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Chemical complementarity between immune receptor CDR3s and IDH1 mutants correlates with increased survival for lower grade glioma

Oncogene volume 39, pages 1773–1783 (2020)Cite this article

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Abstract

Focusing on highly specific aspects of the immune response is likely to answer a number of basic questions, and in some cases even resolve basic contradictions, in cancer immunology. For example, there are many cases, where chronic inflammation is associated with cancer development, and many other cases where an immune response represents an anticancer process. In this study, using bioinformatics algorithms, we examined the chemical relationships between the amino acid sequences of the complementarity-determining region-3 (CDR3) represented by immune receptors associated with lower grade glioma and isocitrate dehydrogenase-1 (IDH1) mutants. In particular, we developed a chemical complementarity scoring approach to classify tumors based on the complementarity of CDR3s and mutant IDH1 amino acids, relying on net charge per residue and hydropathy parameters. There was a strong correlation between the increased survival in low-grade glioma (LGG) and complementarity of IDH1 mutants to the CDR3 domain of the T-cell receptor beta chain (TRB). Similar results were obtained for TRB CDR3s and NRAS mutants in melanoma. Furthermore, the clear connection between increased survival rates and immune receptor-IDH1 mutant complementarities may also, partially, explain the better LGG prognosis for patients with IDH1 mutants.

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Code availability

SOM and https://github.com/bchobrut-USF/lgg_idh1.

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Acknowledgements

Authors thank USF research computing and the taxpayers of the State of Florida. BIC, SZ, SF, MY and AD were recipients of USF Morsani College of Medicine RISE fellowships.

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Authors and Affiliations

  1. Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA

    Boris I. Chobrutskiy, Michelle Yeagley, Price Tipping, Saif Zaman, Andrea Diviney, Dhruv N. Patel, Shayan Falasiri, Vladimir N. Uversky & George Blanck

  2. Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA

    Saif Zaman & George Blanck

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  1. Boris I. Chobrutskiy
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Correspondence to George Blanck.

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Chobrutskiy, B.I., Yeagley, M., Tipping, P. et al. Chemical complementarity between immune receptor CDR3s and IDH1 mutants correlates with increased survival for lower grade glioma. Oncogene 39, 1773–1783 (2020). https://doi.org/10.1038/s41388-019-1101-2

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