Pan-cancer analysis of longitudinal metastatic tumors reveals genomic alterations and immune landscape dynamics associated with pembrolizumab sensitivity

S. Y. Cindy Yang, Scott C. Lien, Ben X. Wang, Derek L. Clouthier, Youstina Hanna, Iulia Cirlan, Kelsey Zhu, Jeffrey P. Bruce, Samah El Ghamrasni, Marco A. J. Iafolla, Marc Oliva, Aaron R. Hansen, Anna Spreafico, Philippe L. Bedard, Stephanie Lheureux, Albiruni Razak, Vanessa Speers, Hal K. Berman, Alexey Aleshin, Benjamin Haibe-Kains, David G. Brooks, Tracy L. McGaha, Marcus O. Butler, Scott V. Bratman, Pamela S. Ohashi, Lillian L. Siu () and Trevor J. Pugh ()
Additional contact information
S. Y. Cindy Yang: University of Toronto
Scott C. Lien: University of Toronto
Ben X. Wang: University Health Network
Derek L. Clouthier: University Health Network
Youstina Hanna: University Health Network
Iulia Cirlan: University Health Network
Kelsey Zhu: University Health Network
Jeffrey P. Bruce: University Health Network
Samah El Ghamrasni: University Health Network
Marco A. J. Iafolla: University Health Network
Marc Oliva: University Health Network
Aaron R. Hansen: University Health Network
Anna Spreafico: University Health Network
Philippe L. Bedard: University Health Network
Stephanie Lheureux: University Health Network
Albiruni Razak: University Health Network
Vanessa Speers: University Health Network
Hal K. Berman: University Health Network
Alexey Aleshin: Natera, Inc.
Benjamin Haibe-Kains: University of Toronto
David G. Brooks: University of Toronto
Tracy L. McGaha: University of Toronto
Marcus O. Butler: University of Toronto
Scott V. Bratman: University of Toronto
Pamela S. Ohashi: University of Toronto
Lillian L. Siu: University Health Network
Trevor J. Pugh: University of Toronto

Nature Communications, 2021, vol. 12, issue 1, 1-15

Abstract: Abstract Serial circulating tumor DNA (ctDNA) monitoring is emerging as a non-invasive strategy to predict and monitor immune checkpoint blockade (ICB) therapeutic efficacy across cancer types. Yet, limited data exist to show the relationship between ctDNA dynamics and tumor genome and immune microenvironment in patients receiving ICB. Here, we present an in-depth analysis of clinical, whole-exome, transcriptome, and ctDNA profiles of 73 patients with advanced solid tumors, across 30 cancer types, from a phase II basket clinical trial of pembrolizumab (NCT02644369) and report changes in genomic and immune landscapes (primary outcomes). Patients stratified by ctDNA and tumor burden dynamics correspond with survival and clinical benefit. High mutation burden, high expression of immune signatures, and mutations in BRCA2 are associated with pembrolizumab molecular sensitivity, while abundant copy-number alterations and B2M loss-of-heterozygosity corresponded with resistance. Upon treatment, induction of genes expressed by T cell, B cell, and myeloid cell populations are consistent with sensitivity and resistance. We identified the upregulated expression of PLA2G2D, an immune-regulating phospholipase, as a potential biomarker of adaptive resistance to ICB. Together, these findings provide insights into the diversity of immunogenomic mechanisms that underpin pembrolizumab outcomes.

Date: 2021
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-25432-7

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DOI: 10.1038/s41467-021-25432-7

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