to impaired cel- lular function and ultimately cell death. One of those mechanisms is macroautophagy (hereafter called auto- phagy), a lysosome-dependent degradation pathway that allows the recycling of damaged or superfluous cytoplasmic content, such as proteins and organelles. During autophagy, an isolation membrane, or phagophore, hijacks portions of the cytoplasm, giving rise to the autophagosome. This dou- ble-membrane vesicle subsequently fuses with the lysosome, where the enclosed material will be released and degraded by lysosomal enzymes. Such process yields cell metabolic precursors that can be used for ATP generation or protein synthesis, for example (Fig. 1) [15–19]. The autophagic pathway can be activated under different stimuli, such as starvation [17], endoplasmic reticulum stress [20], DNA damage [21], and reactive oxygen species (ROS) [22], thereby eliciting a cytoprotective response that helps cells to overcome those stressful situations. Deregulation of this pathway has been linked to several pathologies, such as neurodegenerative and cardiac disorders, cancer, and aging [15,23–25]. In this article, we will summarize recent evidences showing that autophagy plays an important role in stem cell maintenance and differentiation. We will also discuss a possible role for autophagy during cellular reprogramming and iPS cell generation. Autophagy Acts as a Cell Remodeling Mechanism During Cell Differentiation As previously described, autophagy acts as an intracellu- lar quality control mechanism through degradation of damaged or obsolete organelles and proteins. For instance, T lymphocytes deficient for the autophagy genes, Atg3, 5, or 7, show abnormal mitochondria accumulation and expanded endoplasmic reticulum due to impaired organelle homeo- stasis. As a result, there is an increase in ROS production and elevation in intracellular calcium that further impairs cal- cium influx, affecting the survival of T lymphocytes [26–28]. Besides acting as quality control mechanism in differenti- ated cells, autophagy was also shown to participate in dif- ferentiation, as a cell remodeling mechanism that promotes morphological and structural changes. During adipogenesis, preadipocytes differentiate into adipocytes, a cell type that 1 Department of Microbiology, Institute of Biomedical Sciences, University of Sa ˜o Paulo, Sa ˜ o Paulo, Brazil. 2 Department of Pediatrics/Rady Children’s Hospital, Department of Cellular and Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, California. 3 Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of Sa ˜o Paulo, Sa ˜ o Paulo, Brazil. STEM CELLS AND DEVELOPMENT Volume 21, Number 4, 2012 Ó Mary Ann Liebert, Inc. DOI: 10.1089/scd.2011.0526 513