IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v12y2021i1d10.1038_s41467-021-26745-3.html
   My bibliography  Save this article

Focal amplifications are associated with chromothripsis events and diverse prognoses in gastric cardia adenocarcinoma

Author

Listed:
  • Xue-Ke Zhao

    (Zhengzhou University)

  • Pengwei Xing

    (Uppsala University)

  • Xin Song

    (Zhengzhou University)

  • Miao Zhao

    (Uppsala University)

  • Linxuan Zhao

    (Uppsala University)

  • Yonglong Dang

    (Uppsala University)

  • Ling-Ling Lei

    (Zhengzhou University)

  • Rui-Hua Xu

    (Zhengzhou University)

  • Wen-Li Han

    (Zhengzhou University)

  • Pan-Pan Wang

    (Zhengzhou University)

  • Miao-Miao Yang

    (Zhengzhou University)

  • Jing-Feng Hu

    (Zhengzhou University)

  • Kan Zhong

    (Zhengzhou University)

  • Fu-You Zhou

    (Zhengzhou University)

  • Xue-Na Han

    (Zhengzhou University)

  • Chao-Long Meng

    (Zhengzhou University)

  • Jia-Jia Ji

    (Zhengzhou University)

  • Xingqi Chen

    (Uppsala University)

  • Li-Dong Wang

    (Zhengzhou University)

Abstract

The role of focal amplifications and extrachromosomal DNA (ecDNA) is unknown in gastric cardia adenocarcinoma (GCA). Here, we identify frequent focal amplifications and ecDNAs in Chinese GCA patient samples, and find focal amplifications in the GCA cohort are associated with the chromothripsis process and may be induced by accumulated DNA damage due to local dietary habits. We observe diverse correlations between the presence of oncogene focal amplifications and prognosis, where ERBB2 focal amplifications positively correlate with prognosis and EGFR focal amplifications negatively correlate with prognosis. Large-scale ERBB2 immunohistochemistry results from 1668 GCA patients show survival probability of ERBB2 positive patients is lower than that of ERBB2 negative patients when their surviving time is under 2 years, however, the tendency is opposite when their surviving time is longer than 2 years. Our observations indicate that the ERBB2 focal amplifications may represent a good prognostic marker in GCA patients.

Suggested Citation

  • Xue-Ke Zhao & Pengwei Xing & Xin Song & Miao Zhao & Linxuan Zhao & Yonglong Dang & Ling-Ling Lei & Rui-Hua Xu & Wen-Li Han & Pan-Pan Wang & Miao-Miao Yang & Jing-Feng Hu & Kan Zhong & Fu-You Zhou & Xu, 2021. "Focal amplifications are associated with chromothripsis events and diverse prognoses in gastric cardia adenocarcinoma," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26745-3
    DOI: 10.1038/s41467-021-26745-3
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-021-26745-3
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-021-26745-3?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Michael S. Lawrence & Petar Stojanov & Paz Polak & Gregory V. Kryukov & Kristian Cibulskis & Andrey Sivachenko & Scott L. Carter & Chip Stewart & Craig H. Mermel & Steven A. Roberts & Adam Kiezun & Pe, 2013. "Mutational heterogeneity in cancer and the search for new cancer-associated genes," Nature, Nature, vol. 499(7457), pages 214-218, July.
    2. Natalia Voronina & John K. L. Wong & Daniel Hübschmann & Mario Hlevnjak & Sebastian Uhrig & Christoph E. Heilig & Peter Horak & Simon Kreutzfeldt & Andreas Mock & Albrecht Stenzinger & Barbara Hutter , 2020. "The landscape of chromothripsis across adult cancer types," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
    3. Swee Seong Wong & Kyoung-Mee Kim & Jason C. Ting & Kun Yu & Jake Fu & Shawn Liu & Razvan Cristescu & Michael Nebozhyn & Lara Gong & Yong Gang Yue & Jian Wang & Chen Ronghua & Andrey Loboda & James Har, 2014. "Genomic landscape and genetic heterogeneity in gastric adenocarcinoma revealed by whole-genome sequencing," Nature Communications, Nature, vol. 5(1), pages 1-12, December.
    4. Ofer Shoshani & Simon F. Brunner & Rona Yaeger & Peter Ly & Yael Nechemia-Arbely & Dong Hyun Kim & Rongxin Fang & Guillaume A. Castillon & Miao Yu & Julia S. Z. Li & Ying Sun & Mark H. Ellisman & Bing, 2021. "Chromothripsis drives the evolution of gene amplification in cancer," Nature, Nature, vol. 591(7848), pages 137-141, March.
    5. Jens Luebeck & Ceyda Coruh & Siavash R. Dehkordi & Joshua T. Lange & Kristen M. Turner & Viraj Deshpande & Dave A. Pai & Chao Zhang & Utkrisht Rajkumar & Julie A. Law & Paul S. Mischel & Vineet Bafna, 2020. "AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    6. Manasi Ratnaparkhe & John K. L. Wong & Pei-Chi Wei & Mario Hlevnjak & Thorsten Kolb & Milena Simovic & Daniel Haag & Yashna Paul & Frauke Devens & Paul Northcott & David T. W. Jones & Marcel Kool & An, 2018. "Defective DNA damage repair leads to frequent catastrophic genomic events in murine and human tumors," Nature Communications, Nature, vol. 9(1), pages 1-13, December.
    7. Huimin Li & Dong Han & Yawen Hou & Huilin Chen & Zheng Chen, 2015. "Statistical Inference Methods for Two Crossing Survival Curves: A Comparison of Methods," PLOS ONE, Public Library of Science, vol. 10(1), pages 1-18, January.
    8. Christopher A Miller & Oliver Hampton & Cristian Coarfa & Aleksandar Milosavljevic, 2011. "ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Sequencing Reads," PLOS ONE, Public Library of Science, vol. 6(1), pages 1-7, January.
    9. Henrik Devitt Møller & Marghoob Mohiyuddin & Iñigo Prada-Luengo & M. Reza Sailani & Jens Frey Halling & Peter Plomgaard & Lasse Maretty & Anders Johannes Hansen & Michael P. Snyder & Henriette Pilegaa, 2018. "Circular DNA elements of chromosomal origin are common in healthy human somatic tissue," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    10. Kristen M. Turner & Viraj Deshpande & Doruk Beyter & Tomoyuki Koga & Jessica Rusert & Catherine Lee & Bin Li & Karen Arden & Bing Ren & David A. Nathanson & Harley I. Kornblum & Michael D. Taylor & Sh, 2017. "Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity," Nature, Nature, vol. 543(7643), pages 122-125, March.
    11. Ofer Shoshani & Simon F. Brunner & Rona Yaeger & Peter Ly & Yael Nechemia-Arbely & Dong Hyun Kim & Rongxin Fang & Guillaume A. Castillon & Miao Yu & Julia S. Z. Li & Ying Sun & Mark H. Ellisman & Bing, 2021. "Publisher Correction: Chromothripsis drives the evolution of gene amplification in cancer," Nature, Nature, vol. 591(7850), pages 19-19, March.
    12. Sihan Wu & Kristen M. Turner & Nam Nguyen & Ramya Raviram & Marcella Erb & Jennifer Santini & Jens Luebeck & Utkrisht Rajkumar & Yarui Diao & Bin Li & Wenjing Zhang & Nathan Jameson & M. Ryan Corces &, 2019. "Circular ecDNA promotes accessible chromatin and high oncogene expression," Nature, Nature, vol. 575(7784), pages 699-703, November.
    13. Cheng-Zhong Zhang & Alexander Spektor & Hauke Cornils & Joshua M. Francis & Emily K. Jackson & Shiwei Liu & Matthew Meyerson & David Pellman, 2015. "Chromothripsis from DNA damage in micronuclei," Nature, Nature, vol. 522(7555), pages 179-184, June.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Chunyang Bao & Richard W. Tourdot & Gregory J. Brunette & Chip Stewart & Lili Sun & Hideo Baba & Masayuki Watanabe & Agoston T. Agoston & Kunal Jajoo & Jon M. Davison & Katie S. Nason & Gad Getz & Ken, 2023. "Genomic signatures of past and present chromosomal instability in Barrett’s esophagus and early esophageal adenocarcinoma," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
    2. Jinxin Phaedo Chen & Constantin Diekmann & Honggui Wu & Chong Chen & Giulia Chiara & Enrico Berrino & Konstantinos L. Georgiadis & Britta A. M. Bouwman & Mohit Virdi & Luuk Harbers & Sara Erika Bellom, 2024. "scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    3. Robin Aguilar & Conor K. Camplisson & Qiaoyi Lin & Karen H. Miga & William S. Noble & Brian J. Beliveau, 2024. "Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    4. Shixiang Wang & Chen-Yi Wu & Ming-Ming He & Jia-Xin Yong & Yan-Xing Chen & Li-Mei Qian & Jin-Ling Zhang & Zhao-Lei Zeng & Rui-Hua Xu & Feng Wang & Qi Zhao, 2024. "Machine learning-based extrachromosomal DNA identification in large-scale cohorts reveals its clinical implications in cancer," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    5. Francesc Muyas & Manuel José Gómez Rodriguez & Rita Cascão & Angela Afonso & Carolin M. Sauer & Claudia C. Faria & Isidro Cortés-Ciriano & Ignacio Flores, 2024. "The ALT pathway generates telomere fusions that can be detected in the blood of cancer patients," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    6. Ambrocio Sanchez & Pedro Ortega & Ramin Sakhtemani & Lavanya Manjunath & Sunwoo Oh & Elodie Bournique & Alexandrea Becker & Kyumin Kim & Cameron Durfee & Nuri Alpay Temiz & Xiaojiang S. Chen & Reuben , 2024. "Mesoscale DNA features impact APOBEC3A and APOBEC3B deaminase activity and shape tumor mutational landscapes," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    7. Love Michael I. & Myšičková Alena & Sun Ruping & Kalscheuer Vera & Vingron Martin & Haas Stefan A., 2011. "Modeling Read Counts for CNV Detection in Exome Sequencing Data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 10(1), pages 1-30, November.
    8. Anna Luiza Silva Almeida Vicente & Alexei Novoloaca & Vincent Cahais & Zainab Awada & Cyrille Cuenin & Natália Spitz & André Lopes Carvalho & Adriane Feijó Evangelista & Camila Souza Crovador & Rui Ma, 2022. "Cutaneous and acral melanoma cross-OMICs reveals prognostic cancer drivers associated with pathobiology and ultraviolet exposure," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    9. Heathcliff Dorado García & Fabian Pusch & Yi Bei & Jennifer Stebut & Glorymar Ibáñez & Kristina Guillan & Koshi Imami & Dennis Gürgen & Jana Rolff & Konstantin Helmsauer & Stephanie Meyer-Liesener & N, 2022. "Therapeutic targeting of ATR in alveolar rhabdomyosarcoma," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    10. Rotem Katzir & Noam Rudberg & Keren Yizhak, 2022. "Estimating tumor mutational burden from RNA-sequencing without a matched-normal sample," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    11. Kathrin Möllenhoff & Achim Tresch, 2023. "Investigating non-inferiority or equivalence in time-to-event data under non-proportional hazards," Lifetime Data Analysis: An International Journal Devoted to Statistical Methods and Applications for Time-to-Event Data, Springer, vol. 29(3), pages 483-507, July.
    12. Oriol Pich & Iker Reyes-Salazar & Abel Gonzalez-Perez & Nuria Lopez-Bigas, 2022. "Discovering the drivers of clonal hematopoiesis," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    13. Nathan Cunningham & Jim E. Griffin & David L. Wild, 2020. "ParticleMDI: particle Monte Carlo methods for the cluster analysis of multiple datasets with applications to cancer subtype identification," Advances in Data Analysis and Classification, Springer;German Classification Society - Gesellschaft für Klassifikation (GfKl);Japanese Classification Society (JCS);Classification and Data Analysis Group of the Italian Statistical Society (CLADAG);International Federation of Classification Societies (IFCS), vol. 14(2), pages 463-484, June.
    14. Charlotte K. Y. Ng & Eva Dazert & Tuyana Boldanova & Mairene Coto-Llerena & Sandro Nuciforo & Caner Ercan & Aleksei Suslov & Marie-Anne Meier & Thomas Bock & Alexander Schmidt & Sylvia Ketterer & Xuey, 2022. "Integrative proteogenomic characterization of hepatocellular carcinoma across etiologies and stages," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    15. Farshad Farshidfar & Kahn Rhrissorrakrai & Chaya Levovitz & Cong Peng & James Knight & Antonella Bacchiocchi & Juan Su & Mingzhu Yin & Mario Sznol & Stephan Ariyan & James Clune & Kelly Olino & Laxmi , 2022. "Integrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    16. Martin Boström & Erik Larsson, 2022. "Somatic mutation distribution across tumour cohorts provides a signal for positive selection in cancer," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    17. Stamatis Papathanasiou & Styliani Markoulaki & Logan J. Blaine & Mitchell L. Leibowitz & Cheng-Zhong Zhang & Rudolf Jaenisch & David Pellman, 2021. "Whole chromosome loss and genomic instability in mouse embryos after CRISPR-Cas9 genome editing," Nature Communications, Nature, vol. 12(1), pages 1-7, December.
    18. Yanli Liu & Zhong Wu & Jin Zhou & Dinesh K. A. Ramadurai & Katelyn L. Mortenson & Estrella Aguilera-Jimenez & Yifei Yan & Xiaojun Yang & Alison M. Taylor & Katherine E. Varley & Jason Gertz & Peter S., 2021. "A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    19. Jennifer B. Shah & Dana Pueschl & Bradley Wubbenhorst & Mengyao Fan & John Pluta & Kurt D’Andrea & Anna P. Hubert & Jake S. Shilan & Wenting Zhou & Adam A. Kraya & Alba Llop Guevara & Catherine Ruan &, 2022. "Analysis of matched primary and recurrent BRCA1/2 mutation-associated tumors identifies recurrence-specific drivers," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    20. Akshaya Ramakrishnan & Aikaterini Symeonidi & Patrick Hanel & Katharina T. Schmid & Maria L. Richter & Michael Schubert & Maria Colomé-Tatché, 2023. "epiAneufinder identifies copy number alterations from single-cell ATAC-seq data," Nature Communications, Nature, vol. 14(1), pages 1-10, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26745-3. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.