Interrogating the precancerous evolution of pathway dysfunction in lung squamous cell carcinoma using XTABLE

  1. Matthew Roberts
  2. Julia Ogden
  3. A S Md Mukarram Hossain
  4. Anshuman Chaturvedi
  5. Alastair RW Kerr
  6. Caroline Dive
  7. Jennifer Ellen Beane
  8. Carlos Lopez-Garcia  Is a corresponding author
  1. University of Manchester, United Kingdom
  2. Cancer Research UK Manchester Institute, United Kingdom
  3. The Christie Hospital, United Kingdom
  4. Boston University, United States

Abstract

Lung squamous cell carcinoma (LUSC) is a type of lung cancer with a dismal prognosis that lacks adequate therapies and actionable targets. This disease is characterized by a sequence of low and high-grade preinvasive stages with increasing probability of malignant progression. Increasing our knowledge about the biology of these premalignant lesions (PMLs) is necessary to design new methods of early detection and prevention, and to identify the molecular processes that are key for malignant progression. To facilitate this research, we have designed XTABLE, an open-source application that integrates the most extensive transcriptomic databases of PMLs published so far. With this tool, users can stratify samples using multiple parameters and interrogate PML biology in multiple manners, such as two and multiple group comparisons, interrogation of genes of interests and transcriptional signatures. Using XTABLE, we have carried out a comparative study of the potential role of chromosomal instability scores as biomarkers of PML progression and mapped the onset of the most relevant LUSC pathways to the sequence of LUSC developmental stages. XTABLE will critically facilitate new research for the identification of early detection biomarkers and acquire a better understanding of the LUSC precancerous stages.

Data availability

The current manuscript makes use of previously published databases, so no data have been generated for this manuscript. All analyses shown in the manuscript has been carried out using XTABLE and can be reproduced easily by any user.

The following previously published data sets were used

Article and author information

Author details

  1. Matthew Roberts

    Cancer Biomarker Centre, University of Manchester, Alderley Edge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  2. Julia Ogden

    Cancer Research UK Manchester Institute, Alderley Edge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  3. A S Md Mukarram Hossain

    Cancer Biomarker Centre, University of Manchester, Alderley Edge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. Anshuman Chaturvedi

    Department of Histopathology, The Christie Hospital, Manchester, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  5. Alastair RW Kerr

    Cancer Biomarker Centre, University of Manchester, Edinburgh, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9207-6050
  6. Caroline Dive

    Cancer Biomarker Centre, University of Manchester, Alderley Edge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  7. Jennifer Ellen Beane

    School of Medicine, Boston University, Boston, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Carlos Lopez-Garcia

    Cancer Research UK Manchester Institute, Alderley Edge, United Kingdom
    For correspondence
    carlos.lopezgarcia@cruk.manchester.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9848-8216

Funding

Cancer Research UK (A25146)

  • Julia Ogden
  • A S Md Mukarram Hossain
  • Anshuman Chaturvedi
  • Alastair RW Kerr
  • Caroline Dive
  • Carlos Lopez-Garcia

Manchester Biomedical Research Centre

  • Matthew Roberts

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2023, Roberts et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Matthew Roberts
  2. Julia Ogden
  3. A S Md Mukarram Hossain
  4. Anshuman Chaturvedi
  5. Alastair RW Kerr
  6. Caroline Dive
  7. Jennifer Ellen Beane
  8. Carlos Lopez-Garcia
(2023)
Interrogating the precancerous evolution of pathway dysfunction in lung squamous cell carcinoma using XTABLE
eLife 12:e77507.
https://doi.org/10.7554/eLife.77507

Share this article

https://doi.org/10.7554/eLife.77507

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