Genetic Variability Overrides the Impact of Parental Cell Type and Determines iPSC Differentiation Potential

Stem Cell Reports
Aija KyttäläRas Trokovic

Abstract

Reports on the retention of somatic cell memory in induced pluripotent stem cells (iPSCs) have complicated the selection of the optimal cell type for the generation of iPSC biobanks. To address this issue we compared transcriptomic, epigenetic, and differentiation propensities of genetically matched human iPSCs derived from fibroblasts and blood, two tissues of the most practical relevance for biobanking. Our results show that iPSC lines derived from the same donor are highly similar to each other. However, genetic variation imparts a donor-specific expression and methylation profile in reprogrammed cells that leads to variable functional capacities of iPSC lines. Our results suggest that integration-free, bona fide iPSC lines from fibroblasts and blood can be combined in repositories to form biobanks. Due to the impact of genetic variation on iPSC differentiation, biobanks should contain cells from large numbers of donors.

References

Jul 21, 1998·Annals of the New York Academy of Sciences·B G Forget
Apr 20, 2001·Proceedings of the National Academy of Sciences of the United States of America·V G TusherG Chu
Sep 4, 2003·Genome Research·Paul D ThomasApurva Narechania
Feb 3, 2004·Journal of Cell Science·J Michael Sorrell, Arnold I Caplan
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Oct 15, 2005·Nucleic Acids Research·Alexander MeissnerRudolf Jaenisch
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Gordon K Smyth
Jun 19, 2007·Nature Biotechnology·UNKNOWN International Stem Cell InitiativeWeidong Zhang
Jun 20, 2007·Nucleic Acids Research·Shannan J Ho SuiWyeth W Wasserman
Feb 19, 2008·Nature Biotechnology·Kenji OsafuneDouglas A Melton
Aug 2, 2008·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Laura L EloTero Aittokallio
Aug 24, 2010·Cell Stem Cell·Jason TchieuKathrin Plath
Sep 15, 2010·Nature Reviews. Genetics·Jeffrey T LeekRafael A Irizarry
Mar 8, 2011·Nature Methods·Franz-Josef MüllerJeanne F Loring
Apr 16, 2011·Bioinformatics·Felix Krueger, Simon R Andrews
Oct 18, 2011·BMC Genomics·M Aleksi KallioEija I Korpelainen
Jul 18, 2012·Proceedings of the National Academy of Sciences of the United States of America·Masatoshi KajiwaraShinya Yamanaka
Oct 4, 2012·Molecular Therapy : the Journal of the American Society of Gene Therapy·Kaifeng ShaoWolfgang Wagner
Dec 4, 2012·Stem Cell Research & Therapy·Min Zhang, Bing Huang
Jun 27, 2013·Nature Neuroscience·Jackson Sandoe, Kevin Eggan
Aug 5, 2014·Laboratory Investigation; a Journal of Technical Methods and Pathology·Katherine E SantostefanoNaohiro Terada
Oct 31, 2014·Stem Cells Translational Medicine·Ras TrokovicAija Kyttälä
Feb 15, 2015·Stem Cell Reports·Roger E RönnNiels-Bjarne Woods
Mar 31, 2015·The EMBO Journal·Buhe NashunPetra Hajkova

❮ Previous
Next ❯

Citations

Mar 24, 2016·Upsala Journal of Medical Sciences·Timo Otonkoski
May 8, 2016·Cell Stem Cell·Dirk Hockemeyer, Rudolf Jaenisch
Jul 28, 2016·Cell Stem Cell·Natalia Tapia, Hans R Schöler
Sep 20, 2016·British Journal of Pharmacology·Luca SalaChristine L Mummery
Oct 21, 2016·The European Journal of Neuroscience·Ulrich SauerzopfMatthäus Willeit
Apr 8, 2017·Biopreservation and Biobanking·Aikaterini NtaiIda Biunno
Jul 8, 2016·Experimental Biology and Medicine·Katrin ZeilingerFanny Knöspel
May 11, 2017·Nature·Helena KilpinenDaniel J Gaffney
Mar 22, 2018·International Journal of Molecular Sciences·Hirofumi NoguchiYoshiki Nakashima
Mar 9, 2018·International Journal of Molecular Sciences·Anke HoffmannDietmar Spengler
Jan 19, 2018·Stem Cells·Ana Artero CastroSlaven Erceg
Aug 29, 2017·Nature Cell Biology·Maria SkamagkiKitai Kim
Jun 14, 2018·Alcoholism, Clinical and Experimental Research·Iya PrytkovaPaul A Slesinger
Oct 21, 2016·Human Gene Therapy·Qingxi ZhangTongxiang Lin
Dec 6, 2018·International Journal of Molecular Sciences·Anke HoffmannDietmar Spengler
Oct 26, 2018·Annual Review of Pathology·Rodrigo GrandyLudovic Vallier
Jan 19, 2019·The European Journal of Neuroscience·Beatrice WeykopfOliver Brüstle
Mar 7, 2018·Nature Communications·Shin-Il KimKnut Woltjen
Feb 27, 2020·Nature Reviews. Endocrinology·Nicole A J Krentz, Anna L Gloyn
Dec 30, 2016·Oncotarget·Su Min LimSeung Hyun Kim
Aug 29, 2020·Journal of Molecular Medicine : Official Organ of the Gesellschaft Deutscher Naturforscher Und Ärzte·Tristan Frum, Jason R Spence
Feb 10, 2019·Nature Reviews. Genetics·R Grant Rowe, George Q Daley
Aug 28, 2019·Cold Spring Harbor Perspectives in Medicine·Eirini P Papapetrou
Dec 13, 2019·Stem Cells International·Yngvild BjørlykkeHelge Ræder
May 26, 2017·Stem Cells and Development·Ludovic ZimmerlinElias T Zambidis
Sep 5, 2018·Frontiers in Cardiovascular Medicine·Marianna TsifakiAndriana Margariti

❮ Previous
Next ❯

Datasets Mentioned

BETA
E-MTAB-3825
E-MTAB-3859

Methods Mentioned

BETA
RRBS
fluorescence-activated cell sorting
biopsies
FACS

Software Mentioned

SAM
PANTHER Classification System
PowerPoint
GSEA
Chipster
R
Homer
DAVID
PluriTest
MethylKit

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.