Researcher, Royan institute
Cell membrane acts like a country toll, give entry/exit permission or receive/send messages to the surrounding environment. The tools of cell membrane to accomplish its responsibilities are proteins. These proteins can be regarded as biomarker so one of the mission of membrane proteomics is finding new biomarkers can be used in clinics. However, as noted by Thierry Rabilloud, Love is possible but so difficult. I have worked on membrane proteomics for more than 9 years since I was MSc student. Moreover, I have been involved in two international Human Proteome Organization initiatives on membrane proteomics. In one of these initiatives, I have prepared standard membrane samples for other countries including Australia, South Korea, China, Japan and Singapore in collaboration with Academia Sinica (Taiwan) and Royan institute (Iran). My PhD thesis was also about organellar proteomics.
In recent years, it has been shown that cells communicate each other by sending some kind of packages name vesicles surrounded by membrane. These packages can be easily find in blood, urine, etc. and providing attractive sources for membrane proteomics specially people loving biomarker discovery. After completion of my PhD, Prof. Baharvand (director of Royan Institute for Stem Cell Biology and Technology) asked me to focus on these vesicles because my previous experiences on membrane isolation and proteomic characterizations. Now, I am trying to establish extracellular vesicle group in Royan institute working on both therapeutic applications and biomarker discovery of extracellular vesicles.
Abstract: Embryonic stem cells (ESCs) are undifferentiated cells with two common remarkable features known as self-renewal and differentiation. Proteomics plays an increasingly important role in understanding molecular mechanisms underlying self-renewal and pluripotency of ESCs and their applications in cell therapy and developmental biology studies. As the function of a protein is strongly associated with its localization in cell, a complete and accurate picture of the proteome of ESCs cannot be achieved without knowing the subcellular locations of proteins. Subcellular fractionation allows enrichment of low abundant proteins and signaling complexes and reduces the complexity of the sample. It also provided insight into tracking proteins that shuttle between different compartments. Despite the substantial interest and efforts in ESC subcellular proteomics area, progress has been relatively limited. In this review, we present an overview on current status of ESCs organelle proteomics research and discuss challenges in subcellular proteomics.
Pub.: 06 Jul '14, Pinned: 29 Jul '17
Abstract: Human embryonic stem cells (hESCs) have great potential for use in developmental biology studies, functional genomics applications, drug screening, and regenerative medicine. A detailed understanding of the molecular mechanisms that are responsible for maintaining the undifferentiated and pluripotent nature of hESCs is essential for their effective therapeutic application. It has become evident that many complex cellular processes are carried out by assemblies of protein molecules (protein complexes). Blue native polyacrylamide gel electrophoresis (BN-PAGE) has been used to separate protein complexes from whole cell lysates. Using BN-PAGE, we resolved cytoplasmic and membrane-associated complexes from hESCs and characterised their composition, stoichiometry, and dynamics by denaturing SDS-PAGE. The reliability of the fractionation was examined by western blot analysis of membrane and cytosolic markers. MALDI TOF/TOF mass spectrometry identified 119 cytosolic and 69 membrane proteins from the BN-PAGE proteome maps. Potential protein complexes were validated by computational prediction of possible protein-protein interactions using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database. Based on BN-PAGE gels and validation by databases, 82 heteromultimeric and 47 homomultimeric protein complexes have been found in hESCs. Resolving some of the protein complexes provided insight into the function of previously uncharacterised complexes in hESCs.
Pub.: 06 Jul '11, Pinned: 29 Jul '17
Abstract: The data presented here pertain to the research article entitled "Proteome Analysis of Human Embryonic Stem Cell Organelles" (Shekariet al., 2017 ). In the present article we endeavour to locate new proteins and pathways in human embryonic stem cells (hESCs) by mass spectrometry and bioinformatics analysis. We have analyzed total and mitochondrial proteins extracted from three biological replicates of the hESC H9 cell line according to mass spectrometry proteomics and bioinformatics investigations.
Pub.: 01 Jul '17, Pinned: 29 Jul '17
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.
Pub.: 20 Apr '17, Pinned: 29 Jul '17
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