TY - JOUR
T1 - Global Proteomic and Methylome Analysis in Human Induced Pluripotent Stem Cells Reveals Overexpression of a Human TLR3 Affecting Proper Innate Immune Response Signaling
AU - Requena, Jordi
AU - Belen Alvarez-Palomo, Ana
AU - Codina-Pascual, Montserrat
AU - Delgado-Morales, Raul
AU - Moran, Sebastian
AU - Esteller, Manel
AU - Sal, Marti
AU - Juan, Manel
AU - Boronat Barado, Anna
AU - Consiglio, Antonella
AU - Addeleccia Bogle, Orleigh
AU - Wolvetang, Ernst
AU - Ovchinnikov, Dmitry
AU - Alvarez, Inaki
AU - Jaraquemada, Dolores
AU - Mezquita-Pla, Jovita
AU - Oliva, Rafael
AU - Edel, Michael J.
N1 - Funding Information:
We acknowledge the support of the following people: Angel Raya Centre for Regenerative Medicine Barcelona (CMRB), John Christo-doulou of the University of Sydney, Eduard Palou Rivera for HLA analysis, Josep Maria Estanyol of the Technological and Scientific Centre at the University of Barcelona, a member of the ProteoRed network (http://www.proteored.org/) for assistance in the proteo-mic analysis, Montserrat Pau for technical assistance, Carmen Bar-rot for RT-PCR analysis. Isabel Crespo Torres, Responsable Plataforma Citometria IDIBAPS. MJE is supported in part by the Program Ramon y Cajal (RYC-2010-06512), FBG project 307900, MINECO project grant BFU2011–26596, BFU2014-54467-P, TV3 Marato project grant /FBG309768 and Talent Retention program, University of Barcelona. The proteomic analysis was supported by projects from the Ministerio de Economica y Competitividad P113/00699 and EU-PF7-PEOPLE-2011-ITN289880 to RO. Dr. Manel Esteller laboratory is supported by, among other institutions, the EU Joint Programme – Neurodegenerative Disease Research (JPND); Cellex Foundation; the Health and Science Departments of the Catalan Government (Generalitat de Catalunya); the E-Rare (ERA-Net for research programs on rare diseases) and EuroRETT (a European network on Rett syndrome, funded by the European Commission under its 6th Framework Program since 2006). Dr. Manel Esteller is an ICREA Research Professor. Anto-nella Consiglio laboratory is supported by the European Research Council-ERC (2012-StG-311736-PD-HUMMODEL), the Spanish Ministry of Economy and Competitiveness-MINECO (BFU2016-80870-P), Instituto de Salud Carlos III-ISCIII/ FEDER (Red de Terapia Celular - TerCel RD16/0011/0024), AGAUR (2017-SGR-899). Contact R. Delgado-Morales and M. Esteller for comments on the methylome array. Contact R. Oliva for comments on the proteomic screen.
Funding Information:
We acknowledge the support of the following people: Angel Raya Centre for Regenerative Medicine Barcelona (CMRB), John Christodoulou of the University of Sydney, Eduard Palou Rivera for HLA analysis, Josep Maria Estanyol of the Technological and Scientific Centre at the University of Barcelona, a member of the ProteoRed network (http://www.proteored.org/) for assistance in the proteomic analysis, Montserrat Pau for technical assistance, Carmen Barrot for RT-PCR analysis. Isabel Crespo Torres, Responsable Plataforma Citometria IDIBAPS. MJE is supported in part by the Program Ramon y Cajal (RYC-2010-06512), FBG project 307900, MINECO project grant BFU2011?26596, BFU2014-54467-P, TV3 Marato project grant /FBG309768 and Talent Retention program, University of Barcelona. The proteomic analysis was supported by projects from the Ministerio de Economica y Competitividad P113/00699 and EU-PF7-PEOPLE-2011-ITN289880 to RO. Dr. Manel Esteller laboratory is supported by, among other institutions, the EU Joint Programme ? Neurodegenerative Disease Research (JPND); Cellex Foundation; the Health and Science Departments of the Catalan Government (Generalitat de Catalunya); the E-Rare (ERA-Net for research programs on rare diseases) and EuroRETT (a European network on Rett syndrome, funded by the European Commission under its 6th Framework Program since 2006). Dr. Manel Esteller is an ICREA Research Professor. Antonella Consiglio laboratory is supported by the European Research Council-ERC (2012-StG-311736- PD-HUMMODEL), the Spanish Ministry of Economy and Competitiveness-MINECO (BFU2016-80870-P), Instituto de Salud Carlos III-ISCIII/FEDER (Red de Terapia Celular - TerCel RD16/0011/0024), AGAUR (2017-SGR-899). Contact R. Delgado-Morales and M. Esteller for comments on the methylome array. Contact R. Oliva for comments on the proteomic screen.
Publisher Copyright:
©2019 The Authors. Stem Cells published by Wiley Periodicals, Inc. on behalf of AlphaMed Press 2019
PY - 2019/4
Y1 - 2019/4
N2 - When considering the clinical applications of autologous cell replacement therapy of human induced pluripotent stem cells (iPSC)-derived cells, there is a clear need to better understand what the immune response will be before we embark on extensive clinical trials to treat or model human disease. We performed a detailed assessment comparing human fibroblast cell lines (termed F1) reprogrammed into human iPSC and subsequently differentiated back to fibroblast cells (termed F2) or other human iPSC-derived cells including neural stem cells (NSC) made from either retroviral, episomal, or synthetic mRNA cell reprogramming methods. Global proteomic analysis reveals the main differences in signal transduction and immune cell protein expression between F1 and F2 cells, implicating wild type (WT) toll like receptor protein 3 (TLR3). Furthermore, global methylome analysis identified an isoform of the human TLR3 gene that is not epigenetically reset correctly upon differentiation to F2 cells resulting in a hypomethylated transcription start site in the TLR3 isoform promoter and overexpression in most human iPSC-derived cells not seen in normal human tissue. The human TLR3 isoform in human iPSC-NSC functions to suppress NF-KB p65 signaling pathway in response to virus (Poly IC), suggesting suppressed immunity of iPSC-derived cells to viral infection. The sustained WT TLR3 and TLR3 isoform overexpression is central to understanding the altered immunogenicity of human iPSC-derived cells calling for screening of human iPSC-derived cells for TLR3 expression levels before applications. Stem Cells2019;37:476-488
AB - When considering the clinical applications of autologous cell replacement therapy of human induced pluripotent stem cells (iPSC)-derived cells, there is a clear need to better understand what the immune response will be before we embark on extensive clinical trials to treat or model human disease. We performed a detailed assessment comparing human fibroblast cell lines (termed F1) reprogrammed into human iPSC and subsequently differentiated back to fibroblast cells (termed F2) or other human iPSC-derived cells including neural stem cells (NSC) made from either retroviral, episomal, or synthetic mRNA cell reprogramming methods. Global proteomic analysis reveals the main differences in signal transduction and immune cell protein expression between F1 and F2 cells, implicating wild type (WT) toll like receptor protein 3 (TLR3). Furthermore, global methylome analysis identified an isoform of the human TLR3 gene that is not epigenetically reset correctly upon differentiation to F2 cells resulting in a hypomethylated transcription start site in the TLR3 isoform promoter and overexpression in most human iPSC-derived cells not seen in normal human tissue. The human TLR3 isoform in human iPSC-NSC functions to suppress NF-KB p65 signaling pathway in response to virus (Poly IC), suggesting suppressed immunity of iPSC-derived cells to viral infection. The sustained WT TLR3 and TLR3 isoform overexpression is central to understanding the altered immunogenicity of human iPSC-derived cells calling for screening of human iPSC-derived cells for TLR3 expression levels before applications. Stem Cells2019;37:476-488
KW - Cytokine
KW - Human leukocyte antigen
KW - Immune response
KW - Induced pluripotent stem cells
KW - Inflammation
KW - MHC-I
KW - Neural stem cells
KW - Toll like receptor
KW - IMMUNOGENICITY
KW - BIOINFORMATICS
KW - EXPRESSION
KW - ACTIVATION
KW - NEURONS
KW - ROLES
U2 - 10.1002/stem.2966
DO - 10.1002/stem.2966
M3 - Article
C2 - 30664289
SN - 1066-5099
VL - 37
SP - 476
EP - 488
JO - Stem Cells
JF - Stem Cells
IS - 4
ER -