Evidence map›Paper›PMID 28844656›Full record

ArticleStem cell reports2017

Methylome Analysis of Human Bone Marrow MSCs Reveals Extensive Age- and Culture-Induced Changes at Distal Regulatory Elements.

Kalyan K Pasumarthy, Naresh Doni Jayavelu, Lotta Kilpinen, Colin Andrus, Stephanie L Battle, Matti Korhonen, Petri Lehenkari, Riikka Lund, Saara Laitinen, R David Hawkins

Open access · goldAbstract read
In one paragraph

Article in Stem cell reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.

0numbers the graph read from it
0cells of the map it votes in
24citing papers in PubMed
1.7field-weighted citation impact, top 16% 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

24 citing papers in PubMed, 35 citations in OpenAlex.

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  12. From Stem Cells to Bone-Forming Cells.International journal of molecular sciences · 2021
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  15. Histone ChIP-Seq identifies differential enhancer usage during chondrogenesis as critical for defining cell-type specificity.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 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 4 institutions in 2 countries.

Kalyan K PasumarthyTurku Centre for Biotechnology, University of Turku, Turku 20520, Finland.
Naresh Doni JayaveluTurku Centre for Biotechnology, University of Turku, Turku 20520, Finland; Division of Medical Genetics, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA.
Lotta KilpinenResearch and Development, Medical Services, Finnish Red Cross Blood Service, Helsinki 00310, Finland.
Colin AndrusDivision of Medical Genetics, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA.
Stephanie L BattleDivision of Medical Genetics, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA.
Matti KorhonenCell Therapy Services, Medical Services, Finnish Red Cross Blood Service, Helsinki 00310, Finland.
Petri LehenkariInstitute of Clinical Medicine, Division of Surgery and Institute of Biomedicine, Department of Anatomy and Cell Biology, University of Oulu, Oulu 90014, Finland; Clinical Research Center, Department of Surgery and Intensive Care, Oulu University Hospital, Oulu 90014, Finland.
Riikka LundTurku Centre for Biotechnology, University of Turku, Turku 20520, Finland; Åbo Akademi University, Turku 20520, Finland.
Saara LaitinenResearch and Development, Medical Services, Finnish Red Cross Blood Service, Helsinki 00310, Finland.
R David HawkinsTurku Centre for Biotechnology, University of Turku, Turku 20520, Finland; Division of Medical Genetics, Department of Medicine, Department of Genome Sciences, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA. Electronic address: rdhawk@uw.edu.
University of Washington · USFinnish Red Cross · FIUniversity of Turku · FIOulu University Hospital · FI

Funding

Functional assessment of distal regulatory SNPs associated with type 1 diabetes.R01DK103667 · NIDDK · UNIVERSITY OF WASHINGTON · PI HAWKINS, RAYMOND DAVID · 2015 to 2019
$2.5M
Functional validation of Rheumatoid Arthritis-associated distal regulatory SNPs iR01AR065952 · NIAMS · UNIVERSITY OF WASHINGTON · PI HAWKINS, RAYMOND DAVID · 2015 to 2018
$1.8M
NIAMS NIH HHS R01 AR065952NIDDK NIH HHS R01 DK103667
6 · The paper itself

Abstract

Human bone marrow stromal cells, or mesenchymal stem cells (BM-MSCs), need expansion prior to use as cell-based therapies in immunological and tissue repair applications. Aging and expansion of BM-MSCs induce epigenetic changes that can impact therapeutic outcomes. By applying sequencing-based methods, we reveal that the breadth of DNA methylation dynamics associated with aging and expansion is greater than previously reported. Methylation changes are enriched at known distal transcription factor binding sites such as enhancer elements, instead of CpG-rich regions, and are associated with changes in gene expression. From this, we constructed hypo- and hypermethylation-specific regulatory networks, including a sub-network of BM-MSC master regulators and their predicted target genes, and identified putatively disrupted signaling pathways. Our genome-wide analyses provide a broader overview of age- and expansion-induced DNA methylation changes and a better understanding of the extent to which these changes alter gene expression and functionality of human BM-MSCs.

Indexed as

AgedAged, 80 and overAge FactorsBinding SitesBone Marrow CellsCells, CulturedCpG IslandsDNA MethylationGene Expression ProfilingGene Regulatory NetworksGenome, HumanHumansMesenchymal Stem CellsMiddle AgedRegulatory Sequences, Nucleic AcidSequence Analysis, DNATranscription Factorsagingbone marrow MSCsDNA methylationenhancer elementsepigeneticsstem cell biology

Identifiers

PMID28844656
PMCPMC5599244
OpenAlexW2749363228

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

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.