Works based on the generation of induced pluripotent stem cells (iPSCs) mediated by expressing Yamanaka cocktail factors (Takahashi and Yamanaka, 2006) have been extensively reported. During somatic cell reprogramming, many organelles get remodeled on multilayer such as organelle morphology, metabolic patterns, and meanwhile epigenetic landscapes and gene expression changes. In the process of organelle plasticity control, lipids, ions, and metabolites are ferried to particular targets. Such reorientations need the aid of membrane trafficking. However, most related mechanisms and physiological/pathological functions remain largely unknown.