Autophagy and cell reprogramming

Abstract

Autophagy is an evolutionarily conserved process that degrades cytoplasmic components, thus contributing to cell survival and tissue homeostasis. Recent studies have demonstrated that autophagy maintains stem cells in relatively undifferentiated states (stemness) and also contributes to differentiation processes. Autophagy likewise plays a crucial role in somatic cell reprogramming, a finely regulated process that resets differentiated cells to a pluripotent state and that requires comprehensive alterations in transcriptional activities and epigenetic signatures. Autophagy assists in manifesting the functional consequences that arise from these alterations by modifying cellular protein expression profiles. The role of autophagy appears to be particularly relevant for early phases of cell reprogramming during the generation of induced pluripotent stems cells (iPSCs). In this review, we provide an overview of the core molecular machinery that constitutes the autophagic degradation system, describe the roles of autophagy in maintenance, self-renewal, and differentiation of stem cells, and discuss the autophagic process and its regulation during cell reprogramming.

Fig. 1

Simplified overview of the autophagic degradation system. Four major complexes are key components of the autophagic molecular machinery. (1) mTORC1 complex. In nutrient-rich conditions, amino acids are sensed and result in the conversion of RAG GTPase heterodimers from RAGA/B-GDP-RAGC/D-GTP to RAGA/B-GTP-RAGC/G-GDP. This facilitates the binding of the small GTPase Rheb to mTOR, resulting in mTOR activation. Upon stimulation with growth factors, the PI3K-AKT pathway is activated to phosphorylate TSC2. TSC2-P inhibits Rheb and promotes the activation of mTORC1. High ADP: ATP ratios activate AMPK, promote TSC1-TSC2 activation by phosphorylation of TSC2, followed by inhibition of Rheb and inhibition of mTORC1. (2) ULK1 complex. During nutrient starvation or other metabolic stresses, the activation of mTORC1 is inhibited to block mTOR-dependent phosphorylation of ULK1, leading to ULK1 autophosphorylation. ULK1 is activated by AMPK-mediated phosphorylation. Phosphorylated ULK1 subsequently phosphorylates and activates FIP200 and mAtg13, resulting in autophagy induction. (3) Vps34 complex. Beclin 1 and Vps34 form the core of this complex. Bif, Ambra1, UVRAG, and Atg14L positively regulate the activity of the Beclin 1-Vps34 complex. Bcl2, WASH, Rubicon, and Cdk1/5 negatively regulate this complex to suppress autophagy. (4) Ubiquitin-like (Ubl) conjugation complex. Two Ubl systems are relevant during autophagy. Atg5 is covalently conjugated to Atg12, and the Atg5-Atg12 conjugate forms an active multimeric complex with Atg16. This first complex then localizes to autophagosomes. The second complex is the LC3-PE system. During autophagy induction, LC3 is conjugated to phosphatidylethanolamine (PE) to form LC3-II. LC3-II then locates to autophagosomes. Autophagosomes then enclose target materials that are degraded upon fusion with lysosomes and the formation of autolysosomes

Fig. 2

Autophagy induction during cell reprogramming. a Autophagy in iPSC reprogramming. In somatic cells, the histones in the promoter region of mTOR are modified by acetylation and methylation (H3K9K14ac, H3K4me1), facilitating mTOR transcription. During early stages of the reprogramming process, Sox2 recruits the NuRD complex to the mTOR promoter, resulting in removal of the epigenetic modifications and causing the suppression of mTOR transcription. Downregulation of mTOR initiates autophagy, which is an indispensable event for cell iPSC reprogramming. Autophagy minimizes ROS levels in somatic cells and provides a suitable microenvironment for reprogramming. b Autophagy in embryonic reprogramming. After fertilization, calcium oscillations trigger an initial induction of autophagy. During the four-to eight-cell stage, Sox2 recruits the NuRD complex to downregulate mTOR expression, thereby leading to the continued induction of autophagy as needed for further development to the blastocyst