Evolution of Delayed Resistance to Immunotherapy in a Melanoma Responder

David Liu*, Jia-Ren Lin* (equal contribution), Emily J Robitschek, Gyulnara G Kasumova, Alex Heyde, Alvin Shi, Adam Kraya, Gao Zhang, Tabea Moll, Dennie T Frederick, Yu-An Chen, Shu Wang, Denis Schapiro, Li-Lun Ho, Kevin Bi, Avinash Sahu, Shaolin Mei, Benchun Miao, Tatyana Sharova, Christopher Alvarez-Breckinridge, Jackson Stocking, Tommy Kim, Riley Fadden, Donald Lawrence, Mai P Hoang, Daniel P Cahill, Mohsen Malehmir, Martin A Nowak, Priscilla K Brastianos, Christine G Lian, Eytan Ruppin, Benjamin Izar, Meenhard Herlyn, Eliezer M Van Allen, Katherine Nathanson, Keith T Flaherty, Ryan J Sullivan, Manolis Kellis, Peter K Sorger, Genevieve M Boland

Nat Med. In press

Despite initial responses, most melanoma patients develop resistance to immune checkpoint blockade (ICB) via poorly understood mechanisms. To understand the evolution of resistance, we studied 37 tumor samples collected over 9 years from a patient with metastatic melanoma and initial response to ICB followed by delayed recurrence and death. Phylogenetic analysis revealed co-evolution of 7 lineages with multiple convergent, but independent resistance-associated alterations (RAAs). All progression tumors emerged from a lineage characterized by loss of chromosome 15q including β2 microglobulin (B2M), with post-treatment resistant clones continuing to acquire additional genomic driver events including genome doubling, CDKN2A biallelic loss, and chromosome 11 loss. Deconvolution of bulk RNAseq and highly-multiplexed immunofluorescence (t-CyCIF) of histological specimens revealed differences in immune composition amongst the different lineages, despite an overall low immune composition. Imaging also revealed an NGFR-High tumor population enriched for PD-L1 expression in close proximity to immune cells with a vasculogenic mimicry phenotype. Rapid autopsy samples demonstrated 2 distinct NGFR spatial patterns with increased polarity and proximity to immune cells in subcutaneous tumors versus a diffuse spatial pattern in lung tumors, suggesting differences in the role and etiology of this neural crest-like program in different tumor microenvironments.

Available images

1169 -22 -55 -62 -1381 27 39 62 76 83 92 109 1028 4 days radiation 1 day radiation MAP2K1 IDH1 Genome doubling Genomedoubling Chr2q partial loss Chr15q loss (B2M) Genome doubling CDKN2A homozygous deletionC15 muts (n=4) C13 Muts (n=17) Chr19q partial loss C24 Muts (n=9) PTEN homozygous deletion Genome doubling Chr11 loss Partial response Partial response Partial response Treatment: Response: Day -30 -60 -1381 0 1169 1849 1862 Nivolumab Nivolumab Anti-PD1TLR-9 Nivolumab Ipilimumab 180 30 60 120 150 720 1028 90 1760 2066 1790 1820 1850 Progression 2066 2 1 4 5 6 3 0 T4 T1 T3 T2 T5 T6 T11 T13 T14 T15 T18 T19 T21 T12 T9 T10 T20 T22 R1 R3.2 R2 T16 T17 T8 T7 AS4 AB1 AS3 AS1 AL3 AS2 AL4 AV1 AB2 AL1 AL2 R3.1



Day -55, Skin Left Forearm

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Day -22, L2 - Skin Right Nasolabial Fold

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Day 27, L6 - Skin Chin

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Day 27, L4 - Skin Upper Lip

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Day 27, L5 - Skin Left Brow

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Day 27, L5 - Skin Right Ear

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Day 39, L2 - Skin Left Arm

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Day 39, L2 - Skin Right Posterior Scalp

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Day 39, L2 - Skin Posterior Neck

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Day 39, L3 - Skin Left Posterior Scalp

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Day 62, L1 - Skin Right Neck

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Day 62, L1 - Skin Left Wrist

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Day 76, L1 - Skin Left Leg

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Day 76, L4 - Skin Right Neck

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Day 76, L4 - Skin Right Nasolabial Fold

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Day 83, L1 - Skin Left Posterior Shoulder

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Day 92, L6 - Skin Left Groin

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Day 92, L1 - Skin Left Neck

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Day 92, L3 - Skin Right Upper Lip

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Day 109, L1 - Skin Left Ring Finger

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Day 1028, L3 - Jejunum

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Day 1849, L3 - Skin Left Neck

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Day 1862, L3 - Skin Left Neck

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Autopsy - Lung, Right Lower Lobe

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Autopsy - Lung, Right Upper Lobe

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Autopsy - Lung, Left Upper Lobe

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Autopsy - Lung, Left Lower Lobe

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Autopsy - Subcutaneous Lesion, Left Mastoid

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Autopsy - Subcutaneous Lesion, left inguinal region

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Autopsy - Subcutaneous Lesion, left scalp

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Autopsy - Subcutaneous Lesion, Left Temporal Bone

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Autopsy - Visceral Organ, Right Adrenal

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Funded by NIH grants P50-GM107618, U54-HL127365, U2C-CA233262, U2C-CA233280, U54-CA225088, the Ludwig Center at Harvard, and the Ludwig Cancer Research Foundation
©2020, Laboratory of Systems Pharmacology. All rights reserved.
Please cite this resource as CyCIF.org, RRID:SCR_016267