7 Citations (Scopus)

Abstract

As the functions of proteins are associated with their cellular localization, the comprehensive sub-cellular proteome knowledge of human embryonic stem cells (hESCs) is indispensable for ensuring a therapeutic effect. Here, we have utilized a sub-cellular proteomics approach to analyze the localization of proteins in the nucleus, mitochondria, crude membrane, cytoplasm, heavy and light microsomes. Out of 2002 reproducibly identified proteins, we detected 762 proteins in a single organelle whereas 160 proteins were found in all sub-cellular fractions. We verified the localization of identified proteins through databases and discussed the consistency of the obtained results. With regards to the ambiguity in the definition of a membrane protein, we tried to clearly define the plasma membrane, peripheral membrane and membrane proteins by annotation of these proteins in databases, along with predictions of transmembrane helices. Among ten enriched signaling pathways highlighted in our results, non-canonical Wnt signaling were analyzed in greater detail. The functions of three novel hESC membrane proteins (ERBB4, GGT1 and ZDHHC13) have been assessed in terms of pluripotency. Our report is the most comprehensive for organellar proteomics of hESCs. Significance Mass spectrometric identification of proteins using a TripleTOF 5600 from nucleus, mitochondria, crude membrane, cytoplasm, heavy and light microsomal fractions highlighted the significance of the non-canonical Wnt signaling in human embryonic stem cells.

Original languageEnglish
Pages (from-to)108-118
Number of pages11
JournalJournal of Proteomics
Volume162
DOIs
Publication statusPublished - Jun 6 2017

Fingerprint

Proteome
Stem cells
Organelles
Protein Databases
Membrane Proteins
Proteins
Proteomics
Mitochondria
Membranes
Cytoplasm
Molecular Sequence Annotation
Therapeutic Uses
Microsomes
Human Embryonic Stem Cells
Cell membranes
Cell Membrane
Light

Keywords

  • Human embryonic stem cell
  • Membrane proteomics
  • Non-canonical Wnt signaling
  • Organellar proteomics
  • Surface marker

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry

Cite this

Shekari, F., Nezari, H., Larijani, M. R., Han, C. L., Baharvand, H., Chen, Y. J., & Salekdeh, G. H. (2017). Proteome analysis of human embryonic stem cells organelles. Journal of Proteomics, 162, 108-118. https://doi.org/10.1016/j.jprot.2017.04.017

Proteome analysis of human embryonic stem cells organelles. / Shekari, Faezeh; Nezari, Hossein; Larijani, Mehran Rezaei; Han, Chia Li; Baharvand, Hossein; Chen, Yu Ju; Salekdeh, Ghasem Hosseini.

In: Journal of Proteomics, Vol. 162, 06.06.2017, p. 108-118.

Research output: Contribution to journalArticle

Shekari, F, Nezari, H, Larijani, MR, Han, CL, Baharvand, H, Chen, YJ & Salekdeh, GH 2017, 'Proteome analysis of human embryonic stem cells organelles', Journal of Proteomics, vol. 162, pp. 108-118. https://doi.org/10.1016/j.jprot.2017.04.017
Shekari F, Nezari H, Larijani MR, Han CL, Baharvand H, Chen YJ et al. Proteome analysis of human embryonic stem cells organelles. Journal of Proteomics. 2017 Jun 6;162:108-118. https://doi.org/10.1016/j.jprot.2017.04.017
Shekari, Faezeh ; Nezari, Hossein ; Larijani, Mehran Rezaei ; Han, Chia Li ; Baharvand, Hossein ; Chen, Yu Ju ; Salekdeh, Ghasem Hosseini. / Proteome analysis of human embryonic stem cells organelles. In: Journal of Proteomics. 2017 ; Vol. 162. pp. 108-118.
@article{7fd38519f4f74b73bd13fa20c8862212,
title = "Proteome analysis of human embryonic stem cells organelles",
abstract = "As the functions of proteins are associated with their cellular localization, the comprehensive sub-cellular proteome knowledge of human embryonic stem cells (hESCs) is indispensable for ensuring a therapeutic effect. Here, we have utilized a sub-cellular proteomics approach to analyze the localization of proteins in the nucleus, mitochondria, crude membrane, cytoplasm, heavy and light microsomes. Out of 2002 reproducibly identified proteins, we detected 762 proteins in a single organelle whereas 160 proteins were found in all sub-cellular fractions. We verified the localization of identified proteins through databases and discussed the consistency of the obtained results. With regards to the ambiguity in the definition of a membrane protein, we tried to clearly define the plasma membrane, peripheral membrane and membrane proteins by annotation of these proteins in databases, along with predictions of transmembrane helices. Among ten enriched signaling pathways highlighted in our results, non-canonical Wnt signaling were analyzed in greater detail. The functions of three novel hESC membrane proteins (ERBB4, GGT1 and ZDHHC13) have been assessed in terms of pluripotency. Our report is the most comprehensive for organellar proteomics of hESCs. Significance Mass spectrometric identification of proteins using a TripleTOF 5600 from nucleus, mitochondria, crude membrane, cytoplasm, heavy and light microsomal fractions highlighted the significance of the non-canonical Wnt signaling in human embryonic stem cells.",
keywords = "Human embryonic stem cell, Membrane proteomics, Non-canonical Wnt signaling, Organellar proteomics, Surface marker",
author = "Faezeh Shekari and Hossein Nezari and Larijani, {Mehran Rezaei} and Han, {Chia Li} and Hossein Baharvand and Chen, {Yu Ju} and Salekdeh, {Ghasem Hosseini}",
year = "2017",
month = "6",
day = "6",
doi = "10.1016/j.jprot.2017.04.017",
language = "English",
volume = "162",
pages = "108--118",
journal = "Journal of Proteomics",
issn = "1874-3919",
publisher = "Elsevier",

}

TY - JOUR

T1 - Proteome analysis of human embryonic stem cells organelles

AU - Shekari, Faezeh

AU - Nezari, Hossein

AU - Larijani, Mehran Rezaei

AU - Han, Chia Li

AU - Baharvand, Hossein

AU - Chen, Yu Ju

AU - Salekdeh, Ghasem Hosseini

PY - 2017/6/6

Y1 - 2017/6/6

N2 - As the functions of proteins are associated with their cellular localization, the comprehensive sub-cellular proteome knowledge of human embryonic stem cells (hESCs) is indispensable for ensuring a therapeutic effect. Here, we have utilized a sub-cellular proteomics approach to analyze the localization of proteins in the nucleus, mitochondria, crude membrane, cytoplasm, heavy and light microsomes. Out of 2002 reproducibly identified proteins, we detected 762 proteins in a single organelle whereas 160 proteins were found in all sub-cellular fractions. We verified the localization of identified proteins through databases and discussed the consistency of the obtained results. With regards to the ambiguity in the definition of a membrane protein, we tried to clearly define the plasma membrane, peripheral membrane and membrane proteins by annotation of these proteins in databases, along with predictions of transmembrane helices. Among ten enriched signaling pathways highlighted in our results, non-canonical Wnt signaling were analyzed in greater detail. The functions of three novel hESC membrane proteins (ERBB4, GGT1 and ZDHHC13) have been assessed in terms of pluripotency. Our report is the most comprehensive for organellar proteomics of hESCs. Significance Mass spectrometric identification of proteins using a TripleTOF 5600 from nucleus, mitochondria, crude membrane, cytoplasm, heavy and light microsomal fractions highlighted the significance of the non-canonical Wnt signaling in human embryonic stem cells.

AB - As the functions of proteins are associated with their cellular localization, the comprehensive sub-cellular proteome knowledge of human embryonic stem cells (hESCs) is indispensable for ensuring a therapeutic effect. Here, we have utilized a sub-cellular proteomics approach to analyze the localization of proteins in the nucleus, mitochondria, crude membrane, cytoplasm, heavy and light microsomes. Out of 2002 reproducibly identified proteins, we detected 762 proteins in a single organelle whereas 160 proteins were found in all sub-cellular fractions. We verified the localization of identified proteins through databases and discussed the consistency of the obtained results. With regards to the ambiguity in the definition of a membrane protein, we tried to clearly define the plasma membrane, peripheral membrane and membrane proteins by annotation of these proteins in databases, along with predictions of transmembrane helices. Among ten enriched signaling pathways highlighted in our results, non-canonical Wnt signaling were analyzed in greater detail. The functions of three novel hESC membrane proteins (ERBB4, GGT1 and ZDHHC13) have been assessed in terms of pluripotency. Our report is the most comprehensive for organellar proteomics of hESCs. Significance Mass spectrometric identification of proteins using a TripleTOF 5600 from nucleus, mitochondria, crude membrane, cytoplasm, heavy and light microsomal fractions highlighted the significance of the non-canonical Wnt signaling in human embryonic stem cells.

KW - Human embryonic stem cell

KW - Membrane proteomics

KW - Non-canonical Wnt signaling

KW - Organellar proteomics

KW - Surface marker

UR - http://www.scopus.com/inward/record.url?scp=85019158704&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85019158704&partnerID=8YFLogxK

U2 - 10.1016/j.jprot.2017.04.017

DO - 10.1016/j.jprot.2017.04.017

M3 - Article

C2 - 28435121

AN - SCOPUS:85019158704

VL - 162

SP - 108

EP - 118

JO - Journal of Proteomics

JF - Journal of Proteomics

SN - 1874-3919

ER -