Kinome-wide Functional Analysis Highlights the Role of Cytoskeletal Remodeling in Somatic Cell Reprogramming

Overview

Journal Cell Stem Cell

Publisher Cell Press

Specialty Cell Biology

Date 2014 Apr 8

PMID 24702998

Citations 38

Authors

Kumi Sakurai

Indrani Talukdar

Veena S Patil

Jason Dang

Zhonghan Li

Kung-Yen Chang

Chih-Chung Lu

Violaine Delorme-Walker

Celine DerMardirossian

Karen Anderson

Dorit Hanein

Chao-Shun Yang

Dongmei Wu

Yang Liu

Tariq M Rana

Affiliations

Soon will be listed here.

Abstract

The creation of induced pluripotent stem cells (iPSCs) from somatic cells by ectopic expression of transcription factors has galvanized the fields of regenerative medicine and developmental biology. Here, we report a kinome-wide RNAi-based analysis to identify kinases that regulate somatic cell reprogramming to iPSCs. We prepared 3,686 small hairpin RNA (shRNA) lentiviruses targeting 734 kinase genes covering the entire mouse kinome and individually examined their effects on iPSC generation. We identified 59 kinases as barriers to iPSC generation and characterized seven of them further. We found that shRNA-mediated knockdown of the serine/threonine kinases TESK1 or LIMK2 promoted mesenchymal-to-epithelial transition, decreased COFILIN phosphorylation, and disrupted Actin filament structures during reprogramming of mouse embryonic fibroblasts. Similarly, knockdown of TESK1 in human fibroblasts also promoted reprogramming to iPSCs. Our study reveals the breadth of kinase networks regulating pluripotency and identifies a role for cytoskeletal remodeling in modulating the somatic cell reprogramming process.

Citing Articles

The interferon γ pathway enhances pluripotency and X-chromosome reactivation in iPSC reprogramming.

Barrero M, Lazarenkov A, Blanco E, Palma L, Lopez-Rubio A, Bauer M Sci Adv. 2024; 10(32):eadj8862.

PMID: 39110794 PMC: 11305397. DOI: 10.1126/sciadv.adj8862.

PIM1 promotes hepatic conversion by suppressing reprogramming-induced ferroptosis and cell cycle arrest.

Yuan Y, Wang C, Zhuang X, Lin S, Luo M, Deng W Nat Commun. 2022; 13(1):5237.

PMID: 36068222 PMC: 9448736. DOI: 10.1038/s41467-022-32976-9.

Chaperonin-Containing TCP1 Subunit 5 Protects Against the Effect of Mer Receptor Tyrosine Kinase Knockdown in Retinal Pigment Epithelial Cells by Interacting With Filamentous Actin and Activating the LIM-Kinase 1/Cofilin Pathway.

Feng L, Li H, Du Y, Zhang T, Zhu Y, Li Z Front Med (Lausanne). 2022; 9:861371.

PMID: 35492354 PMC: 9043132. DOI: 10.3389/fmed.2022.861371.

An shRNA kinase screen identifies regulators of UHRF1 stability and activity in mouse embryonic stem cells.

Rushton M, Saunderson E, Patani H, Green M, Ficz G Epigenetics. 2022; 17(12):1590-1607.

PMID: 35324392 PMC: 9621053. DOI: 10.1080/15592294.2022.2044126.

The Role of LIM Kinases during Development: A Lens to Get a Glimpse of Their Implication in Pathologies.

Ribba A, Fraboulet S, Sadoul K, Lafanechere L Cells. 2022; 11(3).

PMID: 35159213 PMC: 8834001. DOI: 10.3390/cells11030403.

References

Lu Z, Hunter T . Degradation of activated protein kinases by ubiquitination. Annu Rev Biochem. 2009; 78:435-75. PMC: 2776765. DOI: 10.1146/annurev.biochem.013008.092711. View

Wernig M, Meissner A, Foreman R, Brambrink T, Ku M, Hochedlinger K . In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature. 2007; 448(7151):318-24. DOI: 10.1038/nature05944. View

Ruiz S, Panopoulos A, Herrerias A, Bissig K, Lutz M, Berggren W . A high proliferation rate is required for cell reprogramming and maintenance of human embryonic stem cell identity. Curr Biol. 2010; 21(1):45-52. PMC: 3034649. DOI: 10.1016/j.cub.2010.11.049. View

Li Z, Rana T . A kinase inhibitor screen identifies small-molecule enhancers of reprogramming and iPS cell generation. Nat Commun. 2012; 3:1085. PMC: 3658009. DOI: 10.1038/ncomms2059. View

Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P . The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res. 2010; 39(Database issue):D561-8. PMC: 3013807. DOI: 10.1093/nar/gkq973. View

Silva J, Barrandon O, Nichols J, Kawaguchi J, Theunissen T, Smith A . Promotion of reprogramming to ground state pluripotency by signal inhibition. PLoS Biol. 2008; 6(10):e253. PMC: 2570424. DOI: 10.1371/journal.pbio.0060253. View

Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K . Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell. 2007; 131(5):861-72. DOI: 10.1016/j.cell.2007.11.019. View

Yu J, Vodyanik M, Smuga-Otto K, Antosiewicz-Bourget J, Frane J, Tian S . Induced pluripotent stem cell lines derived from human somatic cells. Science. 2007; 318(5858):1917-20. DOI: 10.1126/science.1151526. View

Wiggan O, Shaw A, DeLuca J, Bamburg J . ADF/cofilin regulates actomyosin assembly through competitive inhibition of myosin II binding to F-actin. Dev Cell. 2012; 22(3):530-43. PMC: 3306597. DOI: 10.1016/j.devcel.2011.12.026. View

10.

Vardouli L, Moustakas A, Stournaras C . LIM-kinase 2 and cofilin phosphorylation mediate actin cytoskeleton reorganization induced by transforming growth factor-beta. J Biol Chem. 2005; 280(12):11448-57. DOI: 10.1074/jbc.M402651200. View

11.

Li R, Liang J, Ni S, Zhou T, Qing X, Li H . A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts. Cell Stem Cell. 2010; 7(1):51-63. DOI: 10.1016/j.stem.2010.04.014. View

12.

Li W, Wei W, Zhu S, Zhu J, Shi Y, Lin T . Generation of rat and human induced pluripotent stem cells by combining genetic reprogramming and chemical inhibitors. Cell Stem Cell. 2008; 4(1):16-9. DOI: 10.1016/j.stem.2008.11.014. View

13.

Lee D, Su J, Ang Y, Carvajal-Vergara X, Mulero-Navarro S, Pereira C . Regulation of embryonic and induced pluripotency by aurora kinase-p53 signaling. Cell Stem Cell. 2012; 11(2):179-94. PMC: 3413175. DOI: 10.1016/j.stem.2012.05.020. View

14.

Lengner C, Camargo F, Hochedlinger K, Welstead G, Zaidi S, Gokhale S . Oct4 expression is not required for mouse somatic stem cell self-renewal. Cell Stem Cell. 2007; 1(4):403-15. PMC: 2151746. DOI: 10.1016/j.stem.2007.07.020. View

15.

Kligys K, Claiborne J, Debiase P, Hopkinson S, Wu Y, Mizuno K . The slingshot family of phosphatases mediates Rac1 regulation of cofilin phosphorylation, laminin-332 organization, and motility behavior of keratinocytes. J Biol Chem. 2007; 282(44):32520-8. PMC: 2754063. DOI: 10.1074/jbc.M707041200. View

16.

Shi Y, Desponts C, Do J, Hahm H, Scholer H, Ding S . Induction of pluripotent stem cells from mouse embryonic fibroblasts by Oct4 and Klf4 with small-molecule compounds. Cell Stem Cell. 2008; 3(5):568-74. DOI: 10.1016/j.stem.2008.10.004. View

17.

Park I, Zhao R, West J, Yabuuchi A, Huo H, Ince T . Reprogramming of human somatic cells to pluripotency with defined factors. Nature. 2007; 451(7175):141-6. DOI: 10.1038/nature06534. View

18.

Burdon T, Stracey C, Chambers I, Nichols J, Smith A . Suppression of SHP-2 and ERK signalling promotes self-renewal of mouse embryonic stem cells. Dev Biol. 1999; 210(1):30-43. DOI: 10.1006/dbio.1999.9265. View

19.

Takahashi K, Yamanaka S . Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006; 126(4):663-76. DOI: 10.1016/j.cell.2006.07.024. View

20.

Samavarchi-Tehrani P, Golipour A, David L, Sung H, Beyer T, Datti A . Functional genomics reveals a BMP-driven mesenchymal-to-epithelial transition in the initiation of somatic cell reprogramming. Cell Stem Cell. 2010; 7(1):64-77. DOI: 10.1016/j.stem.2010.04.015. View