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Clonal driver neoantigen loss under EGFR TKI and immune selection pressures

Maise Al Bakir
James L. Reading
Samuel Gamble
Rachel Rosenthal
Imran Uddin
Andrew Rowan
Joanna Przewrocka
Amber Rogers
Yien Ning Sophia Wong
Amalie K. Bentzen
Selvaraju Veeriah
Sophia Ward
Aaron T. Garnett
Paula Kalavakur
Carlos Martínez-Ruiz
Clare Puttick
Ariana Huebner
Daniel E. Cook
David A. Moore
Chris Abbosh
Crispin T. Hiley
Cristina Naceur-Lombardelli
Thomas B. K. Watkins
Marina Petkovic
Roland F. Schwarz
Felipe Gálvez-Cancino
Kevin Litchfield
Peter Meldgaard
Boe Sandahl Sorensen
Line Bille Madsen
Dirk Jäger
Martin D. Forster
Tobias Arkenau
Clara Domingo-Vila
Timothy I. M. Tree
Mohammad Kadivar
Sine Reker Hadrup
Benny Chain
Sergio A. Quezada
Nicholas McGranahan
Charles Swanton

February 19, 2025

Neoantigen vaccines are under investigation for various cancers, including epidermal growth factor receptor (EGFR)-driven lung cancers1,2. We tracked the phylogenetic history of an EGFR mutant lung cancer treated with erlotinib, osimertinib, radiotherapy and a personalized neopeptide vaccine (NPV) targeting ten somatic mutations, including EGFR exon 19 deletion (ex19del). The ex19del mutation was clonal, but is likely to have appeared after a whole-genome doubling (WGD) event. Following osimertinib and NPV treatment, loss of the ex19del mutation was identified in a progressing small-cell-transformed liver metastasis. Circulating tumour DNA analyses tracking 467 somatic variants revealed the presence of this EGFR wild-type clone before vaccination and its expansion during osimertinib/NPV therapy. Despite systemic T cell reactivity to the vaccine-targeted ex19del neoantigen, the NPV failed to halt disease progression. The liver metastasis lost vaccine-targeted neoantigens through chromosomal instability and exhibited a hostile microenvironment, characterized by limited immune infiltration, low CXCL9 and elevated M2 macrophage levels. Neoantigens arising post-WGD were more likely to be absent in the progressing liver metastasis than those occurring pre-WGD, suggesting that prioritizing pre-WGD neoantigens may improve vaccine design. Data from the TRACERx 421 cohort3 provide evidence that pre-WGD mutations better represent clonal variants, and owing to their presence at multiple copy numbers, are less likely to be lost in metastatic transition. These data highlight the power of phylogenetic disease tracking and functional T cell profiling to understand mechanisms of immune escape during combination therapies.