Transcriptional immunogenomic analysis reveals distinct immunological clusters in pediatric nervous system tumours

Nabbi, A.; Beck, P.; Delaidelli, A.; Oldridge, D. A.; Sudhaman, S.; Zhu, K.; Yang, S. Y. C.; Mulder, D. T.; Bruce, J. P.; Paulson, J. N.; Raman, P.; Zhu, Y.; Resnick, A. C.; Sorensen, P. H.; Sill, M.; Brabetz, S.; Lambo, S.; Malkin, D.; Johann, P. D.; Kool, M.; Jones, D. T. W.; Pfister, S. M.; Jäger, N.; Pugh, T. J.

doi:10.1101/2022.09.20.508719

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bioRxiv · 10.1101/2022.09.20.508719

Transcriptional immunogenomic analysis reveals distinct immunological clusters in pediatric nervous system tumours

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Abstract

To inform immunotherapy approaches in children, we performed an immunogenomic analysis of RNA-seq data from 925 treatment-naive pediatric nervous system tumours (pedNST) spanning 12 cancer types from three public data sets. Within pedNST, we uncovered four broad immune clusters: Pediatric Inflamed (10%), Myeloid Predominant (30%), Immune Neutral (43%) and Immune Excluded (17%). We validated these clusters using immunohistochemistry, methylation immune inference, and segmentation analysis of tissue images. We report shared biology of these immune clusters within and across cancer types, and characterization of specific immune-cell frequencies as well as T- and B-cell repertoires. We found no associations between immune infiltration levels and tumour mutational burden, although molecular cancer entities were enriched within specific immune clusters. Given the heterogeneity within pedNST, our findings suggest personalized immunogenomic profiling is needed to guide selection of immunotherapeutic strategies.

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Nabbi, A., Beck, P., Delaidelli, A., Oldridge, D. A., Sudhaman, S., Zhu, K., Yang, S. Y. C., Mulder, D. T., Bruce, J. P., Paulson, J. N., Raman, P., Zhu, Y., Resnick, A. C., Sorensen, P. H., Sill, M., Brabetz, S., Lambo, S., Malkin, D., Johann, P. D., Kool, M., Jones, D. T. W., Pfister, S. M., Jäger, N., Pugh, T. J.. 2022-09-21. Transcriptional immunogenomic analysis reveals distinct immunological clusters in pediatric nervous system tumours. https://doi.org/10.1101/2022.09.20.508719

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