Evidence map›Paper›PMID 39457378›Full record

ArticleGenes2024

Characterization of the Rat Osteosarcoma Cell Line UMR-106 by Long-Read Technologies Identifies a Large Block of Amplified Genes Associated with Human Disease.

Alan F Scott, David W Mohr, William A Littrell, Reshma Babu, Michelle Kokosinski, Victoria Stinnett, Janvi Madhiwala, John Anderson, Ying S Zou, Kathleen L Gabrielson

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genes, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Chorein Regulates Key Osteoblast Genes in UMR-106 Cells.Cell biochemistry and biophysics · 2026
    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.

Alan F ScottGenetic Resources Core Facility, Department of Genetic Medicine, Johns Hopkins University School of Medicine, 600 N. Wolfe St., 1034 Blalock, Baltimore, MD 21287, USA.
David W MohrGenetic Resources Core Facility, Department of Genetic Medicine, Johns Hopkins University School of Medicine, 600 N. Wolfe St., 1034 Blalock, Baltimore, MD 21287, USA.ORCID 0000-0002-2198-3822
William A LittrellGenetic Resources Core Facility, Department of Genetic Medicine, Johns Hopkins University School of Medicine, 600 N. Wolfe St., 1034 Blalock, Baltimore, MD 21287, USA.
Reshma BabuGenetic Resources Core Facility, Department of Genetic Medicine, Johns Hopkins University School of Medicine, 600 N. Wolfe St., 1034 Blalock, Baltimore, MD 21287, USA.
Michelle KokosinskiDepartment of Genetic Medicine, Johns Hopkins Genomics, Johns Hopkins University School of Medicine, 1812 Ashland Ave., Suite 200, Baltimore, MD 21205, USA.
Victoria StinnettCytogenetic Laboratory, Department of Pathology, Johns Hopkins Genomics, Johns Hopkins University School of Medicine, 600 N. Wolfe St., Halsted 281, Baltimore, MD 21287, USA.ORCID 0000-0003-0317-1385
Janvi MadhiwalaDepartment of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA.
John AndersonDepartment of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA.
Ying S ZouCytogenetic Laboratory, Department of Pathology, Johns Hopkins Genomics, Johns Hopkins University School of Medicine, 600 N. Wolfe St., Halsted 281, Baltimore, MD 21287, USA.ORCID 0000-0003-2787-1917
Kathleen L GabrielsonDepartment of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA.

Funding

NIH HHS 5R21CA229582-02
6 · The paper itself

Abstract

BACKGROUND/

objectivesThe rat osteosarcoma cell line UMR-106 is widely used for the study of bone cancer biology but it has not been well characterized with modern genomic methods.

methodsTo better understand the biology of UMR-106 cells we used a combination of optical genome mapping (OGM), long-read sequencing nanopore sequencing and RNA sequencing.The UMR-106 genome was compared to a strain-matched Sprague-Dawley rat for variants associated with human osteosarcoma while expression data were contrasted with a public osteoblast dataset.

resultsUsing the COSMIC database to identify the most affected genes in human osteosarcomas we found somatic mutations in Tp53 and H3f3a. OGM identified a relatively small number of differences between the cell line and a strain-matched control animal but did detect a ~45 Mb block of amplification that included Myc on chromosome 7 which was confirmed by long-read sequencing. The amplified region showed several blocks of non-contiguous rearranged sequence implying complex rearrangements during their formation and included 14 genes reported as biomarkers in human osteosarcoma, many of which also showed increased transcription. A comparison of 5mC methylation from the nanopore reads of tumor and control samples identified genes with distinct differences including the OS marker Cdkn2a.

conclusionsThis dataset illustrates the value of long DNA methods for the characterization of cell lines and how inter-species analysis can inform us about the genetic nature underlying mutations that underpin specific tumor types. The data should be a valuable resource for investigators studying osteosarcoma, in general, and specifically the UMR-106 model.

Indexed as

Bone NeoplasmsOsteosarcomaAnimalsCell Line, TumorChromosome MappingDNA MethylationGene AmplificationHumansMutationNanopore SequencingRatsRats, Sprague-DawleyMyc amplificationnanopore sequencingoptical mappingosteosarcoma

Identifiers

PMID39457378
PMCPMC11507229

What Socratic holds

Textmetadata
LicenceCC BY
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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 Socratic graph.