The envisioned clinical and industrial use of human pluripotent stem cells and their derivatives has given major momentum to the establishment of suspension culture protocols that enable the mass production of cells. Understanding molecular changes accompanying the transfer from adherent to suspension culture is of utmost importance because this information can have a direct effect on the development of optimized culture conditions. In this study we assessed the gene expression of human embryonic stem cells and induced pluripotent stem cells grown in surface-adherent culture (two-dimensional) versus free-floating suspension culture spheroids (three-dimensional). We combined a quantitative proteomic approach based on stable isotope labeling by amino acids in cell culture with deep-sequencing-based transcriptomics. Cells in three-dimensional culture showed reduced expression of proteins forming structural components of cell-cell and cell-extracellular matrix junctions. However, fully unexpected, we found up-regulation of secreted inhibitors of the canonical Wnt signaling pathway and, concomitantly, a reduction in the level of active -catenin and in the expression of Wnt target genes. In Western blot analyses the cysteine protease calpain was shown to cleave E-cadherin and -catenin under three-dimensional culture conditions. Our data al- Human embryonic and induced pluripotent stem cells (hESCs and hiPSCs, respectively) 1 hold the potential for indefinite self-renewal and differentiation into all somatic cell types (1, 2). Beyond their application as models for studying mechanisms of pluripotency, these cells have been considered as a potent source for cell therapies and in vitro assays in pharmacology and toxicology, raising the need for largescale cell production under defined conditions (3). Conventional, surface adherent, two-dimensional culture is not suited to generate billions of human pluripotent stem cells (hPSCs) and their respective progenies required for clinical applications (3). To overcome these limits, three-dimensional culture From the ‡Institute for Cellular Chemistry, Hannover Medical School, 30625 Hannover, Germany; §REBIRTH Cluster of Excellence, Hannover Medical School, 30625 Hannover, Germany; ¶Institute for