title: Quantitative Analysis of Human Pluripotency and Neural Specification by In-Depth (Phospho)Proteomic Profiling.
abstract: Controlled differentiation of human embryonic stem cells (hESCs) can be utilized for precise analysis of cell type identities during early development. We established a highly efficient neural induction strategy and an improved analytical platform, and determined proteomic and phosphoproteomic profiles of hESCs and their specified multipotent neural stem cell derivatives (hNSCs). This quantitative dataset (nearly 13,000 proteins and 60,000 phosphorylation sites) provides unique molecular insights into pluripotency and neural lineage entry. Systems-level comparative analysis of proteins (e.g., transcription factors, epigenetic regulators, kinase families), phosphorylation sites, and numerous biological pathways allowed the identification of distinct signatures in pluripotent and multipotent cells. Furthermore, as predicted by the dataset, we functionally validated an autocrine/paracrine mechanism by demonstrating that the secreted protein midkine is a regulator of neural specification. This resource is freely available to the scientific community, including a searchable website, PluriProt.
authors: Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA. Electronic address: ilyas.singec@nih.gov.
authors: Ilyas
authors: I
authors: Singec
authors: Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
authors: Andrew M
authors: AM
authors: Crain
authors: Proteomics Facility, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
authors: Junjie
authors: J
authors: Hou
authors: Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
authors: Brian T D
authors: BTD
authors: Tobe
authors: Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
authors: Maria
authors: M
authors: Talantova
authors: Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
authors: Alicia A
authors: AA
authors: Winquist
authors: Informatics and Data Management, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
authors: Kutbuddin S
authors: KS
authors: Doctor
authors: Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
authors: Jennifer
authors: J
authors: Choy
authors: Informatics and Data Management, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
authors: Xiayu
authors: X
authors: Huang
authors: Department of Biology, Vrije Universiteit Brussel, 1050 Brussels, Belgium.
authors: Esther
authors: E
authors: La Monaca
authors: Thermo Fisher Scientific Inc., San Jose, CA 95134, USA.
authors: David M
authors: DM
authors: Horn
authors: Proteomics Facility, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
authors: Dieter A
authors: DA
authors: Wolf
authors: Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
authors: Stuart A
authors: SA
authors: Lipton
authors: Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; Department of Biology, Vrije Universiteit Brussel, 1050 Brussels, Belgium.
authors: Gustavo J
authors: GJ
authors: Gutierrez
authors: Proteomics Facility, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA. Electronic address: lbrill@san.rr.com.
authors: Laurence M
authors: LM
authors: Brill
authors: Center for Stem Cells and Regenerative Medicine, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA. Electronic address: esnyder@sbpdiscovery.org.
authors: Evan Y
authors: EY
authors: Snyder
mesh_terms: D000818:Animals; D002454:Cell Differentiation / Q000235:genetics; D019070:Cell Lineage / Q000235:genetics; D002478:Cells, Cultured; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D055785:Gene Knockdown Techniques; D006801:Humans; D009474:Neurons / Q000166:cytology / Q000378:metabolism*; D010750:Phosphoproteins / Q000378:metabolism*; D039904:Pluripotent Stem Cells / Q000166:cytology* / Q000378:metabolism*; D020543:Proteome; D040901:Proteomics / Q000379:methods; D015398:Signal Transduction; D059467:Transcriptome
chemical_list: D010750:Phosphoproteins; D020543:Proteome