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Updated: Aug 6, 2025

Multiplexed Immunofluorescence Analysis and Quantification of Intratumoral PD-1+ Tim-3+ CD8+ T Cells
Published on: February 8, 2018
The molecular and functional landscape of resistance to immune checkpoint blockade in melanoma
Su Yin Lim1,2, Elena Shklovskaya1,2, Jenny H Lee1,2,3
1Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia.
Abstract:
Resistance to immune checkpoint inhibitor therapies in melanoma is common and remains an intractable clinical challenge. In this study, we comprehensively profile immune checkpoint inhibitor resistance mechanisms in short-term tumor cell lines and matched tumor samples from melanoma patients progressing on immune checkpoint inhibitors. Combining genome, transcriptome, and high dimensional flow cytometric profiling with functional analysis, we identify three distinct programs of immunotherapy resistance. Here we show that resistance programs include (1) the loss of wild-type antigen expression, resulting from tumor-intrinsic IFNγ signaling and melanoma de-differentiation, (2) the disruption of antigen presentation via multiple independent mechanisms affecting MHC expression, and (3) immune cell exclusion associated with PTEN loss. The dominant role of compromised antigen production and presentation in melanoma resistance to immune checkpoint inhibition highlights the importance of treatment salvage strategies aimed at the restoration of MHC expression, stimulation of innate immunity, and re-expression of wild-type differentiation antigens.
Insights
Melanoma patients often resist immune checkpoint inhibitors. This study identifies three resistance mechanisms: lost antigen expression, disrupted antigen presentation, and immune cell exclusion, guiding new treatment strategies.
Area of Science:
- Oncology
- Immunology
- Genetics
Background:
- Immune checkpoint inhibitor (ICI) therapy has revolutionized melanoma treatment.
- However, resistance to ICI therapies is a significant clinical hurdle, limiting treatment efficacy for many patients.
Purpose of the Study:
- To comprehensively profile the mechanisms of resistance to immune checkpoint inhibitors in melanoma.
- To identify distinct molecular and cellular programs driving immunotherapy resistance in melanoma patients.
Main Methods:
- Analysis of short-term melanoma cell lines and matched tumor samples from patients progressing on ICIs.
- Integration of genomic, transcriptomic, and high-dimensional flow cytometry profiling.
- Functional assays to elucidate resistance mechanisms.
Main Results:
- Identification of three distinct immunotherapy resistance programs in melanoma.
- Program 1: Loss of wild-type antigen expression due to tumor-intrinsic interferon-gamma (IFNγ) signaling and melanoma de-differentiation.
- Program 2: Disruption of antigen presentation affecting Major Histocompatibility Complex (MHC) expression through multiple mechanisms.
- Program 3: Immune cell exclusion linked to phosphatase and tensin homolog (PTEN) loss.
Conclusions:
- Compromised antigen production and presentation are dominant factors in melanoma ICI resistance.
- Salvage strategies should focus on restoring MHC expression, stimulating innate immunity, and re-expressing wild-type differentiation antigens.
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