Loss of tumor-infiltrating lymphocytes and poor response to immunotherapy in IDH GOF mutant melanoma
Emma Specht, Lakshmi Pakanati, Meng-Ju Wu, Russell W. Jenkins, Derek N. Effiom, Nabeel Bardeesy, Bradley E. Bernstein, Moshe Sade-Feldman, Christine G. Lian, Genevieve M. Boland, Elena Torlai Triglia, Sonia Cohen
Emma Specht, Lakshmi Pakanati, Meng-Ju Wu, Russell W. Jenkins, Derek N. Effiom, Nabeel Bardeesy, Bradley E. Bernstein, Moshe Sade-Feldman, Christine G. Lian, Genevieve M. Boland, Elena Torlai Triglia, Sonia Cohen
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Research Article Genetics Immunology Oncology

Loss of tumor-infiltrating lymphocytes and poor response to immunotherapy in IDH GOF mutant melanoma

Abstract

Recent innovations in melanoma treatment with immune checkpoint blockade (ICB) have improved overall outcomes for patients; however, over 50% of patients still develop resistance to treatment. These patients either have intrinsic resistance and never respond to therapy or develop acquired resistance months or years into treatment. The mechanisms underlying ICB resistance remain poorly understood. Our data show that patients with isocitrate dehydrogenase gain-of-function (IDH GOF) mutant melanoma have a worse response to anti-PD1 immunotherapy. IDH mutations have been found to be oncogenic and associated with differential methylation in multiple cancers but are not yet characterized in human melanoma. Here, we investigate the clinical, immune, and transcriptional phenotypes of IDH GOF melanomas through analyses of clinical response, single-cell RNA-seq, bulk RNA-seq, and DNA methylation data. Single-cell data analysis showed decreased immune infiltrate and activity in the IDH GOF tumors. Bulk sequencing data demonstrated the association among IDH mutation, immune exclusion, and disruptions in global DNA methylation. The melanoma-derived genomic data presented support previously described resistance mechanisms of IDH mutation in other cancer types and is the first demonstration to our knowledge of the role of IDH GOF in the human melanoma tumor microenvironment.

Authors

Emma Specht, Lakshmi Pakanati, Meng-Ju Wu, Russell W. Jenkins, Derek N. Effiom, Nabeel Bardeesy, Bradley E. Bernstein, Moshe Sade-Feldman, Christine G. Lian, Genevieve M. Boland, Elena Torlai Triglia, Sonia Cohen

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Figure 2

Single-cell RNA-seq shows a decrease in TIL in IDH GOF melanoma.

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Single-cell RNA-seq shows a decrease in TIL in IDH GOF melanoma. Single-...
Single-cell gene expression profiles from IDH GOF melanoma (n = 3 patients; 33,076 total high-quality cells; 6,566–20,786 cells per patient) were compared with profiles from well-matched IDH WT melanoma (n = 6 patients; 38,850 total high-quality cells; 4,129–10,641 per patient) in the pretreatment setting (Supplemental Figure 2). Labels M1–M3 refer to samples from IDH GOF patients. Labels WT4–WT9 refer to samples from IDH WT patients. (A) Cell gene-expression profiles (dots) were annotated by cell types (clusters) and colored by the mutational status of the tumors. Patient tumor samples were analyzed and cell types classified using Leiden clustering in conjunction with marker genes (Methods). (B) Box plot of cell type distribution in IDH GOF vs. IDH WT melanoma with dots representing individual melanomas. (A and B) Analysis with scCODA revealed that IDH GOF tumors had a larger proportion of tumor cells. (D) UMAPs representing the expression of marker genes show the normalized expression (red). (E) Dot plot showing expression of marker genes in classified T cell type groups. (D and E) Gene expression profile analysis with Hotspot on all T cells demonstrated 6 modules corresponding to T cell states. (C) Cells were assigned to their top module, and genes in each module were used to identify the modules identity (Methods). (D and E) Well-defined modules of T cell state exhibit distinctly higher expression of state-defining marker genes compared with other modules. (F) Mutant tumors had low proportions of T cells compared with WT tumors. (G) Comparing the IDH GOF and IDH WT samples, on average mutant samples included proportionally more regulatory and memory T cells and fewer CD8+ cytotoxic and exhausted T cells, representing a cold environment. (H) T cells from IDH WT tumors displayed higher expression of the CXCL13/CXCR5 signaling pathway, consistent with published work (12) understanding ICB melanoma responders.