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Analysis of immune subtypes across the epithelial-mesenchymal plasticity spectrum.

Publication ,  Journal Article
Chakraborty, P; Chen, EL; McMullen, I; Armstrong, AJ; Kumar Jolly, M; Somarelli, JA
Published in: Comput Struct Biotechnol J
2021

Epithelial-mesenchymal plasticity plays a critical role in many solid tumor types as a mediator of metastatic dissemination and treatment resistance. In addition, there is also a growing appreciation that the epithelial/mesenchymal status of a tumor plays a role in immune evasion and immune suppression. A deeper understanding of the immunological features of different tumor types has been facilitated by the availability of large gene expression datasets and the development of methods to deconvolute bulk RNA-Seq data. These resources have generated powerful new ways of characterizing tumors, including classification of immune subtypes based on differential expression of immunological genes. In the present work, we combine scoring algorithms to quantify epithelial-mesenchymal plasticity with immune subtype analysis to understand the relationship between epithelial plasticity and immune subtype across cancers. We find heterogeneity of epithelial-mesenchymal transition (EMT) status both within and between cancer types, with greater heterogeneity in the expression of EMT-related factors than of MET-related factors. We also find that specific immune subtypes have associated EMT scores and differential expression of immune checkpoint markers.

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Published In

Comput Struct Biotechnol J

DOI

ISSN

2001-0370

Publication Date

2021

Volume

19

Start / End Page

3842 / 3851

Location

Netherlands

Related Subject Headings

  • 4601 Applied computing
  • 3101 Biochemistry and cell biology
  • 0802 Computation Theory and Mathematics
  • 0103 Numerical and Computational Mathematics
 

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Chakraborty, P., Chen, E. L., McMullen, I., Armstrong, A. J., Kumar Jolly, M., & Somarelli, J. A. (2021). Analysis of immune subtypes across the epithelial-mesenchymal plasticity spectrum. Comput Struct Biotechnol J, 19, 3842–3851. https://doi.org/10.1016/j.csbj.2021.06.023
Chakraborty, Priyanka, Emily L. Chen, Isabelle McMullen, Andrew J. Armstrong, Mohit Kumar Jolly, and Jason A. Somarelli. “Analysis of immune subtypes across the epithelial-mesenchymal plasticity spectrum.Comput Struct Biotechnol J 19 (2021): 3842–51. https://doi.org/10.1016/j.csbj.2021.06.023.
Chakraborty P, Chen EL, McMullen I, Armstrong AJ, Kumar Jolly M, Somarelli JA. Analysis of immune subtypes across the epithelial-mesenchymal plasticity spectrum. Comput Struct Biotechnol J. 2021;19:3842–51.
Chakraborty, Priyanka, et al. “Analysis of immune subtypes across the epithelial-mesenchymal plasticity spectrum.Comput Struct Biotechnol J, vol. 19, 2021, pp. 3842–51. Pubmed, doi:10.1016/j.csbj.2021.06.023.
Chakraborty P, Chen EL, McMullen I, Armstrong AJ, Kumar Jolly M, Somarelli JA. Analysis of immune subtypes across the epithelial-mesenchymal plasticity spectrum. Comput Struct Biotechnol J. 2021;19:3842–3851.
Journal cover image

Published In

Comput Struct Biotechnol J

DOI

ISSN

2001-0370

Publication Date

2021

Volume

19

Start / End Page

3842 / 3851

Location

Netherlands

Related Subject Headings

  • 4601 Applied computing
  • 3101 Biochemistry and cell biology
  • 0802 Computation Theory and Mathematics
  • 0103 Numerical and Computational Mathematics