Evidence map›Paper›PMID 30674975›Full record

ArticleScientific reports2019

Identification of candidate neoantigens produced by fusion transcripts in human osteosarcomas.

Susan K Rathe, Flavia E Popescu, James E Johnson, Adrienne L Watson, Tracy A Marko, Branden S Moriarity, John R Ohlfest, David A Largaespada

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

Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.

0numbers the graph read from it
0cells of the map it votes in
25citing papers in PubMed
2.3field-weighted citation impact, top 11% 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

25 citing papers in PubMed, 37 citations in OpenAlex.

  1. Review
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  11. Sources of Cancer Neoantigens beyond Single-Nucleotide Variants.International journal of molecular sciences · 2022
    Review
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  17. S100A4 mRNA-protein relationship uncovered by measurement noise reduction.Journal of molecular medicine (Berlin, Germany) · 2020
    Article
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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

8 authors at 2 institutions in 1 country.

Susan K RatheMasonic Cancer Center, University of Minnesota, Minneapolis, MN, USA. rath0096@umn.edu.
Flavia E PopescuMasonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
James E JohnsonSupercomputing Institute, University of Minnesota, Minneapolis, MN, USA.
Adrienne L WatsonMasonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
Tracy A MarkoMasonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
Branden S MoriarityMasonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
John R OhlfestDepartment of Pediatrics, University of Minnesota, Minneapolis, MN, USA.
David A LargaespadaMasonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
University of Minnesota Medical Center · USUniversity of Minnesota · US

Funding

Sleeping Beauty for uncovering cancer genes in miceR01CA113636 · NCI · UNIVERSITY OF MINNESOTA · PI LARGAESPADA, DAVID ANDREW · 2006 to 2016
$2.5M
Recurrent Tumor-Specific Alternately Processed Transcripts as a Source of Neoantigens for NF1-associated Malignant Peripheral Nerve Sheath Tumor ImmunopreventionUG3CA244687 · NCI · UNIVERSITY OF MINNESOTA · PI LARGAESPADA, DAVID ANDREW · 2019 to 2020
$1.5M
NCI NIH HHS R01 CA113636NCI NIH HHS UG3 CA244687
6 · The paper itself

Abstract

Osteosarcomas are characterized by highly disrupted genomes. Although osteosarcomas lack common fusions, we find evidence of many tumour specific gene-gene fusion transcripts, likely due to chromosomal rearrangements and expression of transcription-induced chimeras. Most of the fusions result in out-of-frame transcripts, potentially capable of producing long novel protein sequences and a plethora of neoantigens. To identify fusions, we explored RNA-sequencing data to obtain detailed knowledge of transcribed fusions, by creating a novel program to compare fusions identified by deFuse to de novo transcripts generated by Trinity. This allowed us to confirm the deFuse results and identify unusual splicing patterns associated with fusion events. Using various existing tools combined with this custom program, we developed a pipeline for the identification of fusion transcripts applicable as targets for immunotherapy. In addition to identifying candidate neoantigens associated with fusions, we were able to use the pipeline to establish a method for measuring the frequency of fusion events, which correlated to patient outcome, as well as highlight some similarities between canine and human osteosarcomas. The results of this study of osteosarcomas underscores the numerous benefits associated with conducting a thorough analysis of fusion events within cancer samples.

Indexed as

AnimalsAntigens, NeoplasmAntiportersBone NeoplasmsCation Transport ProteinsCD8-Positive T-LymphocytesCell Line, TumorCLOCK ProteinsComputational BiologyEpitopesGene Expression ProfilingGenetic LociGenomic InstabilityHigh-Throughput Nucleotide SequencingMiceOncogene Proteins, FusionAntigens, NeoplasmAntiportersCation Transport ProteinsCLOCK protein, humanCLOCK ProteinsEpitopesOncogene Proteins, FusionTMEM165 protein, mouse

Identifiers

PMID30674975
PMCPMC6344567
OpenAlexW2913727097

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.