Evidence map›Paper›PMID 34439147›Full record

ArticleCancers2021

PPAR-Responsive Elements Enriched with Alu Repeats May Contribute to Distinctive PPARγ-DNMT1 Interactions in the Genome.

Amit Sharma, Fabian Tobar-Tosse, Tikam Chand Dakal, Hongde Liu, Arijit Biswas, Athira Menon, Anoosha Paruchuri, Panagiotis Katsonis, Olivier Lichtarge, M Michael Gromiha and 5 more

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In one paragraph

Article in Cancers, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
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

3 citing papers in PubMed.

  1. Review
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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

15 authors.

Amit SharmaDepartment of Ophthalmology, University Hospital Bonn, 53127 Bonn, Germany.ORCID 0000-0002-2216-5389
Fabian Tobar-TosseDepartment of Basic Sciences for Health, Pontificia Universidad Javeriana Cali, Cali 760031, Colombia.ORCID 0000-0001-5334-4286
Tikam Chand DakalDepartment of Biotechnology, Mohanlal Sukhadia University Udaipur, Udaipur 313001, India.
Hongde LiuState Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China.ORCID 0000-0001-8768-764X
Arijit BiswasInstitute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, 53127 Bonn, Germany.ORCID 0000-0002-4103-5854
Athira MenonDepartment of Biotechnology, Mohanlal Sukhadia University Udaipur, Udaipur 313001, India.
Anoosha ParuchuriDepartment of Internal Medicine, Division of Medical Oncology and Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA.
Panagiotis KatsonisComputational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX 77030, USA.ORCID 0000-0002-7172-1644
Olivier LichtargeComputational and Integrative Biomedical Research Center, Baylor College of Medicine, Houston, TX 77030, USA.
M Michael GromihaDepartment of Biotechnology, Bhupat and Jyoti Mehta School of BioSciences, Indian Institute of Technology Madras, Chennai 600036, India.ORCID 0000-0002-1776-4096
Michael LudwigDepartment of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany.ORCID 0000-0003-2287-5281
Ingo G H Schmidt-WolfDepartment of Integrated Oncology, CIO Bonn, University Hospital Bonn, 53127 Bonn, Germany.
Frank G HolzDepartment of Ophthalmology, University Hospital Bonn, 53127 Bonn, Germany.
Karin U LoefflerDepartment of Ophthalmology, University Hospital Bonn, 53127 Bonn, Germany.
Martina C Herwig-CarlDepartment of Ophthalmology, University Hospital Bonn, 53127 Bonn, Germany.ORCID 0000-0002-5943-7675

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundPPARγ (peroxisome proliferator-activated receptor gamma) is involved in the pathology of numerous diseases, including UM and other types of cancer. Emerging evidence suggests that an interaction between PPARγ and DNMTs (DNA methyltransferase) plays a role in cancer that is yet to be defined.

methodsThe configuration of the repeating elements was performed with CAP3 and MAFFT, and the structural modelling was conducted with HDOCK. An evolutionary action scores algorithm was used to identify oncogenic variants. A systematic bioinformatic appraisal of PPARγ and DNMT1 was performed across 29 tumor types and UM available in The Cancer Genome Atlas (TCGA).

resultsPPAR-responsive elements (PPREs) enriched with Alu repeats are associated with different genomic regions, particularly the promotor region of DNMT1. PPARγ-DNMT1 co-expression is significantly associated with several cancers. C-terminals of PPARγ and DNMT1 appear to be the potential protein-protein interaction sites where disease-specific mutations may directly impair the respective protein functions. Furthermore, PPARγ expression could be identified as an additional prognostic marker for UM.

conclusionsWe hypothesize that the function of PPARγ requires an additional contribution of Alu repeats which may directly influence the DNMT1 network. Regarding UM, PPARγ appears to be an additional discriminatory prognostic marker, in particular in disomy 3 tumors.

Indexed as

Alu repeatscancerDNMT1evolutionary action scorePPARγrepetitive sequencesuveal melanoma

Identifiers

PMID34439147
PMCPMC8391462

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