Subcellular Proteome Landscape of Human Embryonic Stem Cells Revealed Missing Membrane Proteins

Abstract

Human embryonic stem cells (hESCs) have the capacity for self-renewal and multilineage differentiation, which are of clinical importance for regeneration medicine. Despite the significant progress of hESC study, the complete hESC proteome atlas, especially the surface protein composition, awaits delineation. According to the latest release of neXtProt database (January 17, 2018; 19 658 PE1, 2, 3, and 4 human proteins), membrane proteins present the major category (1047; 48%) among all 2186 missing proteins (MPs). We conducted a deep subcellular proteomics analysis of hESCs to identify the nuclear, cytoplasmic, and membrane proteins in hESCs and to mine missing membrane proteins in the very early cell status. To our knowledge, our study achieved the largest data set with confident identification of 11 970 unique proteins (1% false discovery rate at peptide, protein, and PSM levels), including the most-comprehensive description of 6 138 annotated membrane proteins in hESCs. Following the HPP guideline, we identified 26 gold (neXtProt PE2, 3, and 4 MPs) and 87 silver (potential MP candidates with a single unique peptide detected) MPs, of which 69 were membrane proteins, and the expression of 21 gold MPs was further verified either by multiple reaction monitoring mass spectrometry or by matching synthetic peptides in the Peptide Atlas database. Functional analysis of the MPs revealed their potential roles in the pluripotency-related pathways and the lineage- and tissue-specific differentiation processes. Our proteome map of hESCs may provide a rich resource not only for the identification of MPs in the human proteome but also for the investigation on self-renewal and differentiation of hESC. All mass spectrometry data were deposited in ProteomeXchange via jPOST with identifier PXD009840.

Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project

“…Figure 3 depicts the contributions of the top 10 data sets to this increase in the number of proteins, accounting for 292 (59%) of the 495. The three data sets contributing the most canonical proteins (a total of 161) were PXD009737, 22 PXD010630, 25 and PXD009840, 24 all resulting from the sixth HPP special issue in this journal (2018). It is impressive that major progress has been made with membrane proteins.…”

Cell-Surface Proteomics Identifies Differences in Signaling and Adhesion Protein Expression between Naive and Primed Human Pluripotent Stem Cells

“…However, cell-surface proteins are typically underrepresented in these studies due to their low abundance and biochemical properties. In response to this limitation, several methods for measuring plasma membrane proteins by MS have been developed (Elschenbroich et al, 2010;Josic and Clifton, 2007) that are compatible with primed hPSC (Boheler et al, 2014;Dormeyer et al, 2008;Weldemariam et al, 2018).…”

Asia-Oceania HUPO: Past, Present, and Future

“…The main aim of AOHUPO is not only to promote and coordinate the activities of each regional proteomics community, but also to facilitate the inter-community activities through AOHUPO initiatives such as Membrane Proteome Initiative (MPI) led by Bill Jordan (New Zealand) [3]. Recently, attempts to unveil missing proteins, including the MPI results [4], have resulted in reporting a 90.4% complete high-stringency human proteome blueprint through the chromosome-based human proteome project in HUPO (cHPP) [5]. Two more initiatives such as Chemical Proteomics and Nuclear Proteomics led by two prominent scientists Ho Jeong Kwon and Jun Qin, respectively, are on-going with participation by the AOHUPO community [6].…”