Evidence map›Paper›PMID 26437031›Full record

ArticleNature genetics2015

Integrated molecular analysis of adult T cell leukemia/lymphoma.

Keisuke Kataoka, Yasunobu Nagata, Akira Kitanaka, Yuichi Shiraishi, Teppei Shimamura, Jun-Ichirou Yasunaga, Yasushi Totoki, Kenichi Chiba, Aiko Sato-Otsubo, Genta Nagae and 49 more

Abstract read
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In one paragraph

Article in Nature genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 549 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
549citing papers in PubMed, 1 pooled it
30.0field-weighted citation impact, top 1% 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

549 citing papers in PubMed, 1 synthesis or guideline pooled it, 830 citations in OpenAlex.

  1. Pooled it
  2. Trial
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  5. Article
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  10. Loss of HTLV-1-specific CD8Blood neoplasia · 2026
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489 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

59 authors at 14 institutions in 2 countries.

Keisuke KataokaDepartment of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Yasunobu NagataDepartment of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Akira KitanakaDepartment of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
Yuichi ShiraishiLaboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Teppei ShimamuraDivision of Systems Biology, Center for Neurological Disease and Cancer, Graduate School of Medicine, Nagoya University, Nagoya, Japan.
Jun-Ichirou YasunagaLaboratory of Virus Control, Institute for Virus Research, Kyoto University, Kyoto, Japan.
Yasushi TotokiDivision of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan.
Kenichi ChibaLaboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Aiko Sato-OtsuboDepartment of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Genta NagaeGenome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
Ryohei IshiiDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.ORCID http://orcid.org/0000-0003-2486-1393
Satsuki MutoGraduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.
Shinichi KotaniDepartment of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Yosaku WatataniDepartment of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
June TakedaDepartment 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.
Hiroko TanakaLaboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Hiromichi SuzukiDepartment 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.
Yusuke ShiozawaDepartment of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Tetsuichi YoshizatoDepartment 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.
Hideki MakishimaDepartment of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Masako IwanagaDepartment of Frontier Life Science, Nagasaki University Graduate School of Biomedical Science, Nagasaki, Japan.
Guangyong MaLaboratory of Virus Control, Institute for Virus Research, Kyoto University, Kyoto, Japan.
Kisato NosakaDepartment of Hematology, Kumamoto University School of Medicine, Kumamoto, Japan.
Masakatsu HishizawaDepartment of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Hidehiro ItonagaDepartment of Hematology, Sasebo City General Hospital, Sasebo, Japan.
Yoshitaka ImaizumiDepartment of Hematology, Atomic Bomb Disease and Hibakusya Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan.
Wataru MunakataDepartment of Hematology, National Cancer Center Hospital, Tokyo, Japan.
Hideaki OgasawaraKAN Research Institute, Inc., Kobe, Japan.
Toshitaka SatoKAN Research Institute, Inc., Kobe, Japan.
Ken SasaiKAN Research Institute, Inc., Kobe, Japan.
Kenzo MuramotoKAN Research Institute, Inc., Kobe, Japan.
Marina PenovaCenter for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Takahisa KawaguchiCenter for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Hiromi NakamuraDivision of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan.
Natsuko HamaDivision of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan.
Kotaro ShideDepartment of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
Yoko KubukiDepartment of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
Tomonori HidakaDepartment of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
Takuro KamedaDepartment of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
Tsuyoshi NakamakiDivision of Hematology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan.
Ken IshiyamaDepartment of Hematology and Oncology, Kanazawa University Hospital, Kanazawa, Japan.
Shuichi MiyawakiDivision of Hematology, Department of Internal Medicine, Tokyo Metropolitan Ohtsuka Hospital, Tokyo, Japan.
Sung-Soo YoonDepartment of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.
Kensei TobinaiDepartment of Hematology, National Cancer Center Hospital, Tokyo, Japan.ORCID http://orcid.org/0000-0002-7859-3227
Yasushi MiyazakiDepartment of Hematology, Atomic Bomb Disease and Hibakusya Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan.
Akifumi Takaori-KondoDepartment of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.ORCID http://orcid.org/0000-0001-7678-4284
Fumihiko MatsudaCenter for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Kengo TakeuchiPathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.
Osamu NurekiDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
Hiroyuki AburataniGenome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
Toshiki WatanabeGraduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.
Tatsuhiro ShibataDivision of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan.
Masao MatsuokaLaboratory of Virus Control, Institute for Virus Research, Kyoto University, Kyoto, Japan.ORCID http://orcid.org/0000-0002-0473-754X
Satoru MiyanoLaboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
Kazuya ShimodaDepartment of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
Seishi OgawaDepartment of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
Kyoto University · JPThe University of Tokyo · JPUniversity of Miyazaki · JPKAN Research Institute · JPNagasaki University · JPTokyo National Hospital · JPJapanese Foundation For Cancer Research · JPKanazawa University Hospital · JPKumamoto University · JPNagoya University · JPSasebo City General Hospital · JPSeoul National University · KRShowa University · JPTokyo Metropolitan Ohtsuka Hospital · JP

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Adult T cell leukemia/lymphoma (ATL) is a peripheral T cell neoplasm of largely unknown genetic basis, associated with human T cell leukemia virus type-1 (HTLV-1) infection. Here we describe an integrated molecular study in which we performed whole-genome, exome, transcriptome and targeted resequencing, as well as array-based copy number and methylation analyses, in a total of 426 ATL cases. The identified alterations overlap significantly with the HTLV-1 Tax interactome and are highly enriched for T cell receptor-NF-κB signaling, T cell trafficking and other T cell-related pathways as well as immunosurveillance. Other notable features include a predominance of activating mutations (in PLCG1, PRKCB, CARD11, VAV1, IRF4, FYN, CCR4 and CCR7) and gene fusions (CTLA4-CD28 and ICOS-CD28). We also discovered frequent intragenic deletions involving IKZF2, CARD11 and TP73 and mutations in GATA3, HNRNPA2B1, GPR183, CSNK2A1, CSNK2B and CSNK1A1. Our findings not only provide unique insights into key molecules in T cell signaling but will also guide the development of new diagnostics and therapeutics in this intractable tumor.

Indexed as

DNA MethylationAdultAmino Acid SequenceDNA Copy Number VariationsExomeGene Products, taxGenome, HumanHEK293 CellsHost-Pathogen InteractionsHumansHuman T-lymphotropic virus 1Jurkat CellsLeukemia-Lymphoma, Adult T-CellMolecular Sequence DataMutationSequence Analysis, DNAGene Products, taxtax protein, Human T-lymphotrophic virus 1

Identifiers

PMID26437031
OpenAlexW1849097877

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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.