Evidence map›Paper›PMID 26822956›Full record

ArticleNature communications2016

Non-CG DNA methylation is a biomarker for assessing endodermal differentiation capacity in pluripotent stem cells.

Lee M Butcher, Mitsuteru Ito, Minodora Brimpari, Tiffany J Morris, Filipa A C Soares, Lars Ährlund-Richter, Nessa Carey, Ludovic Vallier, Anne C Ferguson-Smith, Stephan Beck

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.

0numbers the graph read from it
0cells of the map it votes in
28citing papers in PubMed
4.0field-weighted citation impact, top 6% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

28 citing papers in PubMed, 50 citations in OpenAlex.

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  15. Existence and possible roles of independent non-CpG methylation in the mammalian brain.DNA research : an international journal for rapid publication of reports on genes and genomes · 2020
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors at 7 institutions in 2 countries.

Lee M ButcherUCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK.
Mitsuteru ItoDepartment of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.
Minodora BrimpariAnne McLaren Laboratory, Department of Surgery, Wellcome Trust and Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK.
Tiffany J MorrisUCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK.
Filipa A C SoaresAnne McLaren Laboratory, Department of Surgery, Wellcome Trust and Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK.
Lars Ährlund-RichterDivision of Paediatric Oncology, Department of Women's and Children's Health, Karolinska Institutet,171 76 Stockholm, Sweden.
Nessa CareyPraxisUnico, The Jeffreys Building, St John's Innovation Park, Cambridge CB4 0DE, UK.
Ludovic VallierAnne McLaren Laboratory, Department of Surgery, Wellcome Trust and Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge CB2 0SZ, UK.
Anne C Ferguson-SmithDepartment of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.
Stephan BeckUCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK.
University of Cambridge · GBUniversity College London · GBImperial College London · GBKarolinska Institutet · SEPraxis (United Kingdom) · GBWellcome/MRC Cambridge Stem Cell Institute · GBWellcome Sanger Institute · GB

Funding

Medical Research Council G0800784Medical Research Council G1000847Medical Research Council MC_PC_12009Medical Research Council MR/J001597/1Wellcome Trust 084071Wellcome Trust 095606Wellcome Trust WT098503
6 · The paper itself

Abstract

Non-CG methylation is an unexplored epigenetic hallmark of pluripotent stem cells. Here we report that a reduction in non-CG methylation is associated with impaired differentiation capacity into endodermal lineages. Genome-wide analysis of 2,670 non-CG sites in a discovery cohort of 25 phenotyped human induced pluripotent stem cell (hiPSC) lines revealed unidirectional loss (Δβ=13%, P<7.4 × 10(-4)) of non-CG methylation that correctly identifies endodermal differentiation capacity in 23 out of 25 (92%) hiPSC lines. Translation into a simplified assay of only nine non-CG sites maintains predictive power in the discovery cohort (Δβ=23%, P<9.1 × 10(-6)) and correctly identifies endodermal differentiation capacity in nine out of ten pluripotent stem cell lines in an independent replication cohort consisting of hiPSCs reprogrammed from different cell types and different delivery systems, as well as human embryonic stem cell (hESC) lines. This finding infers non-CG methylation at these sites as a biomarker when assessing endodermal differentiation capacity as a readout.

Indexed as

Cell DifferentiationDNA MethylationBiomarkersCohort StudiesEndodermHumansInduced Pluripotent Stem CellsBiomarkers

Identifiers

PMID26822956
PMCPMC4740175
OpenAlexW2273488592

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.