NEW YORK – A research team led by investigators at the Dana-Farber Cancer Institute and the Broad Institute has uncovered somatic mutations linked to immunotherapy resistance in metastatic melanoma patients who experienced disease recurrence and acquired drug resistance after an initial response to immune checkpoint immunotherapy (ICI).
Rather than identifying a single somatic mutation source for the acquired resistance observed in the metastatic melanoma cases, the team flagged mutations in several genes that seemed to boost resistance to immune checkpoint immunotherapy over time — from known resistance-related mutations in the JAK1/2 or B2M genes to previously unappreciated changes in genes coding for protein-export complex members.
"[N]o highly recurrent tumor-intrinsic resistance-associated alteration was observed in this cohort," co-senior authors Rizwan Haq and Eliezer Van Allen, medical oncology researchers affiliated with the Dana-Farber Cancer Institute and the Broad Institute, and their colleagues wrote in Cancer Cell on Monday, noting that "the mechanisms of intrinsic or acquired resistance to ICIs are likely more varied and complex and may be driven by the behavior of immune cells not captured by tumor-focused sequencing."
For their analysis, the investigators used exome sequencing to assess formalin-fixed paraffin-embedded pre- and post-treatment tumor samples from 25 metastatic melanoma patients treated with anti-PD-1 or combined anti-PD-1 and anti-CLA-4 immunotherapy. They then searched for single-nucleotide variants, small insertions and deletions, and copy number variants associated with immunotherapy resistance by comparing tumor exome sequences to one another and to matched normal peripheral lymphocyte sequences.
"Due to the rarity of isolated or acquired resistance, assembling a larger group of samples was challenging, making it difficult to draw meaningful conclusions on the cohort level," the authors explained. "However, the relatively small cohort nonetheless was sufficient to identify previously discovered and putative resistance mechanisms."
In particular, the team saw cases marked by B2M or JAK1/2 mutations, while uncovering three metastatic melanoma cases with immunotherapy resistance in the SEC24C and SEC24D genes — contributors to a COPII complex that transports an immunity-related nucleic acid sensing "stimulator of interferon genes" (STING) protein and other proteins from the endoplasmic reticulum to the Golgi apparatus.
Based on prior studies pointing to a role for COPII and subsequent STING signaling in inflammatory cytokine induction, innate immune signaling, and immunodeficiency, the authors speculated that "alterations in COPII, such as the SEC24C and SEC24D, may have dominant roles in immunity," while SEC24C missense mutations may "contribute to anti-PD-1 therapy resistance through the loss of STING activity."
Indeed, the researchers detected an apparent dip in nucleic acid sensing and interferon target gene induction when they used CRISPR-Cas9-based gene editing to lop the SEC24 gene out of human metastatic melanoma or acute monocytic leukemia cell lines. While those shifts could be reversed by introducing the wild-type version of SEC24C into the cells, the changes were not mitigated with versions of the gene that contained immunotherapy-related mutations.
Even so, the team cautioned that there may be yet-unappreciated contributors to immunotherapy resistance in metastatic melanoma, including gene expression or regulatory changes in the tumor microenvironment, that may be revealed in future efforts to untangle drug resistance adaptations.
"Future work should focus on characterizing mechanisms of acquired resistance in a cohort large enough to evaluate for recurrent patterns and to use RNA sequencing (RNA-seq) to identify changes in expression in these patients," the authors suggested. "Our work suggests that certain patients may benefit from therapies that upregulate type I IFN production to circumvent SEC24/STING-mediated resistance."