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Niwayama S, Zabet-Moghaddam M, Kurono S, Kattanguru P, Shaikh AL. Synthesis of d-labeled and unlabeled ethyl succinic anhydrides and application to quantitative analysis of peptides by isotope differential mass spectrometry. Bioorg Med Chem Lett 2016; 26:5073-5077. [PMID: 27624079 DOI: 10.1016/j.bmcl.2016.08.079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 08/19/2016] [Accepted: 08/24/2016] [Indexed: 11/18/2022]
Abstract
Ethyl succinic anhydride and its d5-labeled version have been synthesized and applied to quantitative analysis of peptides in combination with MALDI or ESI mass spectrometry. These modifiers react with amino groups in the N-termini and lysine side chains in proteins, and therefore the combination of these modifiers was shown to be a useful tool for quantification of peptides and hence for proteomics research.
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Affiliation(s)
- Satomi Niwayama
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA; Department of Ophthalmology and Visual Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Graduate School of Engineering, Muroran Institute of Technology, Muroran, Hokkaido 050-8585, Japan.
| | - Masoud Zabet-Moghaddam
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Sadamu Kurono
- Joint Research Laboratory of Molecular Signature Analysis, Division of Health Sciences, Osaka University Graduate School of Medicine, 1-7 Yamadaoka, Suita, Osaka 565-0871, Japan; Laboratory and Specialty Chemicals Division, Wako Pure Chemical Industries, Ltd, 3-1-2 Doshomachi, Chuo-ku, Osaka, Osaka 540-8605, Japan
| | - Pullaiah Kattanguru
- Graduate School of Engineering, Muroran Institute of Technology, Muroran, Hokkaido 050-8585, Japan
| | - Aarif L Shaikh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
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2
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Scheerlinck E, Van Steendam K, Daled S, Govaert E, Vossaert L, Meert P, Van Nieuwerburgh F, Van Soom A, Peelman L, De Sutter P, Heindryckx B, Dhaenens M, Deforce D. Assessing the impact of minimizing arginine conversion in fully defined SILAC culture medium in human embryonic stem cells. Proteomics 2016; 16:2605-2614. [PMID: 27392809 PMCID: PMC5096064 DOI: 10.1002/pmic.201600174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 05/23/2016] [Accepted: 07/05/2016] [Indexed: 11/29/2022]
Abstract
We present a fully defined culture system (adapted Essential8TM [E8TM] medium in combination with vitronectin) for human embryonic stem cells that can be used for SILAC purposes. Although a complete incorporation of the labels was observed after 4 days in culture, over 90% of precursors showed at least 10% conversion. To reduce this arginine conversion, E8TM medium was modified by adding (1) l‐proline, (2) l‐ornithine, (3) Nω‐hydroxy‐nor‐l‐arginine acetate, or by (4) lowering the arginine concentration. Reduction of arginine conversion was best obtained by adding 5 mM l‐ornithine, followed by 3.5 mM l‐proline and by lowering the arginine concentration in the medium to 99.5 μM. No major changes in pluripotency and cell amount could be observed for the adapted E8TM media with ornithine and proline. However, our subsequent ion mobility assisted data‐independent acquisition (high‐definition MS) proteome analysis cautions for ongoing changes in the proteome when aiming at longer term suppression of arginine conversion.
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Affiliation(s)
- Ellen Scheerlinck
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Katleen Van Steendam
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Simon Daled
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Elisabeth Govaert
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Liesbeth Vossaert
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Paulien Meert
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Ann Van Soom
- Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Luc Peelman
- Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Petra De Sutter
- Ghent Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - Björn Heindryckx
- Ghent Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - Maarten Dhaenens
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Dieter Deforce
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium.
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Billing AM, Ben Hamidane H, Bhagwat AM, Cotton RJ, Dib SS, Kumar P, Hayat S, Goswami N, Suhre K, Rafii A, Graumann J. Complementarity of SOMAscan to LC-MS/MS and RNA-seq for quantitative profiling of human embryonic and mesenchymal stem cells. J Proteomics 2016; 150:86-97. [PMID: 27613379 DOI: 10.1016/j.jprot.2016.08.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/01/2016] [Accepted: 08/29/2016] [Indexed: 11/16/2022]
Abstract
Dynamic range limitations are challenging to proteomics, particularly in clinical samples. Affinity proteomics partially overcomes this, yet suffers from dependence on reagent quality. SOMAscan, an aptamer-based platform for over 1000 proteins, avoids that issue using nucleic acid binders. Targets include low expressed proteins not easily accessible by other approaches. Here we report on the potential of SOMAscan for the study of differently sourced mesenchymal stem cells (MSC) in comparison to LC-MS/MS and RNA sequencing. While targeting fewer analytes, SOMAscan displays high precision and dynamic range coverage, allowing quantification of proteins not measured by the other platforms. Expression between cell types (ESC and MSC) was compared across techniques and uncovered the expected large differences. Sourcing was investigated by comparing subtypes: bone marrow-derived, standard in clinical studies, and ESC-derived MSC, thought to hold similar potential but devoid of inter-donor variability and proliferating faster in vitro. We confirmed subtype-equivalency, as well as vesicle and extracellular matrix related processes in MSC. In contrast, the proliferative nature of ESC was captured less by SOMAscan, where nuclear proteins are underrepresented. The complementary of SOMAscan allowed the comprehensive exploration of CD markers and signaling molecules, not readily accessible otherwise and offering unprecedented potential in subtype characterization. SIGNIFICANCE Mesenchymal stem cells (MSC) represent promising stem cell-derived therapeutics as indicated by their application in >500 clinical trials currently registered with the NIH. Tissue-derived MSC require invasive harvesting and imply donor-to-donor differences, to which embryonic stem cell (ESC)-derived MSC may provide an alternative and thus warrant thorough characterization. In continuation of our previous study where we compared in depth embryonic stem cells (ESC) and MSC from two sources (bone marrow and ESC-derived), we included the aptamer-based SOMAscan assay, complementing LC-MS/MS and RNA-seq data. Furthermore, SOMAscan, a targeted proteomics platform developed for analyzing clinical samples, has been benchmarked against established analytical platforms (LC-MS/MS and RNA-seq) using stem cell comparisons as a model.
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Affiliation(s)
- Anja M Billing
- Research Division, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | | | - Aditya M Bhagwat
- Research Division, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Richard J Cotton
- Research Division, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Shaima S Dib
- Research Division, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Pankaj Kumar
- Research Division, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Shahina Hayat
- Research Division, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Neha Goswami
- Research Division, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Karsten Suhre
- Research Division, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Arash Rafii
- Research Division, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Johannes Graumann
- Research Division, Weill Cornell Medical College in Qatar, Doha, Qatar.
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Comprehensive transcriptomic and proteomic characterization of human mesenchymal stem cells reveals source specific cellular markers. Sci Rep 2016; 6:21507. [PMID: 26857143 PMCID: PMC4746666 DOI: 10.1038/srep21507] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 01/26/2016] [Indexed: 12/13/2022] Open
Abstract
Mesenchymal stem cells (MSC) are multipotent cells with great potential in therapy, reflected by more than 500 MSC-based clinical trials registered with the NIH. MSC are derived from multiple tissues but require invasive harvesting and imply donor-to-donor variability. Embryonic stem cell-derived MSC (ESC-MSC) may provide an alternative, but how similar they are to ex vivo MSC is unknown. Here we performed an in depth characterization of human ESC-MSC, comparing them to human bone marrow-derived MSC (BM-MSC) as well as human embryonic stem cells (hESC) by transcriptomics (RNA-seq) and quantitative proteomics (nanoLC-MS/MS using SILAC). Data integration highlighted and validated a central role of vesicle-mediated transport and exosomes in MSC biology and also demonstrated, through enrichment analysis, their versatility and broad application potential. Particular emphasis was placed on comparing profiles between ESC-MSC and BM-MSC and assessing their equivalency. Data presented here shows that differences between ESC-MSC and BM-MSC are similar in magnitude to those reported for MSC of different origin and the former may thus represent an alternative source for therapeutic applications. Finally, we report an unprecedented coverage of MSC CD markers, as well as membrane associated proteins which may benefit immunofluorescence-based applications and contribute to a refined molecular description of MSC.
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Abdesselem H, Madani A, Hani A, Al-Noubi M, Goswami N, Ben Hamidane H, Billing AM, Pasquier J, Bonkowski MS, Halabi N, Dalloul R, Sheriff MZ, Mesaeli N, ElRayess M, Sinclair DA, Graumann J, Mazloum NA. SIRT1 Limits Adipocyte Hyperplasia through c-Myc Inhibition. J Biol Chem 2015; 291:2119-35. [PMID: 26655722 PMCID: PMC4732199 DOI: 10.1074/jbc.m115.675645] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Indexed: 01/14/2023] Open
Abstract
The expansion of fat mass in the obese state is due to increased adipocyte hypertrophy and hyperplasia. The molecular mechanism that drives adipocyte hyperplasia remains unknown. The NAD(+)-dependent protein deacetylase sirtuin 1 (SIRT1), a key regulator of mammalian metabolism, maintains proper metabolic functions in many tissues, counteracting obesity. Here we report that differentiated adipocytes are hyperplastic when SIRT1 is knocked down stably in mouse 3T3-L1 preadipocytes. This phenotype is associated with dysregulated adipocyte metabolism and enhanced inflammation. We also demonstrate that SIRT1 is a key regulator of proliferation in preadipocytes. Quantitative proteomics reveal that the c-Myc pathway is altered to drive enhanced proliferation in SIRT1-silenced 3T3-L1 cells. Moreover, c-Myc is hyperacetylated, levels of p27 are reduced, and cyclin-dependent kinase 2 (CDK2) is activated upon SIRT1 reduction. Remarkably, differentiating SIRT1-silenced preadipocytes exhibit enhanced mitotic clonal expansion accompanied by reduced levels of p27 as well as elevated levels of CCAAT/enhancer-binding protein β (C/EBPβ) and c-Myc, which is also hyperacetylated. c-Myc activation and enhanced proliferation phenotype are also found to be SIRT1-dependent in proliferating mouse embryonic fibroblasts and differentiating human SW872 preadipocytes. Reducing both SIRT1 and c-Myc expression in 3T3-L1 cells simultaneously does not induce the adipocyte hyperplasia phenotype, confirming that SIRT1 controls adipocyte hyperplasia through c-Myc regulation. A better understanding of the molecular mechanisms of adipocyte hyperplasia will open new avenues toward understanding obesity.
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Affiliation(s)
| | - Aisha Madani
- From the Departments of Microbiology and Immunology
| | - Ahmad Hani
- From the Departments of Microbiology and Immunology
| | | | | | | | | | - Jennifer Pasquier
- Genetic Medicine, Weill Cornell Medicine Qatar, Qatar Foundation, Education City, P.O. Box 24144, Doha, Qatar
| | - Michael S Bonkowski
- the Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, and
| | - Najeeb Halabi
- Genetic Medicine, Weill Cornell Medicine Qatar, Qatar Foundation, Education City, P.O. Box 24144, Doha, Qatar
| | | | | | | | - Mohamed ElRayess
- the Life Sciences Research Division, Anti-Doping Lab Qatar, P.O. Box 27775, Doha, Qatar
| | - David A Sinclair
- the Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, and
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Billing AM, Ben Hamidane H, Graumann J. Quantitative Proteomic Approaches in Mouse: Stable Isotope Incorporation by Metabolic (SILAC) or Chemical Labeling (Reductive Dimethylation) Combined with High-Resolution Mass Spectrometry. ACTA ACUST UNITED AC 2015; 5:1-20. [DOI: 10.1002/9780470942390.mo140156] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Blanc V, Park E, Schaefer S, Miller M, Lin Y, Kennedy S, Billing AM, Hamidane HB, Graumann J, Mortazavi A, Nadeau JH, Davidson NO. Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver. Genome Biol 2014; 15:R79. [PMID: 24946870 PMCID: PMC4197816 DOI: 10.1186/gb-2014-15-6-r79] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 06/19/2014] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND RNA editing encompasses a post-transcriptional process in which the genomically templated sequence is enzymatically altered and introduces a modified base into the edited transcript. Mammalian C-to-U RNA editing represents a distinct subtype of base modification, whose prototype is intestinal apolipoprotein B mRNA, mediated by the catalytic deaminase Apobec-1. However, the genome-wide identification, tissue-specificity and functional implications of Apobec-1-mediated C-to-U RNA editing remain incompletely explored. RESULTS Deep sequencing, data filtering and Sanger-sequence validation of intestinal and hepatic RNA from wild-type and Apobec-1-deficient mice revealed 56 novel editing sites in 54 intestinal mRNAs and 22 novel sites in 17 liver mRNAs, all within 3' untranslated regions. Eleven of 17 liver RNAs shared editing sites with intestinal RNAs, while 6 sites are unique to liver. Changes in RNA editing lead to corresponding changes in intestinal mRNA and protein levels for 11 genes. Analysis of RNA editing in vivo following tissue-specific Apobec-1 adenoviral or transgenic Apobec-1 overexpression reveals that a subset of targets identified in wild-type mice are restored in Apobec-1-deficient mouse intestine and liver following Apobec-1 rescue. We find distinctive polysome profiles for several RNA editing targets and demonstrate novel exonic editing sites in nuclear preparations from intestine but not hepatic apolipoprotein B RNA. RNA editing is validated using cell-free extracts from wild-type but not Apobec-1-deficient mice, demonstrating that Apobec-1 is required. CONCLUSIONS These studies define selective, tissue-specific targets of Apobec-1-dependent RNA editing and show the functional consequences of editing are both transcript- and tissue-specific.
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Affiliation(s)
- Valerie Blanc
- Department of Medicine, Washington University St Louis, St Louis, MO 63110, USA
| | - Eddie Park
- Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Sabine Schaefer
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | - Melanie Miller
- Department of Medicine, Washington University St Louis, St Louis, MO 63110, USA
| | - Yiing Lin
- Departments of Surgery, Washington University St Louis, St Louis, MO 63110, USA
| | - Susan Kennedy
- Department of Medicine, Washington University St Louis, St Louis, MO 63110, USA
| | - Anja M Billing
- Proteomics Core, Weill Cornell Medical College in Qatar, Doha, Qatar
| | | | - Johannes Graumann
- Proteomics Core, Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Ali Mortazavi
- Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - Joseph H Nadeau
- Pacific Northwest Research Institute, Seattle, WA 98122, USA
| | - Nicholas O Davidson
- Department of Medicine, Washington University St Louis, St Louis, MO 63110, USA
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