Single-cell characterization of anti–LAG-3 and anti–PD-1 combination treatment in patients with melanoma
Jani Huuhtanen, Henna Kasanen, Katriina Peltola, Tapio Lönnberg, Virpi Glumoff, Oscar Brück, Olli Dufva, Karita Peltonen, Johanna Vikkula, Emmi Jokinen, Mette Ilander, Moon Hee Lee, Siru Mäkelä, Marta Nyakas, Bin Li, Micaela Hernberg, Petri Bono, Harri Lähdesmäki, Anna Kreutzman, Satu Mustjoki
Jani Huuhtanen, Henna Kasanen, Katriina Peltola, Tapio Lönnberg, Virpi Glumoff, Oscar Brück, Olli Dufva, Karita Peltonen, Johanna Vikkula, Emmi Jokinen, Mette Ilander, Moon Hee Lee, Siru Mäkelä, Marta Nyakas, Bin Li, Micaela Hernberg, Petri Bono, Harri Lähdesmäki, Anna Kreutzman, Satu Mustjoki
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Clinical Research and Public Health Immunology Oncology

Single-cell characterization of anti–LAG-3 and anti–PD-1 combination treatment in patients with melanoma

Abstract

Background Relatlimab plus nivolumab (anti–lymphocyte-activation gene 3 plus anti–programmed death 1 [anti–LAG-3+anti–PD-1]) has been approved by the FDA as a first-line therapy for stage III/IV melanoma, but its detailed effect on the immune system is unknown.Methods We evaluated blood samples from 40 immunotherapy-naive or prior immunotherapy–refractory patients with metastatic melanoma treated with anti–LAG-3+anti–PD-1 in a phase I trial using single-cell RNA and T cell receptor sequencing (scRNA+TCRαβ-Seq) combined with other multiomics profiling.Results The highest LAG3 expression was noted in NK cells, Tregs, and CD8+ T cells, and these cell populations underwent the most significant changes during the treatment. Adaptive NK cells were enriched in responders and underwent profound transcriptomic changes during the therapy, resulting in an active phenotype. LAG3+ Tregs expanded, but based on the transcriptome profile, became metabolically silent during the treatment. Last, higher baseline TCR clonality was observed in responding patients, and their expanding CD8+ T cell clones gained a more cytotoxic and NK-like phenotype.Conclusion Anti–LAG-3+anti–PD-1 therapy has profound effects on NK cells and Tregs in addition to CD8+ T cells.Trial registration ClinicalTrials.gov (NCT01968109)Funding Cancer Foundation Finland, Sigrid Juselius Foundation, Signe and Ane Gyllenberg Foundation, Relander Foundation, State funding for university-level health research in Finland, a Helsinki Institute of Life Sciences Fellow grant, Academy of Finland (grant numbers 314442, 311081, 335432, and 335436), and an investigator-initiated research grant from BMS.

Authors

Jani Huuhtanen, Henna Kasanen, Katriina Peltola, Tapio Lönnberg, Virpi Glumoff, Oscar Brück, Olli Dufva, Karita Peltonen, Johanna Vikkula, Emmi Jokinen, Mette Ilander, Moon Hee Lee, Siru Mäkelä, Marta Nyakas, Bin Li, Micaela Hernberg, Petri Bono, Harri Lähdesmäki, Anna Kreutzman, Satu Mustjoki

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Figure 7

Higher baseline clonality is associated with a response to anti–LAG-3+anti–PD-1 therapy.

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Higher baseline clonality is associated with a response to anti–LAG-3+an...
(A) TCR repertoire clonality before and after anti–LAG-3+anti–PD-1 therapy in IO-naive patients (IO-naive n = 9, CR/PR n = 6, SD/PD n = 3, 26 samples) and IO-refractory patients (IO-refractory, n = 25, CR/PR n = 4, SD/PD n = 21, 44 samples). P values were calculated with a 2-sided Mann-Whitney U test. (B) UMAP representation of cells with detected TCRs from 18 scRNA+TCRαβ-Seq samples from patients with melanoma before treatment and 4 weeks and 12 weeks after treatment with anti–LAG-3+anti–PD-1 (n = 6, 18 samples), where the clusters are the same as in Figure 2A but renumbered based on size. (C) Treemap showing the clonal structure of the 500 most abundant clones from scRNA+TCRαβ-Seq–profiled patients, where each facet is a patient’s TCR repertoire at a different time point, and a box denotes a clonotype and the size of the box corresponds to the clonotype’s size. The boxes are colored on the basis of whether the clone is a singleton (gray, i.e., only 1 TCR read found) or persisting (blue; found before and following the therapy), novel (red; found only after the therapy), or contracting (green; found only before the therapy). The CMV serostatus of the patients is highlighted. seropos, seropositive; seroneg, seronegative. (D) The proportion of phenotypes of different clone size bins in pre-therapy samples. Different clones were assigned to different bins based on their size in the repertoire. (E) ORs for the expansion potential of clonotypes between 1 month after therapy and before therapy (baseline) and 3 months after therapy and before therapy (baseline), where higher ORs indicate a higher probability of expansion after therapy.