Citations

Abstract Malignant pleural mesothelioma is a disease primarily associated with exposure to the carcinogen asbestos. Consistent with this carcinogenic exposure, cytogenetic analyses have identified multiple recurrent structural chromosomal abnormalities in this malignancy, but more recent high-throughput sequencing evaluations of point mutations suggest that there is a low mutational burden in mesothelioma. Since tumor mutational burden has been correlated with responses to treatment with immune checkpoint inhibitors such as nivolumab, it was not consistent that patients with mesothelioma and low mutation burdens would have similar response rates in clinical trials with immune checkpoint inhibitors as patients with non-small cell lung cancer which is associated with a high mutation burden. In order to reconcile these differences, and given the potential for an improved understanding of the molecular pathogenesis of mesothelioma to improve therapeutic options, we used mate-pair sequencing (MPseq) and RNA sequencing (RNAseq) to understand how structural variants affect the transcriptome. MPseq differs from standard next generation sequencing approaches by tiling the whole genome with larger fragments (2-5kb) to reliably detect structural variants such as insertions, deletions and rearrangements. Amongst 22 mesothelioma specimens there were 1535 chromosomal rearrangements (median 41, range 3-298 per specimen), that resulted in junctions or novel fusions of non-coding DNA or genes. Six-hundred thirty-seven of these rearrangements (median 22, range 5-103 range per specimen) resulted in novel fusions of genes. Many of these inter- or intra-chromosomal rearrangements were consistent with a pattern of chromoanagesis such as chromoplexy or chromothripsis. Chromosomal rearrangements detected by MPseq were used to guide analysis of RNAseq data and revealed that these chromosomal junctions resulted in the expression of 179 novel amino acid sequences (median 5, 0-51 range per specimen). To determine whether transcription of chromosomal rearrangement-related junctions have neoantigenic potential, we used in silico tools to determine whether any of the expressed junctions contained peptides that could be presented by patient-specific HLA molecules. The top candidate rearrangement-related peptides with neoantigenic potential bound patient-specific HLA molecules nearly as well or as well as a positive control in competitive binding assays. Our findings represent the discovery of potential neoantigen expression driven by structural chromosomal rearrangements. These results may have implications for the development of novel therapeutic strategies, the selection of patients to receive immunotherapy, and blood-based treatment monitoring strategies. Citation Format: Aaron S. Mansfield, Tobias Peikert, James B. Smadbeck, Julia B. Udell, Farhad Kosari, Stephen J. Murphy, Hongzheng Ren, Vishnu V. Serla, Janet L. Schaefer Klein, Giannoula Karagouga, Faye R. Harris, Carlos Sosa, Sarah H. Johnson, Wendy Nevala, Svetomir N. Markovic, Aaron O. Bungum, Eric S. Edell, Haidong Dong, John C. Cheville, Marie Christine Aubry, Jin Jen, George Vasmatzis. Rearrangement-related peptides with neoantigenic potential in malignant pleural mesothelioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5726.

Abstract Background The treatment of metastatic melanoma has been revolutionized by developments in targeted therapy and immunotherapy. BRAF/MEK inhibitors, blockade of cytotoxic T-lymphocyte antigen 4 (CTLA-4) and programmed death (PD-1/L1) receptor have shown durable anti-melanoma effects. The optimal sequence strategy of targeted therapy and immunotherapy in metastatic BRAF-mutated melanoma patients (pts) is unknown and no treatment guidelines exist. Therefore, we report a single-institution experience of different treatment approaches using targeted therapy and immunotherapy and its impact on outcomes. Methods Pts with BRAF-mutated metastatic melanoma treated with targeted therapy and immunotherapy from 2012 to2017 were analyzed. Six groups were identified based on treatment strategy: (1) 1st line BRAF/MEK inhibitors followed by 2nd line immunotherapy; (1.1) 1st line BRAF/MEK inhibitors followed by 2nd line immunotherapy in combination with BRAF/MEK inhibitors (triple therapy);(1.2) same as group 1 followed by triple therapy as 3rd line; (2) 1st line immunotherapy followed by 2nd line BRAF/MEK inhibitors; (2.1) 1st line immunotherapy followed by 2nd line triple therapy; (2.2) same as group2 followed by triple therapy as 3rd line. All time-to-event analysis was calculated using the Kaplan-Meier method and Wilcoxon test. Results Forty four pts were included. The median age at diagnosis was 49 years (range 21-73), 24 (54%) pts were females and 19 (43%) developed brain metastases during their disease course. BRAF V600 mutation was seen in all pts except in 1 pt with p.N581S mutation. The preferred 1st line targeted therapy was dabrafenib/trametinib used in 17 (94%) out of 18 pts, while ipilimumab was the preferred 1st immunotherapy used in 11 (42%) out of 26 pts. For 2nd line therapy, DT was used in 19 (90%) out of 21 pts, while pembrolizumab was used in 16 (69%) out of 23 pts. For 3rd line, DT was used in 5 (83%) out of 6 pts, while pembrolizumab was used in 6 (100%) out of 6 pts. DT was usually the first choice for patients with high burden disease or brain metastases. The most common approach strategy was immunotherapy followed by targeted therapy (group 2), the median duration of treatment was 11 and 19 weeks respectively; for pts started on targeted therapy followed by immunotherapy (group 1), the median duration of treatment was 17 and 14 weeks respectively. (Table 1) Time-to-next therapy (TTNT) following 1st line treatment was similar in pts treated with targeted therapy (median 23 weeks [95% CI: 15-31]) or immunotherapy (median 26 weeks [95% CI: 10-33], p=0.94). Following 2nd line treatment, the TTNT for pts treated with targeted therapy was 18 weeks (95% CI: 4-38), immunotherapy 18 weeks (95% CI: 13-19) and triple therapy 22 weeks (95% CI: 13-41), p=0.48. A trend towards better overall survival (OS) from frontline therapy was seen in pts who received immunotherapy (1st line) followed by targeted therapy (2nd line) (median 7 years [95% CI: 2.7-7.08]) compared to those who received targeted therapy (1st line) followed by immunotherapy (2nd line) (median 2.3 years [95% CI: 1.3-NR], p=0.09. Interestingly, patients who received salvage chemotherapy had significant longer OS in those treated initially with immunotherapy (median 7 years [95% CI: 3.2-7.08]) (n=6) compared to patients started on targeted therapy (median 2 years [95% CI: 0.6-2.4], p=0.03) (n=5). Conclusion A trend towards longer OS was seen in pts treated with 1st line immunotherapy followed by 2nd line targeted therapy with a median therapy time of 11 and 19 weeks respectively. No difference in TTNT was seen with the use immunotherapy, targeted therapy or triple therapy when used as 1st or 2nd line. The significant longer OS benefit with f 1st line immunotherapy was only seen in patients who received chemotherapy later in their treatment course. Table 1.Treatment Characteristics by GroupMedian duration of therapy in weeksGroup(n)1st line therapy(median)2nd line therapy(median)3rd line therapy(median)Totalmedian (range)Chemotherapy (n)1(n=9)Targeted therapy(17)Immunotherapy (14)N/A52 (13-134)51.1(n=7)Targeted therapy(25)Triple therapy (19)Any*(43)69 (22-118)11.2(n=2)Targeted therapy(60)Immunotherapy (16)Triple therapy (21)96 (81-111)12(n=18)Immunotherapy(11)Targeted therapy(19)Any*(24)48 (16-120)52.1(n=4)Immunotherapy(17)Triple therapy (16)Any*(9)41 (25-69)02.2(n=4)Immunotherapy(19)Targeted therapy(16)Triple therapy (19)61 (54-73)1* include any treatment regimen such as immunotherapy, targeted therapy or chemotherapy Citation Format: Jesus Vera-Aguilera, Jonas Paludo, Narjust Duma, Marcella Tschautscher, Cecilia Yu, Svetomir Markovic. A clinical insight into therapeutic sequence in advanced melanoma [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr LB-A32.

Background and ObjectivesTo describe the patterns of failure in patients with in‐transit (IT) melanoma undergoing surgical excision.MethodsA retrospective review of patients who underwent their first IT lesion(s) resection between May 2005 and September 2014. Cumulative incidence of local failure (new lesion within 2 cm of IT resection) was estimated. Associations between clinicopathologic characteristics, local failure, and any recurrence were analyzed.ResultsOne hundred and thirty patients presented to our institution with IT disease over the study period and met the inclusion criteria. The 2‐year cumulative incidence of local failure was 19.5%. Twenty‐four patients developed disease within 2 cm of the resected IT disease; however, only eight were isolated local events. Cumulative incidence of local failure and of any disease differed with respect to less than 1 year disease‐free interval (DFI) from primary melanoma to first IT event, and having greater than 1 IT lesion at presentation. Incidence of local failure was not found to differ with respect to gross margin greater than 5 mm, after adjusting for DFI and greater than 1 IT lesions.ConclusionsPatients with greater than 1 IT lesion and a DFI less than 1 year are at a higher risk of failure after surgical excision of a first IT event. Very few failures were isolated local disease within 2 cm of the IT resection scar, regardless of IT excision margin.

Abstract Using personalized peptide vaccines (PPVs) to target tumor-specific nonself-antigens (neoantigens) is a promising approach to cancer treatment. However, the development of PPVs is hindered by the challenge of identifying tumor-specific neoantigens, in part because current in silico methods for identifying such neoantigens have limited effectiveness. In this article, we report the results of molecular dynamics simulations of 12 oligopeptides bound with an HLA, revealing a previously unrecognized association between the inability of an oligopeptide to elicit a T cell response and the contraction of the peptide-binding groove upon binding of the oligopeptide to the HLA. Our conformational analysis showed that this association was due to incompatibility at the interface between the contracted groove and its αβ–T cell Ag receptor. This structural demonstration that having the capability to bind HLA does not guarantee immunogenicity prompted us to develop an atom-based method (SEFF12MC) to predict immunogenicity through using the structure and energy of a peptide·HLA complex to assess the propensity of the complex for further complexation with its TCR. In predicting the immunogenicities of the 12 oligopeptides, SEFF12MC achieved a 100% success rate, compared with success rates of 25–50% for 11 publicly available residue-based methods including NetMHC-4.0. Although further validation and refinements of SEFF12MC are required, our results suggest a need to develop in silico methods that assess peptide characteristics beyond their capability to form stable binary complexes with HLAs to help remove hurdles in using the patient tumor DNA information to develop PPVs for personalized cancer immunotherapy.

Abstract Genome-wide identification and characterization of long noncoding RNAs (lncRNA) in individual immune cell lineages helps us better understand the driving mechanisms behind melanoma and advance personalized patient treatment. To elucidate the transcriptional landscape in diverse immune cell types of peripheral blood cells (PBC) in stage IV melanoma, we used whole transcriptome RNA sequencing to profile lncRNAs in CD4+, CD8+, and CD14+ PBC from 132 patient samples. Our integrative computational approach identified 27,625 expressed lncRNAs, 2,744 of which were novel. Both T cells (i.e., CD4+ and CD8+ PBC) and monocytes (i.e., CD14+ PBC) exhibited differential transcriptional expression profiles between patients with melanoma and healthy subjects. Cis- and trans-level coexpression analysis suggested that lncRNAs are potentially involved in many important immune-related pathways and the programmed cell death receptor 1 checkpoint pathways. We also identified nine gene coexpression modules significantly associated with melanoma status, all of which were significantly enriched for three mRNA translation processes. Age and melanoma traits closely correlated with each other, implying that melanoma contains age-associated immune changes. Our computational prediction analysis suggests that many cis- and trans-regulatory lncRNAs could interact with multiple transcriptional and posttranscriptional regulatory elements in CD4+, CD8+, and CD14+ PBC, respectively. These results provide novel insights into the regulatory mechanisms involving lncRNAs in individual immune cell types in melanoma and can help expedite cell type-specific immunotherapy treatments for such diseases. Significance: These findings elucidate melanoma-associated changes to the noncoding transcriptional landscape of distinct immune cell classes, thus providing cell type-specific guidance to targeted immunotherapy regimens. Cancer Res; 78(15); 4411–23. ©2018 AACR.

Abstract In patients with metastatic melanoma, high blood levels of galectin‐9 are correlated with worse overall survival and a bias towards a Th2 inflammatory state supportive of tumor growth. Although galectin‐9 signaling through TIM3 on T cells has been described, less is known about the interaction of galectin‐9 with macrophages. We aimed to determine whether galectin‐9 is a binding partner of CD206 on macrophages and whether the result of this interaction is tumor‐supportive. It was determined that incubation of CD68 + macrophages with galectin‐9 or anti‐CD206 blocked target binding and that both CD206 and galectin‐9 were detected by immunoprecipitation of cell lysates. CD206 and galectin‐9 had a binding affinity of 2.8 × 10 −7 m . Galectin‐9 causes CD206 + macrophages to make significantly more FGF2 and monocyte chemoattractant protein (MCP‐1), but less macrophage‐derived chemokine (MDC). Galectin‐9 had no effect on classical monocyte subsets, but caused expansion of the non‐classical populations. Lastly, there was a positive correlation between increasing numbers of CD206 macrophages and galectin‐9 expression in tumors, and high levels of CD206 macrophages correlated negatively with melanoma survival. These results indicate that galectin‐9 binds to CD206 on M2 macrophages, which appear to drive angiogenesis and the production of chemokines that support tumor growth and poor patient prognoses. Targeting this interaction systemically through circulating monocytes may therefore be a novel way to improve local anti‐tumor effects by macrophages. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Although immune checkpoint inhibitors have resulted in durable clinical benefits in a subset of patients with advanced cancer, some patients who did not respond to initial anti–PD-1 therapy have been found to benefit from the addition of salvage chemotherapy. However, the mechanism responsible for the successful chemoimmunotherapy is not completely understood. Here we show that a subset of circulating CD8 + T cells expressing the chemokine receptor CX3CR1 are able to withstand the toxicity of chemotherapy and are increased in patients with metastatic melanoma who responded to chemoimmunotherapy (paclitaxel and carboplatin plus PD-1 blockade). These CX3CR1 + CD8 + T cells have effector memory phenotypes and the ability to efflux chemotherapy drugs via the ABCB1 transporter. In line with clinical observation, our preclinical models identified an optimal sequencing of chemoimmunotherapy that resulted in an increase of CX3CR1 + CD8 + T cells. Taken together, we found a subset of PD-1 therapy–responsive CD8 + T cells that were capable of withstanding chemotherapy and executing tumor rejection with their unique abilities of drug efflux (ABCB1), cytolytic activity (granzyme B and perforin), and migration to and retention (CX3CR1 and CD11a) at tumor sites. Future strategies to monitor and increase the frequency of CX3CR1 + CD8 + T cells may help to design effective chemoimmunotherapy to overcome cancer resistance to immune checkpoint blockade therapy.