Spatially resolved analyses link genomic and immune diversity and reveal unfavorable neutrophil activation in melanoma

Akash Mitra, Miles C. Andrews, Whijae Roh, Marianna Petaccia De Macedo, Courtney W. Hudgens, Fernando Carapeto, Shailbala Singh, Alexandre Reuben, Feng Wang, Xizeng Mao, Xingzhi Song, Khalida Wani, Samantha Tippen, Kwok Shing Ng, Aislyn Schalck, Donald A. Sakellariou-Thompson, Eveline Chen, Sangeetha M. Reddy, Christine N. Spencer, Diana WiesnoskiLatasha D. Little, Curtis Gumbs, Zachary A. Cooper, Elizabeth M. Burton, Patrick Hwu, Michael A. Davies, Jianhua Zhang, Chantale Bernatchez, Nicholas Navin, Padmanee Sharma, James P. Allison, Jennifer A. Wargo, Cassian Yee, Michael T. Tetzlaff, Wen Jen Hwu, Alexander J. Lazar, P. Andrew Futreal

Research output: Contribution to journalArticle

Abstract

Complex tumor microenvironmental (TME) features influence the outcome of cancer immunotherapy (IO). Here we perform immunogenomic analyses on 67 intratumor sub-regions of a PD-1 inhibitor-resistant melanoma tumor and 2 additional metastases arising over 8 years, to characterize TME interactions. We identify spatially distinct evolution of copy number alterations influencing local immune composition. Sub-regions with chromosome 7 gain display a relative lack of leukocyte infiltrate but evidence of neutrophil activation, recapitulated in The Cancer Genome Atlas (TCGA) samples, and associated with lack of response to IO across three clinical cohorts. Whether neutrophil activation represents cause or consequence of local tumor necrosis requires further study. Analyses of T-cell clonotypes reveal the presence of recurrent priming events manifesting in a dominant T-cell clonotype over many years. Our findings highlight the links between marked levels of genomic and immune heterogeneity within the physical space of a tumor, with implications for biomarker evaluation and immunotherapy response.

Original languageEnglish (US)
Article number1839
JournalNature communications
Volume11
Issue number1
DOIs
StatePublished - Dec 1 2020
Externally publishedYes

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

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    Mitra, A., Andrews, M. C., Roh, W., De Macedo, M. P., Hudgens, C. W., Carapeto, F., Singh, S., Reuben, A., Wang, F., Mao, X., Song, X., Wani, K., Tippen, S., Ng, K. S., Schalck, A., Sakellariou-Thompson, D. A., Chen, E., Reddy, S. M., Spencer, C. N., ... Futreal, P. A. (2020). Spatially resolved analyses link genomic and immune diversity and reveal unfavorable neutrophil activation in melanoma. Nature communications, 11(1), [1839]. https://doi.org/10.1038/s41467-020-15538-9