Evidence map›Paper›PMID 33127576›Full record

ArticleBone2022

Comparative analysis of genome-wide DNA methylation identifies patterns that associate with conserved transcriptional programs in osteosarcoma.

Lauren J Mills, Milcah C Scott, Pankti Shah, Anne R Cunanan, Archana Deshpande, Benjamin Auch, Bridget Curtin, Kenneth B Beckman, Logan G Spector, Aaron L Sarver and 3 more

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

Article in Bone, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed
0.4field-weighted citation impact, top 39% 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

10 citing papers in PubMed, 13 citations in OpenAlex.

  1. Review
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  6. Review of Molecular Technologies for Investigating Canine Cancer.Animals : an open access journal from MDPI · 2024
    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

13 authors at 3 institutions in 1 country.

Lauren J MillsMasonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Childhood Cancer Genomics Group, Department of Pediatric, School of Medicine, University of Minnesota, Minneapolis, MN 55455, USA. Electronic address: ljmills@umn.edu.
Milcah C ScottDepartment of Microbiology and Immunology, Center for Immunology, School of Medicine, University of Minnesota, Minneapolis, MN 55455, USA.
Pankti ShahRoche Sequencing Solution, Pleasanton, CA, USA.
Anne R CunananRoche Sequencing Solution, Pleasanton, CA, USA.
Archana DeshpandeUniversity of Minnesota Genomics Center, Minneapolis, MN 55455, USA.
Benjamin AuchUniversity of Minnesota Genomics Center, Minneapolis, MN 55455, USA.
Bridget CurtinDepartment of Surgery, University of Minnesota, Minneapolis, MN 55455, USA.
Kenneth B BeckmanUniversity of Minnesota Genomics Center, Minneapolis, MN 55455, USA.
Logan G SpectorMasonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Childhood Cancer Genomics Group, Department of Pediatric, School of Medicine, University of Minnesota, Minneapolis, MN 55455, USA.
Aaron L SarverMasonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Animal Cancer Care and Research Program, University of Minnesota, St. Paul 55108, USA; Institute of Health Informatics, University of Minnesota, Minneapolis, MN 55455, USA.
Subbaya SubramanianMasonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Department of Surgery, University of Minnesota, Minneapolis, MN 55455, USA.
Todd A RichmondRoche Sequencing Solution, Pleasanton, CA, USA.
Jaime F ModianoMasonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Animal Cancer Care and Research Program, University of Minnesota, St. Paul 55108, USA; Institute of Health Informatics, University of Minnesota, Minneapolis, MN 55455, USA; Department of Veterinary Clinical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA; Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA; Stem Cell Institute, University of Minnesota, UDS Institute for Engineering in Medicine, Minneapolis, MN 55455, USA.
University of Minnesota · USLa Roche College · USUniversity of Minnesota Medical Center · US

Funding

Women's CancerP30CA077598 · NCI · UNIVERSITY OF MINNESOTA TWIN CITIES · PI Douglas Yee · 1998 to 2026
$100.4M
Bioinformatics approaches to solve the "Missing Driver" problem in solid tumorsR50CA211249 · NCI · UNIVERSITY OF MINNESOTA · PI SARVER, AARON L · 2016 to 2020
$565k
(PQ3) Modulation of Osteosarcoma Biology by Inflammation and Immunity Defined through a ComparativeApproachR21CA208529 · NCI · UNIVERSITY OF MINNESOTA · PI MODIANO, JAIME F. · 2016 to 2017
$365k
NCI NIH HHS P30 CA077598NCI NIH HHS R21 CA208529NCI NIH HHS R50 CA211249
6 · The paper itself

Abstract

Osteosarcoma is an aggressive tumor of the bone that primarily affects young adults and adolescents. Osteosarcoma is characterized by genomic chaos and heterogeneity. While inactivation of tumor protein p53 (TP53) is nearly universal other high frequency mutations or structural variations have not been identified. Despite this genomic heterogeneity, key conserved transcriptional programs associated with survival have been identified across human, canine and induced murine osteosarcoma. The epigenomic landscape, including DNA methylation, plays a key role in establishing transcriptional programs in all cell types. The role of epigenetic dysregulation has been studied in a variety of cancers but has yet to be explored at scale in osteosarcoma. Here we examined genome-wide DNA methylation patterns in 24 human and 44 canine osteosarcoma samples identifying groups of highly correlated DNA methylation marks in human and canine osteosarcoma samples. We also link specific DNA methylation patterns to key transcriptional programs in both human and canine osteosarcoma. Building on previous work, we built a DNA methylation-based measure for the presence and abundance of various immune cell types in osteosarcoma. Finally, we determined that the underlying state of the tumor, and not changes in cell composition, were the main driver of differences in DNA methylation across the human and canine samples. SIGNIFICANCE: Genome wide comparison of DNA methylation patterns in osteosarcoma across two species lays the ground work for the exploration of DNA methylation programs that help establish conserved transcriptional programs in the context of varied mutational landscapes.

Indexed as

Bone NeoplasmsOsteosarcomaAnimalsDNA MethylationDogsEpigenomicsGenomicsMiceComparative oncologyDNA methylationEPIGENETICOsteosarcoma

Identifiers

PMID33127576
PMCPMC8076342
OpenAlexW3097669563

What OpenQuestion holds

Textmetadata
LicenceTDM
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.