Epigenetic biomarker to support classification into pluripotent and non-pluripotent cells

Scientific Reports
Michael LenzWolfgang Wagner

Abstract

Quality control of human induced pluripotent stem cells (iPSCs) can be performed by several methods. These methods are usually relatively labor-intensive, difficult to standardize, or they do not facilitate reliable quantification. Here, we describe a biomarker to distinguish between pluripotent and non-pluripotent cells based on DNA methylation (DNAm) levels at only three specific CpG sites. Two of these CpG sites were selected by their discriminatory power in 258 DNAm profiles - they were either methylated in pluripotent or non-pluripotent cells. The difference between these two β-values provides an Epi-Pluri-Score that was validated on independent DNAm-datasets (264 pluripotent and 1,951 non-pluripotent samples) with 99.9% specificity and 98.9% sensitivity. This score was complemented by a third CpG within the gene POU5F1 (OCT4), which better demarcates early differentiation events. We established pyrosequencing assays for the three relevant CpG sites and thereby correctly classified DNA of 12 pluripotent cell lines and 31 non-pluripotent cell lines. Furthermore, DNAm changes at these three CpGs were tracked in the course of differentiation of iPSCs towards mesenchymal stromal cells. The Epi-Pluri-Score does not give informa...Continue Reading

References

Jul 21, 2001·Stem Cells·M Pesce, H R Schöler
Aug 11, 2006·Genome Research·Marina BibikovaJian-Bing Fan
Mar 28, 2009·Journal of Cellular Physiology·Kelly P SmithGary S Stein
Oct 15, 2009·Nature Biotechnology·Elayne M ChanThorsten M Schlaeger
Oct 15, 2010·Nature Biotechnology·Alexander Meissner
Oct 30, 2010·Nature Methods·Martin F Pera
Feb 5, 2011·Nature Biotechnology·Gabriella L BoultingKevin Eggan
Feb 25, 2011·PloS One·Carmen M KochWolfgang Wagner
Mar 8, 2011·Nature Methods·Franz-Josef MüllerJeanne F Loring
May 20, 2011·Epigenetics : Official Journal of the DNA Methylation Society·Juan SandovalManel Esteller
Aug 16, 2011·Genomics·Marina BibikovaRichard Shen
Oct 20, 2011·Stem Cells·Jared SterneckertHans R Schöler
Nov 16, 2011·Cell Research·Junjun DingJianlong Wang
Jan 10, 2012·Aging Cell·Carmen M KochWolfgang Wagner
Oct 4, 2012·Molecular Therapy : the Journal of the American Society of Gene Therapy·Kaifeng ShaoWolfgang Wagner
Oct 20, 2012·Genome Research·Carmen M KochWolfgang Wagner
Dec 4, 2012·Nature Methods·Leo KurianJuan Carlos Izpisua Belmonte
Apr 25, 2013·Stem Cell Research·Christiane ButaGeorg Weitzer
May 18, 2013·Stem Cell Research & Therapy·Michael W Nestor, Scott A Noggle
Oct 22, 2013·Genome Biology·Steve Horvath
Dec 29, 2013·Stem Cell Reports·Jamie A HackettM Azim Surani
Feb 5, 2014·Genome Biology·Carola Ingrid WeidnerWolfgang Wagner
Aug 21, 2014·Methods in Molecular Biology·Jeffrey FergusUma Lakshmipathy

❮ Previous
Next ❯

Citations

Feb 11, 2016·Stem Cell Reports·Danilo Candido de AlmeidaWolfgang Wagner
Aug 4, 2016·Scientific Reports·Jana StanurovaLaura Steenpass
Apr 8, 2017·Biopreservation and Biobanking·Aikaterini NtaiIda Biunno
Apr 18, 2018·Nature Cell Biology·Atilgan YilmazNissim Benvenisty
Sep 16, 2020·Experimental & Molecular Medicine·Yulia PaninaWataru Fujibuchi
Mar 7, 2020·Stem Cell Research & Therapy·Jonathan HollmannWolfgang Wagner
Nov 27, 2020·Frontiers in Bioengineering and Biotechnology·Andreas ElanzewOliver Brüstle

❮ Previous
Next ❯

Datasets Mentioned

BETA
GSE42646

Methods Mentioned

BETA
flow cytometry
PCR

Software Mentioned

Pluri
PyroMark CpG SW
Score
Epi
PluriTest
- Score

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.

Related Papers

Zhongguo yi xue ke xue yuan xue bao. Acta Academiae Medicinae Sinicae
Ju WangZong-yao Zhou
Zhonghua shao shang za zhi = Zhonghua shaoshang zazhi = Chinese journal of burns
Yong-Tie LiQun-Hong Yu
© 2022 Meta ULC. All rights reserved