Evidence map›Paper›PMID 27164004›Full record

ArticleJournal of immunological methods2016

DNA cytosine hydroxymethylation levels are distinct among non-overlapping classes of peripheral blood leukocytes.

Natalie M Hohos, Kevin Lee, Lexiang Ji, Miao Yu, Muthugapatti M Kandasamy, Bradley G Phillips, Clifton A Baile, Chuan He, Robert J Schmitz, Richard B Meagher

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

Article in Journal of immunological methods, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
0.2field-weighted citation impact, top 36% 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

4 citing papers in PubMed, 6 citations in OpenAlex.

  1. Article
  2. Article
  3. Article
  4. CD4Obesity (Silver Spring, Md.) · 2018
    Article
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 3 institutions in 1 country.

Natalie M HohosDepartment of Foods and Nutrition, University of Georgia, Athens, GA, USA. Electronic address: nhohos@uga.edu.
Kevin LeeDepartment of Genetics, University of Georgia, Athens, GA, USA. Electronic address: klee84@uga.edu.
Lexiang JiInstitute of Bioinformatics, University of Georgia, Athens, GA, USA. Electronic address: lxji@uga.edu.
Miao YuDepartment of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA. Electronic address: miaoyu1988@uchicago.edu.
Muthugapatti M KandasamyDepartment of Genetics, University of Georgia, Athens, GA, USA. Electronic address: kandu@uga.edu.
Bradley G PhillipsClinical and Administrative Pharmacy, University of Georgia, Athens, GA, USA. Electronic address: bgp@uga.edu.
Clifton A BaileDepartment of Foods and Nutrition, University of Georgia, Athens, GA, USA.
Chuan HeDepartment of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA. Electronic address: chuanhe@uchicago.edu.
Robert J SchmitzDepartment of Genetics, University of Georgia, Athens, GA, USA. Electronic address: schmitz@uga.edu.
Richard B MeagherDepartment of Genetics, University of Georgia, Athens, GA, USA. Electronic address: meagher@uga.edu.
University of Georgia · USHoward Hughes Medical Institute · USUniversity of Chicago · US

Funding

Labeling and sequencing of 5hmC and 5mC in DNA-RenewalR01HG006827 · NHGRI · UNIVERSITY OF CHICAGO · PI HE, CHUAN · 2012 to 2025
$7.2M
Identification and Characterization of Population-Wide Epigenetic VariationR00GM100000 · NIGMS · UNIVERSITY OF GEORGIA · PI SCHMITZ, ROBERT J. · 2013 to 2015
$723k
NUCLEAR CAPTURE FOR CELL-TYPE SPECIFIC EPIGENETIC ANALYSIS OF ADIPOCYTESR01DK100392 · NIDDK · UNIVERSITY OF GEORGIA · PI MEAGHER, RICHARD BRIAN, SMITH, ALICIA K · 2014 to 2015
$670k
Affinity Tagging of Adipocyte Nuclei to Examine Epigenetic Controls in ObesityR21DK096300 · NIDDK · UNIVERSITY OF GEORGIA · PI BAILE, CLIFTON A, MEAGHER, RICHARD BRIAN · 2012 to 2013
$401k
Howard Hughes Medical InstituteNHGRI NIH HHS R01 HG006827NIDDK NIH HHS R01 DK100392NIDDK NIH HHS R21 DK096300NIGMS NIH HHS R00 GM100000
6 · The paper itself

Abstract

backgroundPeripheral blood leukocytes are the most commonly used surrogates to study epigenome-induced risk and epigenomic response to disease-related stress. We considered the hypothesis that the various classes of peripheral leukocytes differentially regulate the synthesis of 5-methylcytosine (5mCG) and its removal via Ten-Eleven Translocation (TET) dioxygenase catalyzed hydroxymethylation to 5-hydroxymethylcytosine (5hmCG), reflecting their responsiveness to environment. Although it is known that reductions in TET1 and/or TET2 activity lead to the over-proliferation of various leukocyte precursors in bone marrow and in development of chronic myelomonocytic leukemia and myeloproliferative neoplasms, the role of 5mCG hydroxymethylation in peripheral blood is less well studied.

resultsWe developed simplified protocols to rapidly and reiteratively isolate non-overlapping leukocyte populations from a single small sample of fresh or frozen whole blood. Among peripheral leukocyte types we found extreme variation in the levels of transcripts encoding proteins involved in cytosine methylation (DNMT1, 3A, 3B), the turnover of 5mC by demethylation (TET1, 2, 3), and DNA repair (GADD45A, B, G) and in the global and gene-region-specific levels of DNA 5hmCG (CD4+ T cells≫CD14+ monocytes>CD16+ neutrophils>CD19+ B cells>CD56+ NK cells>Siglec8+ eosinophils>CD8+ T cells).

conclusionsOur data taken together suggest a potential hierarchy of responsiveness among classes of leukocytes with CD4+, CD8+ T cells and CD14+ monocytes being the most distinctly poised for a rapid methylome response to physiological stress and disease.

Indexed as

DNA Methylation5-MethylcytosineB-LymphocytesCell SeparationDNA-Binding ProteinsDNA RepairEpigenesis, GeneticHumansT-Lymphocytes5-hydroxymethylcytosine5-MethylcytosineDNA-Binding Proteins5-HydroxymethylcytosineCellular memoryDiseaseEpigenetic controlEpigenome-induced riskSurrogate cells

Identifiers

PMID27164004
PMCPMC5131182
OpenAlexW2345374303

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.