Abstract 2099: Multi-spatial whole-lesion molecular heterogeneity analyses of an immunotherapy-resistant metastatic melanoma
Authors: Mitra Akash , Roh Whijae , Reuben Alexandre , Wargo Jennifer , Lazar Alexandar , Futreal Philip A. 
Published: August 2018

Genomic and immune intratumor heterogeneity (ITH) can be a significant obstacle to treating patients with checkpoint blockade immunotherapy. The extent of ITH within a single lesion has begun to be addressed but there have been no comprehensive molecular analyses of an entire lesion, multiply sampled in three dimensions with reconstruction of the tumor in its host microenvironment reported thus far. This approach can allow a portrait of the entire tumor ecosystem to emerge and provide a richer, more comprehensive view of the interplay of microenvironment and tumor not bound by a single planar view of a complex entity. Here, we report on our analyses of an anti-CTLA4/anti-PD1 resistant metastatic lesion in toto with an attendant comparative longitudinal view of pre-immunotherapy lesion.

We performed 3-D reconstruction of metastasis obtained at palliative surgery from a patient progressing on anti-PD1 in the context of prior anti-CTLA4 therapy utilizing combined genomic (gene expression profiling, methylation, whole exome sequencing and neoantigen prediction) and immune (immunohistochemistry, RNA- and DNA- based T cell receptor sequencing) profiling of 67 distinct sampled regions from the entire lesion.

Limited point-mutation heterogeneity was found in melanoma driver genes across regions of metastasis. However, copy number alteration analysis revealed changes over time and space with gain of chromosome 7, loss of chromosome 10, and gain of chromosome 14 in certain regions. Differences in immune signatures were observed across regions of a tumor with pockets of immune activation and suppression throughout the metastasis. TCR profiling revealed the dominance of two distinct T cell clonotypes across different regions of the same met, suggesting spatial differences in tumor immunogenicity and T cell activation status. Neoantigen prediction and expression analyses were performed, revealing persistence of a predicted neoantigen detectable prior to CTLA-4 therapy, enriched in different regions of the tumor post-PD-1 blockade. Gene expression of this potential neo-antigen correlated with the distribution and dominance of a specific T cell subclone, suggesting a potential path of infiltration and migration of T cells through the lesion.

Our findings shed light on the three-dimensional genomic and immune landscape in metastatic melanoma in the context of treatment and resistance to immune checkpoint blockade. In particular, even when essentially “gated” on a relatively monotonous mutation landscape, immune intra-tumor heterogeneity can be substantial. This suggests that as immune markers move into the mainstream for use as biomarkers, the use of single biopsies to inform treatment choice may be confounded. These data further impress the need for comprehensive, integrated molecular phenotyping approaches to unravel immunotherapy response and resistance in metastatic melanoma.

Citation Format: Akash Mitra, Whijae Roh, Alexandre Reuben, Jennifer Wargo, Alexandar Lazar, Philip A. Futreal. Multi-spatial whole-lesion molecular heterogeneity analyses of an immunotherapy-resistant metastatic melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2099.