Evidence map›Paper›PMID 26643872›Full record

ArticleOncotarget2015

Genomic landscape of liposarcoma.

Deepika Kanojia, Yasunobu Nagata, Manoj Garg, Dhong Hyun Lee, Aiko Sato, Kenichi Yoshida, Yusuke Sato, Masashi Sanada, Anand Mayakonda, Christoph Bartenhagen and 18 more

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

Article in Oncotarget, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers.

0numbers the graph read from it
0cells of the map it votes in
81citing papers in PubMed
5.0field-weighted citation impact, top 4% 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

81 citing papers in PubMed, 123 citations in OpenAlex.

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  17. Therapy-Induced Senescence Contributes to the Efficacy of Abemaciclib in Patients with Dedifferentiated Liposarcoma.Clinical cancer research : an official journal of the American Association for Cancer Research · 2024
    Article
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21 more citing papers are in PubMed but not listed here.

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

28 authors at 11 institutions in 5 countries.

Deepika KanojiaCancer Science Institute of Singapore, National University of Singapore, Singapore.
Yasunobu NagataDepartment of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Manoj GargCancer Science Institute of Singapore, National University of Singapore, Singapore.
Dhong Hyun LeeDivision of Hematology/Oncology, Cedars-Sinai Medical Center, University of California, School of Medicine, Los Angeles, California, USA.
Aiko SatoDepartment of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Kenichi YoshidaDepartment of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Yusuke SatoDepartment of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Masashi SanadaDepartment of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Anand MayakondaCancer Science Institute of Singapore, National University of Singapore, Singapore.
Christoph BartenhagenInstitute of Medical Informatics, University of Münster, Münster, Germany.
Hans-Ulrich KleinInstitute of Medical Informatics, University of Münster, Münster, Germany.
Ngan B DoanDepartment of Pathology and Laboratory Medicine, Santa Monica-University of California-Los Angeles Medical Center, Los Angeles, California, USA.
Jonathan W SaidDepartment of Pathology and Laboratory Medicine, Santa Monica-University of California-Los Angeles Medical Center, Los Angeles, California, USA.
S MohithCancer Science Institute of Singapore, National University of Singapore, Singapore.
Swetha GunasekarCancer Science Institute of Singapore, National University of Singapore, Singapore.
Yuichi ShiraishiLaboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Kenichi ChibaLaboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Hiroko TanakaLaboratory of Sequence Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Satoru MiyanoLaboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Ola MyklebostNorwegian Cancer Genomics Consortium and Department of Tumor Biology, Institute of Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway.
Henry YangCancer Science Institute of Singapore, National University of Singapore, Singapore.
Martin DugasInstitute of Medical Informatics, University of Münster, Münster, Germany.
Leonardo A Meza-ZepedaNorwegian Cancer Genomics Consortium and Department of Tumor Biology, Institute of Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway.
Allan W SilbermanDepartment of Surgery, Cedars Sinai Medical Center, Division of Surgical Oncology, Los Angeles, California, USA.
Charles ForscherDivision of Hematology/Oncology, Cedars-Sinai Medical Center, University of California, School of Medicine, Los Angeles, California, USA.
Jeffrey W TynerKnight Cancer Institute, Cell and Developmental Biology, Oregon Health and Science University, Portland, Oregon, USA.
Seishi OgawaDepartment of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
H Phillip KoefflerCancer Science Institute of Singapore, National University of Singapore, Singapore.
Kyoto University · JPNational University of Singapore · SGThe University of Tokyo · JPNorwegian Cancer Society · NOUniversity of Münster · DECedars-Sinai Medical Center · USLos Angeles Medical Center · USNagoya Medical Center · JPNational University Cancer Institute, Singapore · SGNational University Hospital · SGOregon Health & Science University · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Liposarcoma (LPS) is the most common type of soft tissue sarcoma accounting for 20% of all adult sarcomas. Due to absence of clinically effective treatment options in inoperable situations and resistance to chemotherapeutics, a critical need exists to identify novel therapeutic targets. We analyzed LPS genomic landscape using SNP arrays, whole exome sequencing and targeted exome sequencing to uncover the genomic information for development of specific anti-cancer targets. SNP array analysis indicated known amplified genes (MDM2, CDK4, HMGA2) and important novel genes (UAP1, MIR557, LAMA4, CPM, IGF2, ERBB3, IGF1R). Carboxypeptidase M (CPM), recurrently amplified gene in well-differentiated/de-differentiated LPS was noted as a putative oncogene involved in the EGFR pathway. Notable deletions were found at chromosome 1p (RUNX3, ARID1A), chromosome 11q (ATM, CHEK1) and chromosome 13q14.2 (MIR15A, MIR16-1). Significantly and recurrently mutated genes (false discovery rate < 0.05) included PLEC (27%), MXRA5 (21%), FAT3 (24%), NF1 (20%), MDC1 (10%), TP53 (7%) and CHEK2 (6%). Further, in vitro and in vivo functional studies provided evidence for the tumor suppressor role for Neurofibromin 1 (NF1) gene in different subtypes of LPS. Pathway analysis of recurrent mutations demonstrated signaling through MAPK, JAK-STAT, Wnt, ErbB, axon guidance, apoptosis, DNA damage repair and cell cycle pathways were involved in liposarcomagenesis. Interestingly, we also found mutational and copy number heterogeneity within a primary LPS tumor signifying the importance of multi-region sequencing for cancer-genome guided therapy. In summary, these findings provide insight into the genomic complexity of LPS and highlight potential druggable pathways for targeted therapeutic approach.

Indexed as

AnimalsDNA Mutational AnalysisFlow CytometryGene Knockdown TechniquesHeterograftsHigh-Throughput Nucleotide SequencingHumansLiposarcomaMiceMice, Inbred NODMice, SCIDOligonucleotide Array Sequence AnalysisPolymerase Chain ReactionPolymorphism, Single NucleotideSoft Tissue NeoplasmsTranscriptomeexome sequencingintra-tumor heterogeneityliposarcomaSNP arraytherapeutics

Identifiers

PMID26643872
PMCPMC4767443
OpenAlexW2185118998

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.