Abstract
| Original language | English |
|---|---|
| Pages (from-to) | 4138-4151 |
| Number of pages | 14 |
| Journal | Journal of Proteome Research |
| Volume | 17 |
| Issue number | 12 |
| DOIs | |
| Publication status | Published - Dec 7 2018 |
Keywords
- human embryonic stem cells
- membrane proteome
- missing proteins
- subcellular fractionation
ASJC Scopus subject areas
- Biochemistry
- Chemistry(all)
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In: Journal of Proteome Research, Vol. 17, No. 12, 07.12.2018, p. 4138-4151.
Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - Subcellular Proteome Landscape of Human Embryonic Stem Cells Revealed Missing Membrane Proteins
AU - Weldemariam, M.M.
AU - Han, C.-L.
AU - Shekari, F.
AU - Kitata, R.B.
AU - Chuang, C.-Y.
AU - Hsu, W.-T.
AU - Kuo, H.-C.
AU - Choong, W.-K.
AU - Sung, T.-Y.
AU - He, F.-C.
AU - Chung, M.C.M.
AU - Salekdeh, G.H.
AU - Chen, Y.-J.
N1 - Export Date: 25 October 2018 Article in Press CODEN: JPROB Correspondence Address: Han, C.-L.; Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical UniversityTaiwan; email: was@tmu.edu.tw References: Rubin, L.L., Haston, K.M., Stem cell biology and drug discovery (2011) BMC Biol., 9, p. 42; Takahashi, K., Tanabe, K., Ohnuki, M., Narita, M., Ichisaka, T., Tomoda, K., Yamanaka, S., Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors (2007) Cell, 131, pp. 861-872; Lu, T.-Y., Lu, R.-M., Liao, M.-Y., Yu, J., Chung, C.-H., Kao, C.-F., Wu, H.-C., Epithelial Cell Adhesion Molecule Regulation Is Associated with the Maintenance of the Undifferentiated Phenotype of Human Embryonic Stem Cells (2010) J. Biol. Chem., 285, pp. 8719-8732; Hu, Q., Rosenfeld, M.G., Epigenetic regulation of human embryonic stem cells (2012) Front. 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PY - 2018/12/7
Y1 - 2018/12/7
N2 - 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; 19658 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 11970 unique proteins (1% false discovery rate at peptide, protein, and PSM levels), including the most-comprehensive description of 6138 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. Copyright © 2018 American Chemical Society.
AB - 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; 19658 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 11970 unique proteins (1% false discovery rate at peptide, protein, and PSM levels), including the most-comprehensive description of 6138 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. Copyright © 2018 American Chemical Society.
KW - human embryonic stem cells
KW - membrane proteome
KW - missing proteins
KW - subcellular fractionation
UR - http://www.scopus.com/inward/record.url?scp=85054140584&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85054140584&partnerID=8YFLogxK
U2 - 10.1021/acs.jproteome.8b00407
DO - 10.1021/acs.jproteome.8b00407
M3 - Article
SN - 1535-3893
VL - 17
SP - 4138
EP - 4151
JO - Journal of Proteome Research
JF - Journal of Proteome Research
IS - 12
ER -