Combined tumor and immune signals from genomes or transcriptomes predict outcomes of checkpoint inhibition in melanoma

Immune checkpoint blockade (CPB) improves melanoma outcomes, but many patients still do not respond. Tumor mutational burden (TMB) and tumor-infiltrating T cells are associated with response, and integrative models improve survival prediction. However, integrating immune/tumor-intrinsic features using data from a single assay (DNA/RNA) remains underexplored. Here, we analyze whole-exome and bulk RNA sequencing of tumors from new and published cohorts of 189 and 178 patients with melanoma receiving CPB, respectively. Using DNA, we calculate T cell and B cell burdens (TCB/BCB) from rearranged TCR/Ig sequences and find that patients with TMBhigh and TCBhigh or BCBhigh have improved outcomes compared to other patients. By combining pairs of immune- and tumor-expressed genes, we identify three gene pairs associated with response and survival, which validate in independent cohorts. The top model includes lymphocyte-expressed MAP4K1 and tumor-expressed TBX3. Overall, RNA or DNA-based models combining immune and tumor measures improve predictions of melanoma CPB outcomes.

Abstract 6670: Combined signals from tumor and immune cells predict outcomes of checkpoint inhibition in melanoma

Cancer immunotherapy with checkpoint blockade has improved survival and outcomes in melanoma, but still a majority of patients do not respond. Both high tumor mutation burden (TMB) and high T cell infiltration have been associated with response, but integrative models based on DNA or RNA assays have not been comprehensively explored and validated. Focusing on melanomas from patients receiving checkpoint blockade, we generated new and aggregated existing datasets of whole exome sequencing (WES) (n = 189 total) and bulk RNA sequencing (n = 154 total) to derive genomic and transcriptomic factors that predict survival and response to immunotherapy in melanoma.

We quantified T and B cell infiltrates using rearranged T cell receptor (TCR) and immunoglobulin (Ig) sequences, respectively, from DNA or RNA sequencing. High levels of rearranged TCR reads or rearranged Ig reads in RNA-seq were associated with survival (P = 0.0046, P = 0.015) and response (P = 0.0034, P = 0.047). We created RNA-based metrics of T and B cell burden (TCBRNA or BCBRNA) by normalizing the number of rearranged TCR reads by the total number of mapped reads. When we analyzed WES data in patients for whom DNA and RNA were extracted from the same region, we found that the TCBDNA correlated with TCBRNA (rho = 0.73) and BCBDNA with BCBRNA (rho = 0.41), demonstrating that the level of lymphocyte infiltration can be estimated using rearranged TCR or Ig reads from tumor WES alone.

We found that TCBDNA and BCBDNA both associated with survival (P = 0.0023 and 0.0089). In a combined model, patients with high TMB and high TCB DNA survived longer (P = 2.4e-4, HR = 2.68) and had a higher response rate (Fisher P = 0.028). This combined model was superior to models with TMB or TCBDNA alone. Similarly, patients with high TMB and high BCBDNA had longer survival and higher response rates (log-rank P = 0.0029, HR = 2.64, Fisher P = 0.015). We reanalyzed stage III/IV melanomas from TCGA and found that the TMB high, TCBDNA high subgroup had increased survival (P = 0.007).

Next, clustering of tumor transcriptomes identified 5 tumor subtypes based on melanocyte differentiation, immune infiltration and keratin levels. These melanoma subtypes were associated with survival outcomes after immunotherapy (P = 0.019). We found that TBX3, a tumor-expressed transcription factor enriched in poorly differentiated melanomas, was over-expressed among non-responders within the immune-infiltrated subtype and among all patients (P = 3.9e-4, P = 8.7e-5). Patients whose tumors had high immune infiltrate and low expression of TBX3 had longer survival (P = 1.6e-5, HR = 3.39), however this subgroup did not have longer survival in an independent cohort (n = 73, P = 0.10, HR = 2.63). In conclusion, we demonstrate both RNA-based (immune infiltrate and tumor subtype) and DNA-based metrics (TMB/TCB or TMB/BCB) can be used as pre-treatment predictors of survival after checkpoint blockade in melanoma.

Citation Format: Samuel S. Freeman, Moshe Sade-Feldman, Jaegil Kim, Chip Stewart, Arvind Ravi, Monica Arniella, Keren Yizhak, Ignaty Leshchiner, Liudmila Elagina, Oliver Spiro, Dimitri Livitz, Daniel Rosebrock, François Aguet, Jian Carrot-Zhang, Anna Gonye, Gavin Ha, Ziao Lin, Jonathan H. Chen, Dennie T. Frederick, Michal Barzily-Rokni, Marc R. Hammond, Hans Vitzthum, Shauna M. Blackmon, Yunxin J. Jiao, Donald P. Lawrence, Lyn M. Duncan, Anat Stemmer-Rachamimov, Jennifer A. Wargo, Keith T. Flaherty, Genevieve M. Boland, Ryan J. Sullivan, Matthew Meyerson, Gad Getz, Nir Hacohen. Combined signals from tumor and immune cells predict outcomes of checkpoint inhibition in melanoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6670.

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma

Treatment of cancer has been revolutionized by immune checkpoint blockade therapies. Despite the high rate of response in advanced melanoma, the majority of patients succumb to disease. To identify factors associated with success or failure of checkpoint therapy, we profiled transcriptomes of 16,291 individual immune cells from 48 tumor samples of melanoma patients treated with checkpoint inhibitors. Two distinct states of CD8+ T cells were defined by clustering and associated with patient tumor regression or progression. A single transcription factor, TCF7, was visualized within CD8+ T cells in fixed tumor samples and predicted positive clinical outcome in an independent cohort of checkpoint-treated patients. We delineated the epigenetic landscape and clonality of these T cell states and demonstrated enhanced antitumor immunity by targeting novel combinations of factors in exhausted cells. Our study of immune cell transcriptomes from tumors demonstrates a strategy for identifying predictors, mechanisms, and targets for enhancing checkpoint immunotherapy.

Context-dependent miR-204 and miR-211 affect the biological properties of amelanotic and melanotic melanoma cells

Despite increasing amounts of experimental evidence depicting the involvement of non-coding RNAs in cancer, the study of BRAFV600E-regulated genes has thus far focused mainly on protein-coding ones. Here, we identify and study the microRNAs that BRAFV600E regulates through the ERK pathway.

By performing small RNA sequencing on A375 melanoma cells and a vemurafenib-resistant clone that was taken as negative control, we discover miR-204 and miR-211 as the miRNAs most induced by vemurafenib. We also demonstrate that, although belonging to the same family, these two miRNAs have distinctive features. miR-204 is under the control of STAT3 and its expression is induced in amelanotic melanoma cells, where it acts as an effector of vemurafenib's anti-motility activity by targeting AP1S2. Conversely, miR-211, a known transcriptional target of MITF, is induced in melanotic melanoma cells, where it targets EDEM1 and consequently impairs the degradation of TYROSINASE (TYR) through the ER-associated degradation (ERAD) pathway. In doing so, miR-211 serves as an effector of vemurafenib's pro-pigmentation activity. We also show that such an increase in pigmentation in turn represents an adaptive response that needs to be overcome using appropriate inhibitors in order to increase the efficacy of vemurafenib.

In summary, we unveil the distinct and context-dependent activities exerted by miR-204 family members in melanoma cells. Our work challenges the widely accepted “same miRNA family = same function” rule and provides a rationale for a novel treatment strategy for melanotic melanomas that is based on the combination of ERK pathway inhibitors with pigmentation inhibitors.

Induction of Telomere Dysfunction Prolongs Disease Control of Therapy-Resistant Melanoma

Purpose: Telomerase promoter mutations are highly prevalent in human tumors including melanoma. A subset of patients with metastatic melanoma often fail multiple therapies, and there is an unmet and urgent need to prolong disease control for those patients.Experimental Design: Numerous preclinical therapy-resistant models of human and mouse melanoma were used to test the efficacy of a telomerase-directed nucleoside, 6-thio-2'-deoxyguanosine (6-thio-dG). Integrated transcriptomics and proteomics approaches were used to identify genes and proteins that were significantly downregulated by 6-thio-dG.Results: We demonstrated the superior efficacy of 6-thio-dG both in vitro and in vivo that results in telomere dysfunction, leading to apoptosis and cell death in various preclinical models of therapy-resistant melanoma cells. 6-thio-dG concomitantly induces telomere dysfunction and inhibits the expression level of AXL.Conclusions: In summary, this study shows that indirectly targeting aberrant telomerase in melanoma cells with 6-thio-dG is a viable therapeutic approach in prolonging disease control and overcoming therapy resistance. Clin Cancer Res; 24(19); 4771-84. ©2018 AACR See related commentary by Teh and Aplin, p. 4629.

Ex Vivo Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids

Ex vivo systems that incorporate features of the tumor microenvironment and model the dynamic response to immune checkpoint blockade (ICB) may facilitate efforts in precision immuno-oncology and the development of effective combination therapies. Here, we demonstrate the ability to interrogate ex vivo response to ICB using murine- and patient-derived organotypic tumor spheroids (MDOTS/PDOTS). MDOTS/PDOTS isolated from mouse and human tumors retain autologous lymphoid and myeloid cell populations and respond to ICB in short-term three-dimensional microfluidic culture. Response and resistance to ICB was recapitulated using MDOTS derived from established immunocompetent mouse tumor models. MDOTS profiling demonstrated that TBK1/IKKε inhibition enhanced response to PD-1 blockade, which effectively predicted tumor response in vivo Systematic profiling of secreted cytokines in PDOTS captured key features associated with response and resistance to PD-1 blockade. Thus, MDOTS/PDOTS profiling represents a novel platform to evaluate ICB using established murine models as well as clinically relevant patient specimens.Significance: Resistance to PD-1 blockade remains a challenge for many patients, and biomarkers to guide treatment are lacking. Here, we demonstrate feasibility of ex vivo profiling of PD-1 blockade to interrogate the tumor immune microenvironment, develop therapeutic combinations, and facilitate precision immuno-oncology efforts. Cancer Discov; 8(2); 196-215. ©2017 AACR.See related commentary by Balko and Sosman, p. 143See related article by Deng et al., p. 216This article is highlighted in the In This Issue feature, p. 127.

Resistance to checkpoint blockade therapy through inactivation of antigen presentation

Treatment with immune checkpoint blockade (CPB) therapies often leads to prolonged responses in patients with metastatic melanoma, but the common mechanisms of primary and acquired resistance to these agents remain incompletely characterized and have yet to be validated in large cohorts. By analyzing longitudinal tumor biopsies from 17 metastatic melanoma patients treated with CPB therapies, we observed point mutations, deletions or loss of heterozygosity (LOH) in beta-2-microglobulin (B2M), an essential component of MHC class I antigen presentation, in 29.4% of patients with progressing disease. In two independent cohorts of melanoma patients treated with anti-CTLA4 and anti-PD1, respectively, we find that B2M LOH is enriched threefold in non-responders (~30%) compared to responders (~10%) and associated with poorer overall survival. Loss of both copies of B2M is found only in non-responders. B2M loss is likely a common mechanism of resistance to therapies targeting CTLA4 or PD1.

Ki-67, p53, and p16 expression, and G691S RET polymorphism in desmoplastic melanoma (DM): A clinicopathologic analysis of predictors of outcome

BACKGROUND

The prognostic role Ki-67, p53, and p16 immunostains and RET (rearranged during transfection) polymorphism in desmoplastic melanoma has not been evaluated.

OBJECTIVE

We sought to identify potential prognostic markers.

METHODS

We performed Ki-67, p53, and p16 immunostains on 66 desmoplastic melanomas, and sequenced RET G691 polymorphism and recurrent mutations of 17 cancer genes in 55 and 20 cases, respectively.

RESULTS

Recurrence and metastasis were documented in 11 of 66 (17%) and 26 of 66 (39%) patients, respectively. Death was noted in 25 of 55 (45%) patients. Ki-67 expression (≥10%, 43%) correlated with male gender (P = .009), ulceration (P = .002), and Breslow depth (P = .009). p53 Expression (≥50%, 28%) correlated with male gender (P = .002) and head and neck location (P = .0228). Using Kaplan-Meier plots, Ki-67 expression (P = .0425) and mitosis (P = .00295) correlated with overall survival, whereas vascular invasion (P = .0292) correlated with disease progression. There was a significant correlation between Ki-67 and p53 expression (P = .003). RET polymorphism was present in 10 of 46 (22%) cases and inversely correlated with Breslow depth (P = .024).

LIMITATION

Our study is small and lacks power to perform a multivariate analysis.

CONCLUSION

Although Ki-67 expression correlated with overall survival, additional studies are needed to determine whether Ki-67 would be an independent prognostic marker in addition to the current routine histopathologic assessment.