A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells

Anja M. Billing, Shaima S. Dib, Aditya M. Bhagwat, Israel T. da Silva, Rodrigo D. Drummond, Shahina Hayat, Rasha Al-Mismar, Hisham Ben-Hamidane, Neha Goswami, Kasper Engholm-Keller, Martin R. Larsen, Karsten Suhre, Arash Rafii, Johannes Graumann

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

Mesenchymal stem/stromal cells (MSCs) are self-renewing multipotent cells with regenerative, secretory and immunomodulatory capabilities that are beneficial for the treatment of various diseases. To avoid the issues that come with using tissue-derived MSCs in therapy, MSCs may be generated by the differentiation of human embryonic stems cells (hESCs) in culture. However, the changes that occur during the differentiation process have not been comprehensively characterized. Here, we combined transcriptome, proteome and phosphoproteome profiling to perform an in-depth, multi-omics study of the hESCs-to-MSCs differentiation process. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation. Among the earliest and strongest induced proteins with extensive differential phosphorylation was AHNAK, which we hypothesized to be a defining factor in MSC biology. We observed two distinct expression waves of developmental HOX genes and an AGO2-to-AGO3 switch in gene silencing. Exploring the kinetic of noncoding ORFs during differentiation, we mapped new functions to well annotated long noncoding RNAs (CARMN, MALAT, NEAT1, LINC00152) as well as new candidates which we identified to be important to the differentiation process. Phosphoproteome analysis revealed ESC and MSC-specific phosphorylation motifs with PAK2 and RAF1 as top predicted upstream kinases in MSCs. Our data represent a rich systems-level resource on ESC-to-MSC differentiation that will be useful for the study of stem cell biology.

OriginalsprogEngelsk
TidsskriftMolecular and Cellular Proteomics
Vol/bind18
Udgave nummer10
Sider (fra-til)1950-1966
ISSN1535-9476
DOI
StatusUdgivet - 1. okt. 2019

Fingeraftryk

Stem cells
Mesenchymal Stromal Cells
Cytology
Phosphorylation
Genes
Human Embryonic Stem Cells
Long Noncoding RNA
Cell Biology
Cell Differentiation
Proteome
Switch Genes
Cell culture
Proteins
Phosphotransferases
Switches
RNA
Tissue
Transcriptome
Open Reading Frames
Kinetics

Citer dette

Billing, Anja M. ; Dib, Shaima S. ; Bhagwat, Aditya M. ; da Silva, Israel T. ; Drummond, Rodrigo D. ; Hayat, Shahina ; Al-Mismar, Rasha ; Ben-Hamidane, Hisham ; Goswami, Neha ; Engholm-Keller, Kasper ; Larsen, Martin R. ; Suhre, Karsten ; Rafii, Arash ; Graumann, Johannes. / A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells. I: Molecular and Cellular Proteomics. 2019 ; Bind 18, Nr. 10. s. 1950-1966.
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abstract = "Mesenchymal stem/stromal cells (MSCs) are self-renewing multipotent cells with regenerative, secretory and immunomodulatory capabilities that are beneficial for the treatment of various diseases. To avoid the issues that come with using tissue-derived MSCs in therapy, MSCs may be generated by the differentiation of human embryonic stems cells (hESCs) in culture. However, the changes that occur during the differentiation process have not been comprehensively characterized. Here, we combined transcriptome, proteome and phosphoproteome profiling to perform an in-depth, multi-omics study of the hESCs-to-MSCs differentiation process. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation. Among the earliest and strongest induced proteins with extensive differential phosphorylation was AHNAK, which we hypothesized to be a defining factor in MSC biology. We observed two distinct expression waves of developmental HOX genes and an AGO2-to-AGO3 switch in gene silencing. Exploring the kinetic of noncoding ORFs during differentiation, we mapped new functions to well annotated long noncoding RNAs (CARMN, MALAT, NEAT1, LINC00152) as well as new candidates which we identified to be important to the differentiation process. Phosphoproteome analysis revealed ESC and MSC-specific phosphorylation motifs with PAK2 and RAF1 as top predicted upstream kinases in MSCs. Our data represent a rich systems-level resource on ESC-to-MSC differentiation that will be useful for the study of stem cell biology.",
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author = "Billing, {Anja M.} and Dib, {Shaima S.} and Bhagwat, {Aditya M.} and {da Silva}, {Israel T.} and Drummond, {Rodrigo D.} and Shahina Hayat and Rasha Al-Mismar and Hisham Ben-Hamidane and Neha Goswami and Kasper Engholm-Keller and Larsen, {Martin R.} and Karsten Suhre and Arash Rafii and Johannes Graumann",
year = "2019",
month = "10",
day = "1",
doi = "10.1074/mcp.RA119.001356",
language = "English",
volume = "18",
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journal = "Molecular and Cellular Proteomics",
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Billing, AM, Dib, SS, Bhagwat, AM, da Silva, IT, Drummond, RD, Hayat, S, Al-Mismar, R, Ben-Hamidane, H, Goswami, N, Engholm-Keller, K, Larsen, MR, Suhre, K, Rafii, A & Graumann, J 2019, 'A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells', Molecular and Cellular Proteomics, bind 18, nr. 10, s. 1950-1966. https://doi.org/10.1074/mcp.RA119.001356

A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells. / Billing, Anja M.; Dib, Shaima S.; Bhagwat, Aditya M.; da Silva, Israel T.; Drummond, Rodrigo D.; Hayat, Shahina; Al-Mismar, Rasha; Ben-Hamidane, Hisham; Goswami, Neha; Engholm-Keller, Kasper; Larsen, Martin R.; Suhre, Karsten; Rafii, Arash; Graumann, Johannes.

I: Molecular and Cellular Proteomics, Bind 18, Nr. 10, 01.10.2019, s. 1950-1966.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells

AU - Billing, Anja M.

AU - Dib, Shaima S.

AU - Bhagwat, Aditya M.

AU - da Silva, Israel T.

AU - Drummond, Rodrigo D.

AU - Hayat, Shahina

AU - Al-Mismar, Rasha

AU - Ben-Hamidane, Hisham

AU - Goswami, Neha

AU - Engholm-Keller, Kasper

AU - Larsen, Martin R.

AU - Suhre, Karsten

AU - Rafii, Arash

AU - Graumann, Johannes

PY - 2019/10/1

Y1 - 2019/10/1

N2 - Mesenchymal stem/stromal cells (MSCs) are self-renewing multipotent cells with regenerative, secretory and immunomodulatory capabilities that are beneficial for the treatment of various diseases. To avoid the issues that come with using tissue-derived MSCs in therapy, MSCs may be generated by the differentiation of human embryonic stems cells (hESCs) in culture. However, the changes that occur during the differentiation process have not been comprehensively characterized. Here, we combined transcriptome, proteome and phosphoproteome profiling to perform an in-depth, multi-omics study of the hESCs-to-MSCs differentiation process. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation. Among the earliest and strongest induced proteins with extensive differential phosphorylation was AHNAK, which we hypothesized to be a defining factor in MSC biology. We observed two distinct expression waves of developmental HOX genes and an AGO2-to-AGO3 switch in gene silencing. Exploring the kinetic of noncoding ORFs during differentiation, we mapped new functions to well annotated long noncoding RNAs (CARMN, MALAT, NEAT1, LINC00152) as well as new candidates which we identified to be important to the differentiation process. Phosphoproteome analysis revealed ESC and MSC-specific phosphorylation motifs with PAK2 and RAF1 as top predicted upstream kinases in MSCs. Our data represent a rich systems-level resource on ESC-to-MSC differentiation that will be useful for the study of stem cell biology.

AB - Mesenchymal stem/stromal cells (MSCs) are self-renewing multipotent cells with regenerative, secretory and immunomodulatory capabilities that are beneficial for the treatment of various diseases. To avoid the issues that come with using tissue-derived MSCs in therapy, MSCs may be generated by the differentiation of human embryonic stems cells (hESCs) in culture. However, the changes that occur during the differentiation process have not been comprehensively characterized. Here, we combined transcriptome, proteome and phosphoproteome profiling to perform an in-depth, multi-omics study of the hESCs-to-MSCs differentiation process. Based on RNA-to-protein correlation, we determined a set of high confidence genes that are important to differentiation. Among the earliest and strongest induced proteins with extensive differential phosphorylation was AHNAK, which we hypothesized to be a defining factor in MSC biology. We observed two distinct expression waves of developmental HOX genes and an AGO2-to-AGO3 switch in gene silencing. Exploring the kinetic of noncoding ORFs during differentiation, we mapped new functions to well annotated long noncoding RNAs (CARMN, MALAT, NEAT1, LINC00152) as well as new candidates which we identified to be important to the differentiation process. Phosphoproteome analysis revealed ESC and MSC-specific phosphorylation motifs with PAK2 and RAF1 as top predicted upstream kinases in MSCs. Our data represent a rich systems-level resource on ESC-to-MSC differentiation that will be useful for the study of stem cell biology.

KW - cell differentiation

KW - developmental biology

KW - differentiation

KW - gene expression

KW - human embryonic stem cells

KW - human mesenchymal stem cells

KW - LC-MS/MS

KW - phosphoproteome

KW - post-translational modifications

KW - quantification

KW - quantitative proteomics

KW - RNA SEQ

KW - stem cells

KW - systems biology

U2 - 10.1074/mcp.RA119.001356

DO - 10.1074/mcp.RA119.001356

M3 - Journal article

C2 - 31332097

AN - SCOPUS:85072849099

VL - 18

SP - 1950

EP - 1966

JO - Molecular and Cellular Proteomics

JF - Molecular and Cellular Proteomics

SN - 1535-9476

IS - 10

ER -