Stochastic modelling of single-cell gene expression adaptation reveals non-genomic contribution to evolution of tumor subclones

Cancer progression is an evolutionary process driven by the selection of cells adapted to gain growth advantage. We present the first formal study on the adaptation of gene expression in subclonal evolution. We model evolutionary changes in gene expression as stochastic Ornstein-Uhlenbeck processes, jointly leveraging the evolutionary history of subclones and single-cell expression data. Applying our model to sublines derived from single cells of a mouse melanoma revealed that sublines with distinct phenotypes are underlined by different patterns of gene expression adaptation, indicating non-genetic mechanisms of cancer evolution. Interestingly, sublines previously observed to be resistant to anti-CTLA-4 treatment showed adaptive expression of genes related to invasion and non-canonical Wnt signaling, whereas sublines that responded to treatment showed adaptive expression of genes related to proliferation and canonical Wnt signaling. Our results suggest that clonal phenotypes emerge as the result of specific adaptivity patterns of gene expression.

Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads

Most current studies rely on short-read sequencing to detect somatic structural variation (SV) in cancer genomes. Long-read sequencing offers the advantage of better mappability and long-range phasing, which results in substantial improvements in germline SV detection. However, current long-read SV detection methods do not generalize well to the analysis of somatic SVs in tumor genomes with complex rearrangements, heterogeneity, and aneuploidy. Here, we present Severus: a method for the accurate detection of different types of somatic SVs using a phased breakpoint graph approach. To benchmark various short- and long-read SV detection methods, we sequenced five tumor/normal cell line pairs with Illumina, Nanopore, and PacBio sequencing platforms; on this benchmark Severus showed the highest F1 scores (harmonic mean of the precision and recall) as compared to long-read and short-read methods. We then applied Severus to three clinical cases of pediatric cancer, demonstrating concordance with known genetic findings as well as revealing clinically relevant cryptic rearrangements missed by standard genomic panels.

Exploring tumor-normal cross-talk with TranNet: Role of the environment in tumor progression

There is a growing awareness that tumor-adjacent normal tissues used as control samples in cancer studies do not represent fully healthy tissues. Instead, they are intermediates between healthy tissues and tumors. The factors that contribute to the deviation of such control samples from healthy state include exposure to the tumor-promoting factors, tumor-related immune response, and other aspects of tumor microenvironment. Characterizing the relation between gene expression of tumor-adjacent control samples and tumors is fundamental for understanding roles of microenvironment in tumor initiation and progression, as well as for identification of diagnostic and prognostic biomarkers for cancers. To address the demand, we developed and validated TranNet, a computational approach that utilizes gene expression in matched control and tumor samples to study the relation between their gene expression profiles. TranNet infers a sparse weighted bipartite graph from gene expression profiles of matched control samples to tumors. The results allow us to identify predictors (potential regulators) of this transition. To our knowledge, TranNet is the first computational method to infer such dependencies. We applied TranNet to the data of several cancer types and their matched control samples from The Cancer Genome Atlas (TCGA). Many predictors identified by TranNet are genes associated with regulation by the tumor microenvironment as they are enriched in G-protein coupled receptor signaling, cell-to-cell communication, immune processes, and cell adhesion. Correspondingly, targets of inferred predictors are enriched in pathways related to tissue remodelling (including the epithelial-mesenchymal Transition (EMT)), immune response, and cell proliferation. This implies that the predictors are markers and potential stromal facilitators of tumor progression. Our results provide new insights into the relationships between tumor adjacent control sample, tumor and the tumor environment. Moreover, the set of predictors identified by TranNet will provide a valuable resource for future investigations.

Noncoding RNA circuitry in melanoma onset, plasticity, and therapeutic response

Melanoma, the cancer of the melanocyte, is the deadliest form of skin cancer with an aggressive nature, propensity to metastasize and tendency to resist therapeutic intervention. Studies have identified that the re-emergence of developmental pathways in melanoma contributes to melanoma onset, plasticity, and therapeutic response. Notably, it is well known that noncoding RNAs play a critical role in the development and stress response of tissues. In this review, we focus on the noncoding RNAs, including microRNAs, long non-coding RNAs, circular RNAs, and other small RNAs, for their functions in developmental mechanisms and plasticity, which drive onset, progression, therapeutic response and resistance in melanoma. Going forward, elucidation of noncoding RNA-mediated mechanisms may provide insights that accelerate development of novel melanoma therapies.

Germline modifiers of the tumor immune microenvironment implicate drivers of cancer risk and immunotherapy response

With the continued promise of immunotherapy for treating cancer, understanding how host genetics contributes to the tumor immune microenvironment (TIME) is essential to tailoring cancer screening and treatment strategies. Here, we study 1084 eQTLs affecting the TIME found through analysis of The Cancer Genome Atlas and literature curation. These TIME eQTLs are enriched in areas of active transcription, and associate with gene expression in specific immune cell subsets, such as macrophages and dendritic cells. Polygenic score models built with TIME eQTLs reproducibly stratify cancer risk, survival and immune checkpoint blockade (ICB) response across independent cohorts. To assess whether an eQTL-informed approach could reveal potential cancer immunotherapy targets, we inhibit CTSS, a gene implicated by cancer risk and ICB response-associated polygenic models; CTSS inhibition results in slowed tumor growth and extended survival in vivo. These results validate the potential of integrating germline variation and TIME characteristics for uncovering potential targets for immunotherapy.

Melanoma clonal subline analysis uncovers heterogeneity-driven immunotherapy resistance mechanisms

Intratumoral heterogeneity (ITH) can promote cancer progression and treatment failure, but the complexity of the regulatory programs and contextual factors involved complicates its study. To understand the specific contribution of ITH to immune checkpoint blockade (ICB) response, we generated single cell-derived clonal sublines from an ICB-sensitive and genetically and phenotypically heterogeneous mouse melanoma model, M4. Genomic and single cell transcriptomic analyses uncovered the diversity of the sublines and evidenced their plasticity. Moreover, a wide range of tumor growth kinetics were observed in vivo , in part associated with mutational profiles and dependent on T cell-response. Further inquiry into melanoma differentiation states and tumor microenvironment (TME) subtypes of untreated tumors from the clonal sublines demonstrated correlations between highly inflamed and differentiated phenotypes with the response to anti-CTLA-4 treatment. Our results demonstrate that M4 sublines generate intratumoral heterogeneity at both levels of intrinsic differentiation status and extrinsic TME profiles, thereby impacting tumor evolution during therapeutic treatment. These clonal sublines proved to be a valuable resource to study the complex determinants of response to ICB, and specifically the role of melanoma plasticity in immune evasion mechanisms.

Exploring tumor-normal cross-talk with TranNet: role of the environment in tumor progression

There is a growing awareness that tumor-adjacent normal tissues used as control samples in cancer studies do not represent fully healthy tissues. Instead, they are intermediates between healthy tissues and tumors. The factors that contribute to the deviation of such control samples from healthy state include exposure to the tumor-promoting factors, tumor-related immune response, and other aspects of tumor microenvironment. Characterizing the relation between gene expression of tumor-adjacent control samples and tumors is fundamental for understanding roles of microenvironment in tumor initiation and progression, as well as for identification of diagnostic and prognostic biomarkers for cancers. To address the demand, we developed and validated TranNet, a computational approach that utilizes gene expression in matched control and tumor samples to study the relation between their gene expression profiles. TranNet infers a sparse weighted bipartite graph from gene expression profiles of matched control samples to tumors. The results allow us to identify predictors (potential regulators) of this transition. To our knowledge, TranNet is the first computational method to infer such regulation. We applied TranNet to the data of several cancer types and their matched control samples from The Cancer Genome Atlas (TCGA). Many predictors identified by TranNet are genes associated with regulation by the tumor microenvironment as they are enriched in G-protein coupled receptor signaling, cell-to-cell communication, immune processes, and cell adhesion. Correspondingly, targets of inferred predictors are enriched in pathways related to tissue remodelling (including the epithelial-mesenchymal Transition (EMT)), immune response, and cell proliferation. This implies that the predictors are markers and potential stromal facilitators of tumor progression. Our results provide new insights for the relationships between tumor adjacent control sample, tumor and the tumor environment. Moreover, the set of predictors identified by TranNet will provide a valuable resource for future investigations. The TranNet method was implemented in python, source codes and the data sets used for and generated during this study are available at the Github site https://github.com/ncbi/TranNet .

Broad misappropriation of developmental splicing profile by cancer in multiple organs

Oncogenesis mimics key aspects of embryonic development. However, the underlying mechanisms are incompletely understood. Here, we demonstrate that the splicing events specifically active during human organogenesis, are broadly reactivated in the organ-specific tumor. Such events are associated with key oncogenic processes and predict proliferation rates in cancer cell lines as well as patient survival. Such events preferentially target nitrosylation and transmembrane-region domains, whose coordinated splicing in multiple genes respectively affect intracellular transport and N-linked glycosylation. We infer critical splicing factors potentially regulating embryonic splicing events and show that such factors are potential oncogenic drivers and are upregulated specifically in malignant cells. Multiple complementary analyses point to MYC and FOXM1 as potential transcriptional regulators of critical splicing factors in brain and liver. Our study provides a comprehensive demonstration of a splicing-mediated link between development and cancer, and suggest anti-cancer targets including splicing events, and their upstream splicing and transcriptional regulators.

DISP-10. A SYSTEMATIC REVIEW OF SEX DIFFERENCES OF INCIDENCE AND OVERALL SURVIVAL IN 15 NON-REPRODUCTIVE CANCERS

Sex is an important factor that influences disease development, progression, and treatment. In multiple non-reproductive cancers, sex differences in incidence, progression, treatment response, survival, and other clinical outcomes are observed. Overall, males have a 20% higher chance of developing cancer over their lifetime, and experience worse clinical outcomes when compared with females. The NIH recognizes the importance of sex as a biologic variable and addressing sex as a biological variable is now required for all researchers submitting NIH grants. While more researchers are investigating the role of sex differences in cancer, a systematic review that examines the patterns of sex differences in incidence and survival across 15 non-reproductive cancers has not yet been published. We performed a systematic review by searching five databases using keywords and controlled vocabulary terms for each concept of interest and limited to English language. Records were included if it reported sex differences in human adults (18+), addressed incidence, mortality, or survival, at least one of the 15 cancers of interest, and were a cohort, cross-sectional, RCT, or case control study. Covidence was used for screening and two reviewers independently screened each record at title/abstract and then full text. Two reviewers independently completed data extraction using Microsoft Excel and the Cochrane RoB 2.0, and JBI tools were used for risk of bias assessment. The searches and pilot of the methods are underway. Understanding the role sex-differences play on incidence and survival are important for adding to our understanding of advances in diagnosis and treatment of individuals with cancer.

Fast intratumor heterogeneity inference from single-cell sequencing data

We introduce HUNTRESS, a computational method for mutational intratumor heterogeneity inference from noisy genotype matrices derived from single-cell sequencing data, the running time of which is linear with the number of cells and quadratic with the number of mutations. We prove that, under reasonable conditions, HUNTRESS computes the true progression history of a tumor with high probability. On simulated and real tumor sequencing data, HUNTRESS is demonstrated to be faster than available alternatives with comparable or better accuracy. Additionally, the progression histories of tumors inferred by HUNTRESS on real single-cell sequencing datasets agree with the best known evolution scenarios for the associated tumors.

Cross-species identification of cancer resistance-associated genes that may mediate human cancer risk

Cancer is a predominant disease across animals. We applied a comparative genomics approach to systematically characterize genes whose conservation levels correlate positively (PC) or negatively (NC) with cancer resistance estimates across 193 vertebrates. Pathway analysis reveals that NC genes are enriched for metabolic functions and PC genes in cell cycle regulation, DNA repair, and immune response, pointing to their corresponding roles in mediating cancer risk. We find that PC genes are less tolerant to loss-of-function (LoF) mutations, are enriched in cancer driver genes, and are associated with germline mutations that increase human cancer risk. Their relevance to cancer risk is further supported via the analysis of mouse functional genomics and cancer mortality of zoo mammals' data. In sum, our study describes a cross-species genomic analysis pointing to candidate genes that may mediate human cancer risk.

Making a mouse out of a molehill: how precision modeling repurposes drugs for congenital giant nevi

Patients with congenital giant nevi (CGN), which can compromise quality of life and progress to melanoma, have limited treatment options. Choi et al. have demonstrated that topical application of a proinflammatory hapten for alopecia treatment [squaric acid dibutylester (SADBE)] caused nevus regression and prevented melanoma in an Nras mouse CGN model. Their results demonstrate the promise of repurposing drugs through precision modeling.

Abstract 576: Shark VNAR single domain-based CAR T cells targeting PD-L1 for cancer therapy

Background: Chimeric antigen receptor (CAR)-T therapy shows great potency against hematological malignancies, whereas it is difficult to transfer CAR T into solid tumors due to lack of appropriate antigenic targets and immunosuppressive tumor microenvironment. Checkpoint molecule PD-L1 is widely overexpressed on multiple tumor types, and PD-1/PD-L1 interaction is a primary mediator of immunosuppression in the TME. Here, we generated anti-PD-L1-specific shark single domain VNAR-based CAR T cell strategy and explored its anti-tumor efficacy in xenograft mouse models.

Methods: We isolated anti-PD-L1 single domain antibodies from semi-synthetic shark VNAR phage display libraries. The binding of isolated VNARs was validated by ELISA, flow cytometry, and Octet. A peptide library based on human PD-L1 was synthesized to predict the epitope of select VNARs. Anti-tumor efficacy of CAR T cells was determined via cell luciferase-based cell assay as well as xenograft mouse models. Two tumor models, MDA-MB-231 (triple-negative breast cancer) and Hep3B (hepatocellular carcinoma or HCC) were used in the present study. Glypican-3 (GPC3) is a tumor-specific target in the Hep3B model.

Results: We identified three anti-PD-L1 phage binders, B2, A11, and F5 from our shark phage libraries. All three binders showed cross-activity to human, mouse, and canine antigens, whereas only B2 functionally blocked the interaction of human PD-1 to PD-L1. Moreover, CAR (B2) T cells specifically lysed both MDA-MB-231 and Hep3B tumor cells by targeting constitutive and inducible expression of PD-L1. Importantly, the combination of anti-GPC3 CAR (hYP7) T cells with CAR (B2) T cells regress Hep3B tumors synergistically in mice.

Conclusions: PD-L1-targeted shark VNAR single domain-based CAR T cell therapy is a novel strategy to treat breast cancer and liver cancer. This work provides a rationale for a potential use of anti-PD-L1 CAR T cells as a monotherapy or combination with a tumor-specific therapy in clinical studies for solid tumors.

Citation Format: Dan Li, Hejiao English, Jessica Hong, Tianyuzhou Liang, Glenn Merlino, Chi-Ping Day, Mitchell Ho. Shark VNAR single domain-based CAR T cells targeting PD-L1 for cancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 576.

Abstract 27: Sex biases in cancer and autoimmune disease incidence are strongly positively correlated with mitochondrial gene expression across human tissues

Cancer occurs more frequently in men while autoimmune diseases (AIDs) occur more frequently in women. To explore whether these sex biases have a common basis, we collected 170 AID incidence studies from many countries for tissues that have both a cancer type and an AID that arise from that tissue. Analyzing a total of 182 country-specific, tissue-matched cancer-AID incidence rate sex bias data pairs, we find that the sex biases observed in the incidence of AIDs and cancers that occur in the same tissue are positively correlated across human tissues. Second, we find that the sex bias in the expression of the 37 genes encoded in the mitochondrial genome stands out as the common key factor whose levels across human tissues are most strongly and positively associated with these incidence rate sex biases.

Citation Format: David Robert Crawford, Sanju Sinha, Nishanth U. Nair, Bríd M. Ryan, Jill Barnholtz-Sloan, Stephen M. Mount, Ayelet Erez, Kenneth Adalpe, Philip E. Castle, Padma S. Rajagopal, Chi-Ping Day, Alejandro A. Schäffer, Eytan Ruppin. Sex biases in cancer and autoimmune disease incidence are strongly positively correlated with mitochondrial gene expression across human tissues [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 27.

Abstract 3825: Germline modifiers of the tumor immune microenvironment reveal drivers of immunotherapy response

With the continued promise of immunotherapy as an avenue for treating cancer, understanding how host genetics contributes to the tumor immune microenvironment (TIME) is essential to tailoring cancer risk screening and treatment strategies. Using genotypes from over 8,000 European individuals in The Cancer Genome Atlas and 137 heritable tumor immune phenotype components (IP components), we identified and investigated 532 TIME-SNPs. Focusing on 77 variants that were relevant to cancer risk, survival, or treatment response, we explored their potential to reveal novel targets for immunotherapy. Many variants overlapped regions with histone marks indicating active transcription, and influenced gene activities in specific immune cell subsets, such as macrophages and dendritic cells. TIME-SNPs implicated genes such as LAIR1, TREX1, CTSS, CTSW and LILRB2 were differentially expressed between responders and non-responders to immune-checkpoint blockade (ICB) in preclinical studies. Of these, LILRB2 and LAIR1 have already been identified as putative targets for immunotherapy. Here we found that inhibition of CTSS led to better tumor control and survival in murine models, alone or in combination with anti-PD-1. Collectively we show that through an integrative approach, it is possible to link host genetics to TIME characteristics, informing novel biomarkers for cancer risk and target identification in immunotherapy.

Citation Format: Meghana Pagadala, Victoria Wu, Eva Pérez-Guijarro, Hyo Kim, Andrea Castro, James Talwar, Cristian Gonzalez-Colin, Steven Cao, Benjamin J. Schmiedel, Timothy Sears, Shervin Goudarzi, Divya Kirani, Rany M. Salem, Gerald P. Morris, Olivier Harismendy, Sandip P. Patel, Jill P. Mesirov, Maurizio Zanetti, Chi-Ping Day, Chun C. Fan, Wesley K. Thompson, Glenn Merlino, J. Silvio Gutkind, Pandurangan Vijayanand, Hannah Carter. Germline modifiers of the tumor immune microenvironment reveal drivers of immunotherapy response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3825.

A novel PD-L1-targeted shark VNAR single-domain-based CAR-T cell strategy for treating breast cancer and liver cancer

Chimeric antigen receptor (CAR)-T cell therapy shows excellent potency against hematological malignancies, but it remains challenging to treat solid tumors, mainly because of a lack of appropriate antigenic targets and an immunosuppressive tumor microenvironment (TME). The checkpoint molecule programmed death-ligand 1 (PD-L1) is widely overexpressed in multiple tumor types, and the programmed death-ligand 1 (PD-1)/PD-L1 interaction is a crucial mediator of immunosuppression in the TME. Here we constructed a semi-synthetic shark V_NAR phage library and isolated anti-PD-L1 single-domain antibodies. Among these V_NARs, B2 showed cross-reactivity to human, mouse, and canine PD-L1, and it partially blocked the interaction of human PD-1 with PD-L1. CAR (B2) T cells specifically lysed human breast cancer and liver cancer cells by targeting constitutive and inducible expression of PD-L1 and hindered tumor metastasis. Combination of PD-L1 CAR (B2) T cells with CAR T cells targeted by GPC3 (a liver cancer-specific antigen) regresses liver tumors in mice. We concluded that PD-L1-targeted shark V_NAR single-domain-based CAR-T therapy is a novel strategy to treat breast and liver cancer. This study provides a rationale for potential use of PD-L1 CAR-T cells as a monotherapy or in combination with a tumor-specific therapy in clinical studies.

Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response

Gut bacteria modulate the response to immune checkpoint blockade (ICB) treatment in cancer, but the effect of diet and supplements on this interaction is not well studied. We assessed fecal microbiota profiles, dietary habits, and commercially available probiotic supplement use in melanoma patients and performed parallel preclinical studies. Higher dietary fiber was associated with significantly improved progression-free survival in 128 patients on ICB, with the most pronounced benefit observed in patients with sufficient dietary fiber intake and no probiotic use. Findings were recapitulated in preclinical models, which demonstrated impaired treatment response to anti–programmed cell death 1 (anti–PD-1)–based therapy in mice receiving a low-fiber diet or probiotics, with a lower frequency of interferon-γ–positive cytotoxic T cells in the tumor microenvironment. Together, these data have clinical implications for patients receiving ICB for cancer.

Myeloid-Derived Suppressive Cell Expansion Promotes Melanoma Growth and Autoimmunity by Inhibiting CD40/IL27 Regulation in Macrophages

The relationship between cancer and autoimmunity is complex. However, the incidence of solid tumors such as melanoma has increased significantly among patients with previous or newly diagnosed systemic autoimmune disease (AID). At the same time, immune checkpoint blockade (ICB) therapy of cancer induces de novo autoinflammation and exacerbates underlying AID, even without evident antitumor responses. Recently, systemic lupus erythematosus (SLE) activity was found to drive myeloid-derived suppressor cell (MDSC) formation in patients, a known barrier to healthy immune surveillance and successful cancer immunotherapy. Cross-talk between MDSCs and macrophages generally drives immune suppressive activity in the tumor microenvironment. However, it remains unclear how peripheral pregenerated MDSC under chronic inflammatory conditions modulates global macrophage immune functions and the impact it could have on existing tumors and underlying lupus nephritis. Here we show that pathogenic expansion of SLE-generated MDSCs by melanoma drives global macrophage polarization and simultaneously impacts the severity of lupus nephritis and tumor progression in SLE-prone mice. Molecular and functional data showed that MDSCs interact with autoimmune macrophages and inhibit cell surface expression of CD40 and the production of IL27. Moreover, low CD40/IL27 signaling in tumors correlated with high tumor-associated macrophage infiltration and ICB therapy resistance both in murine and human melanoma exhibiting active IFNγ signatures. These results suggest that preventing global macrophage reprogramming induced by MDSC-mediated inhibition of CD40/IL27 signaling provides a precision melanoma immunotherapy strategy, supporting an original and advantageous approach to treat solid tumors within established autoimmune landscapes. SIGNIFICANCE: Myeloid-derived suppressor cells induce macrophage reprogramming by suppressing CD40/IL27 signaling to drive melanoma progression, simultaneously affecting underlying autoimmune disease and facilitating resistance to immunotherapy within preexisting autoimmune landscapes.

Abstract LB019: Trisicell: Scalable Tumor Phylogeny Reconstruction and Validation Reveals Developmental Origin and Therapeutic Impact of Intratumoral Heterogeneity

Emerging sets of single-cell sequencing data makes it appealing to apply existing tumor phylogeny reconstruction methods to analyze associated intratumor heterogeneity. Unfortunately, tumor phylogeny inference is an NP-hard problem and existing principled methods typically fail to scale up to handle thousands of cells and mutations observed in emerging single-cell data sets. Even though there are greedy heuristics to build hierarchical clustering of cells and mutations, they suffer from well-documented issues in accuracy. Additionally even when “optimal” solutions are feasible, existing approaches only provide a single “most likely” tree to depict the evolutionary processes that may result in an observed collection of cells and mutations. To make matters worse, the vast majority of single-cell sequencing data sets are transcriptomic and as a result, suffer from considerable variation in coverage across mutational loci.

In this paper, we introduce Trisicell, a computational toolkit for scalable tumor phylogeny reconstruction and validation from single-cell genomic, exomic or transcriptomic sequencing data. Trisicell has three components: (i) Trisicell-DnC, a new tumor phylogeny reconstruction method from genotype matrices derived from single-cell data, (ii) Trisicell-ConT a new algorithm for constructing the consensus for two or more tumor phylogenies - which may be built through the use of different data types on the same set of cells, or built through the use of different methods on the same data, and (iii) Trisicell-PF, a new partition function method for assessing the likelihood of any user-defined subtree/set of cells to be seeded by a given set of mutations in the phylogeny. Collectively, these tools provide means of identifying and validating robust portions of a tumor phylogeny, offering the ability to focus on the most important (sub)clones and the genomic alterations that seed the associated clonal expansion.

We applied Trisicell to a panel of clonal sublines derived from single-cells of a parental mouse melanoma model on which we performed both whole exome and whole transcriptome sequencing. The tumor phylogenies of the clonal sublines built on exomic and transcriptomic mutations by Trisicell-DnC, were shown by Trisicell-ConT to be highly similar and the subtrees comprised of phenotypically similar clonal sublines were shown to be strongly associated by Trisicell-PF to their seeding mutations. In addition, we applied Trisicell to single-cell whole transcriptome sequencing data from a tumor derived from the same parental melanoma cell line, which was subjected to anti-CTLA-4 immunotherapy. The phylogenies generated from both studies featured distinct subtrees, strongly associated with phenotypes including cell differentiation status, tumor growth and therapeutic response. These results suggest that Trisicell can be used for scalable tumor phylogeny reconstruction and validation through both single-cell and clonal-subline sequencing data, which may reveal strong phenotypic associations. In particular, they suggest that the developmental status and phenotypic intratumoral heterogeneity of melanoma originates from observable subclonal variation.

Citation Format: Farid Rashidi Mehrabadi, Salem Malikić, Kerrie L. Marie, Eva Pérez-Guijarro, Erfan Sadeqi Azer, Howard H. Yang, Can Kızılkale, Charli Gruen, Huaitian Liu, Christina Marcelus, Aydın Buluç, Funda Ergün, Maxwell P. Lee, Glenn Merlino, Chi-Ping Day, S. Cenk Sahinalp. Trisicell: Scalable Tumor Phylogeny Reconstruction and Validation Reveals Developmental Origin and Therapeutic Impact of Intratumoral Heterogeneity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB019.

Synthetic Lethal Screens Reveal Cotargeting FAK and MEK as a Multimodal Precision Therapy for GNAQ-Driven Uveal Melanoma

PURPOSE

Uveal melanoma is the most common eye cancer in adults. Approximately 50% of patients with uveal melanoma develop metastatic uveal melanoma (mUM) in the liver, even after successful treatment of the primary lesions. mUM is refractory to current chemo- and immune-therapies, and most mUM patients die within a year. Uveal melanoma is characterized by gain-of-function mutations in GNAQ/GNA11, encoding Gαq proteins. We have recently shown that the Gαq-oncogenic signaling circuitry involves a noncanonical pathway distinct from the classical activation of PLCβ and MEK-ERK. GNAQ promotes the activation of YAP1, a key oncogenic driver, through focal adhesion kinase (FAK), thereby identifying FAK as a druggable signaling hub downstream from GNAQ. However, targeted therapies often activate compensatory resistance mechanisms leading to cancer relapse and treatment failure.

EXPERIMENTAL DESIGN

We performed a kinome-wide CRISPR-Cas9 sgRNA screen to identify synthetic lethal gene interactions that can be exploited therapeutically. Candidate adaptive resistance mechanisms were investigated by cotargeting strategies in uveal melanoma and mUM in vitro and in vivo experimental systems.

RESULTS

sgRNAs targeting the PKC and MEK-ERK signaling pathways were significantly depleted after FAK inhibition, with ERK activation representing a predominant resistance mechanism. Pharmacologic inhibition of MEK and FAK showed remarkable synergistic growth-inhibitory effects in uveal melanoma cells and exerted cytotoxic effects, leading to tumor collapse in uveal melanoma xenograft and liver mUM models in vivo.

CONCLUSIONS

Coupling the unique genetic landscape of uveal melanoma with the power of unbiased genetic screens, our studies reveal that FAK and MEK-ERK cotargeting may provide a new network-based precision therapeutic strategy for mUM treatment.See related commentary by Harbour, p. 2967.

Distinct Biomarker Profiles and TCR Sequence Diversity Characterize the Response to PD-L1 Blockade in a Mouse Melanoma Model

Only a subset of patients responds to immune checkpoint blockade (ICB) in melanoma. A preclinical model recapitulating the clinical activity of ICB would provide a valuable platform for mechanistic studies. We used melanoma tumors arising from an Hgf^tg;Cdk4^R24C/R24C genetically engineered mouse (GEM) model to evaluate the efficacy of an anti-mouse PD-L1 antibody similar to the anti-human PD-L1 antibodies durvalumab and atezolizumab. Consistent with clinical observations for ICB in melanoma, anti-PD-L1 treatment elicited complete and durable response in a subset of melanoma-bearing mice. We also observed tumor growth delay or regression followed by recurrence. For early treatment assessment, we analyzed gene expression profiles, T-cell infiltration, and T-cell receptor (TCR) signatures in regressing tumors compared with tumors exhibiting no response to anti-PD-L1 treatment. We found that CD8⁺ T-cell tumor infiltration corresponded to response to treatment, and that anti-PD-L1 gene signature response indicated an increase in antigen processing and presentation, cytokine-cytokine receptor interaction, and natural killer cell-mediated cytotoxicity. TCR sequence data suggest that an anti-PD-L1-mediated melanoma regression response requires not only an expansion of the TCR repertoire that is unique to individual mice, but also tumor access to the appropriate TCRs. Thus, this melanoma model recapitulated the variable response to ICB observed in patients and exhibited biomarkers that differentiate between early response and resistance to treatment, providing a valuable platform for prediction of successful immunotherapy. IMPLICATIONS: Our melanoma model recapitulates the variable response to anti-PD-L1 observed in patients and exhibits biomarkers that characterize early antibody response, including expansion of the TCR repertoire.

PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem

MOTIVATION

Recent advances in single-cell sequencing (SCS) offer an unprecedented insight into tumor emergence and evolution. Principled approaches to tumor phylogeny reconstruction via SCS data are typically based on general computational methods for solving an integer linear program, or a constraint satisfaction program, which, although guaranteeing convergence to the most likely solution, are very slow. Others based on Monte Carlo Markov Chain or alternative heuristics not only offer no such guarantee, but also are not faster in practice. As a result, novel methods that can scale up to handle the size and noise characteristics of emerging SCS data are highly desirable to fully utilize this technology.

RESULTS

We introduce PhISCS-BnB (phylogeny inference using SCS via branch and bound), a branch and bound algorithm to compute the most likely perfect phylogeny on an input genotype matrix extracted from an SCS dataset. PhISCS-BnB not only offers an optimality guarantee, but is also 10-100 times faster than the best available methods on simulated tumor SCS data. We also applied PhISCS-BnB on a recently published large melanoma dataset derived from the sublineages of a cell line involving 20 clones with 2367 mutations, which returned the optimal tumor phylogeny in <4 h. The resulting phylogeny agrees with and extends the published results by providing a more detailed picture on the clonal evolution of the tumor.

AVAILABILITY AND IMPLEMENTATION

https://github.com/algo-cancer/PhISCS-BnB.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Abstract IA07: UVB-induced tumor heterogeneity directs immune response in melanoma

Little is known regarding the relationship between intra-tumor heterogeneity (ITH) and immune response in melanoma. Here, we explored the role of ITH in tumor rejection by establishing a melanoma mouse model and inducing UVB-derived mutations that increase both ITH and mutational load. This induction gives rise to highly aggressive tumors and decreased cytotoxic activity of tumor infiltrating lymphocytes (TILs). Conversely, single cell-derived melanoma clones with reduced ITH are swiftly rejected. Tumor rejection is accompanied by increased TIL reactivity and increased infiltration into the tumor core. Using phylogenetic tree analyses and mixing experiments of 20 single cell clones that lie along the phylogenetic tee we show that tumor rejection is strongly affected by number of injected clones and genetic diversity. We have, thus set up a novel, highly controlled system that enables us to study the interphase between the immune system and different layers of intra-tumor heterogeneity. Finally, the analysis of melanoma patient data identifies parallel observations, supporting the importance of ITH in determining patient survival and response to checkpoint blockade.

Citation Format: Osnat Bartok, Sushant Patkar, Sapir Cohen, Kevin Litchfield, Hiren Karathia, Joo Sang Lee, Alejandro Jiménez-Sánchez, Chi-Ping Day, Lea Eisenbach, Martin Miller, Glenn Merlino, Eli Pikarsky, Arie Admon, Charles Swanton, Eytan Ruppin, Yardena Samuels, Yochai Wolf. UVB-induced tumor heterogeneity directs immune response in melanoma [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr IA07.

Strength of immune selection in tumors varies with sex and age

Individual MHC genotype constrains the mutational landscape during tumorigenesis. Immune checkpoint inhibition reactivates immunity against tumors that escaped immune surveillance in approximately 30% of cases. Recent studies demonstrated poorer response rates in female and younger patients. Although immune responses differ with sex and age, the role of MHC-based immune selection in this context is unknown. We find that tumors in younger and female individuals accumulate more poorly presented driver mutations than those in older and male patients, despite no differences in MHC genotype. Younger patients show the strongest effects of MHC-based driver mutation selection, with younger females showing compounded effects and nearly twice as much MHC-II based selection. This study presents evidence that strength of immune selection during tumor development varies with sex and age, and may influence the availability of mutant peptides capable of driving effective response to immune checkpoint inhibitor therapy.

Abstract 3863: CODEX high-multiplex imaging reveals distinct tumor microenvironment in mouse melanoma models associated with response to immunotherapy

In order to identify the determinants of melanoma resistance to immunotherapies and predictive biomarkers, we developed a series of immunocompetent syngeneic mouse models that represent diverse subtypes of human melanoma exhibiting a range of sensitivity to immune checkpoint blockade (ICB) therapies (Pérez-Guijarro et al, BioRxiv 2019). Comparative genomic and immunological analysis identified that melanoma plasticity as well as T cell dysfunction and exclusion programs strongly correlated with ICB resistance. However, how interactions between tumor and immune cells influence therapeutic efficacy is still unknown. To address this question, we used CODEX high-multiplex imaging technology that enables quantitative detection of 20+ markers at single cell level resolution preserving spatial context. CODEX does not require cell isolation that may result in variable cell loss. Furthermore, the whole tissue imaging provides insights into tumor/stroma and cellular heterogeneity. Fresh frozen tissues (n=3 for each model) were stained with a panel of 16 antibodies to identify major immune cell phenotypes including cytotoxic and helper T cells, B cells, and subsets of myeloid cells. Quantitative single cell level analysis of images was performed with HALO (Indica Labs) and multiplex analysis viewer (MAV) (Akoya Biosciences) software. Preliminary analysis identified unique tumor architecture, immune cell densities and distribution in each model. Although we found high diversity in the vasculature (CD31+), proliferation (Ki67+) and number of infiltrating leukocytes (CD45+) between the models, these were not associated with resistance. In contrast, high infiltration of cytotoxic T cells and dendritic cells was associated with response to ICBs. These results validated tumor analyses by FACS and gene signatures of immune cells. In addition, CODEX imaging revealed heterogeneity and complex spatial organization in the tumor microenvironment. Importantly, ICB-resistant tumors exhibited compact tumor structure with less stroma infiltration and lack of melanin expression, while ICB-sensitive tumors had complex, nodular and pigmented structures, indicating different differentiation status. Our data also suggested that myeloid phenotypes and functional compartment interactions may contribute to the response to ICBs. The study is expected to provide a higher resolution profiling of tumor-immune cell interactions and facilitate mechanistic understanding of resistance to immune checkpoint therapy.

Citation Format: Noemi Kedei, Eva E. Pérez-Guijarro, Jin-Qiu Chen, Chi-Ping Day, Mariam Q. Malik, David J. Goldstein, Glenn T. Merlino. CODEX high-multiplex imaging reveals distinct tumor microenvironment in mouse melanoma models associated with response to immunotherapy [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 3863.

Multimodel preclinical platform predicts clinical response of melanoma to immunotherapy

Although immunotherapy has revolutionized cancer treatment, only a subset of patients demonstrate durable clinical benefit. Definitive predictive biomarkers and targets to overcome resistance remain unidentified, underscoring the urgency to develop reliable immunocompetent models for mechanistic assessment. Here we characterize a panel of syngeneic mouse models, representing a variety of molecular and phenotypic subtypes of human melanomas and exhibiting their diverse range of responses to immune checkpoint blockade (ICB). Comparative analysis of genomic, transcriptomic and tumor-infiltrating immune cell profiles demonstrated alignment with clinical observations and validated the correlation of T cell dysfunction and exclusion programs with resistance. Notably, genome-wide expression analysis uncovered a melanocytic plasticity signature predictive of patient outcome in response to ICB, suggesting that the multipotency and differentiation status of melanoma can determine ICB benefit. Our comparative preclinical platform recapitulates melanoma clinical behavior and can be employed to identify mechanisms and treatment strategies to improve patient care.

Epigenetic therapy inhibits metastases by disrupting premetastatic niches

Cancer recurrence after surgery remains an unresolved clinical problem^1-3. Myeloid cells derived from bone marrow contribute to the formation of the premetastatic microenvironment, which is required for disseminating tumour cells to engraft distant sites^4-6. There are currently no effective interventions that prevent the formation of the premetastatic microenvironment^6,7. Here we show that, after surgical removal of primary lung, breast and oesophageal cancers, low-dose adjuvant epigenetic therapy disrupts the premetastatic microenvironment and inhibits both the formation and growth of lung metastases through its selective effect on myeloid-derived suppressor cells (MDSCs). In mouse models of pulmonary metastases, MDSCs are key factors in the formation of the premetastatic microenvironment after resection of primary tumours. Adjuvant epigenetic therapy that uses low-dose DNA methyltransferase and histone deacetylase inhibitors, 5-azacytidine and entinostat, disrupts the premetastatic niche by inhibiting the trafficking of MDSCs through the downregulation of CCR2 and CXCR2, and by promoting MDSC differentiation into a more-interstitial macrophage-like phenotype. A decreased accumulation of MDSCs in the premetastatic lung produces longer periods of disease-free survival and increased overall survival, compared with chemotherapy. Our data demonstrate that, even after removal of the primary tumour, MDSCs contribute to the development of premetastatic niches and settlement of residual tumour cells. A combination of low-dose adjuvant epigenetic modifiers that disrupts this premetastatic microenvironment and inhibits metastases may permit an adjuvant approach to cancer therapy.

Melanoblast transcriptome analysis reveals pathways promoting melanoma metastasis

Cutaneous malignant melanoma is an aggressive cancer of melanocytes with a strong propensity to metastasize. We posit that melanoma cells acquire metastatic capability by adopting an embryonic-like phenotype, and that a lineage approach would uncover metastatic melanoma biology. Using a genetically engineered mouse model to generate a rich melanoblast transcriptome dataset, we identify melanoblast-specific genes whose expression contribute to metastatic competence and derive a 43-gene signature that predicts patient survival. We identify a melanoblast gene, KDELR3, whose loss impairs experimental metastasis. In contrast, KDELR1 deficiency enhances metastasis, providing the first example of different disease etiologies within the KDELR-family of retrograde transporters. We show that KDELR3 regulates the metastasis suppressor, KAI1, and report an interaction with the E3 ubiquitin-protein ligase gp78, a regulator of KAI1 degradation. Our work demonstrates that the melanoblast transcriptome can be mined to uncover targetable pathways for melanoma therapy.

UVB-Induced Tumor Heterogeneity Diminishes Immune Response in Melanoma

Although clonal neo-antigen burden is associated with improved response to immune therapy, the functional basis for this remains unclear. Here we study this question in a novel controlled mouse melanoma model that enables us to explore the effects of intra-tumor heterogeneity (ITH) on tumor aggressiveness and immunity independent of tumor mutational burden. Induction of UVB-derived mutations yields highly aggressive tumors with decreased anti-tumor activity. However, single-cell-derived tumors with reduced ITH are swiftly rejected. Their rejection is accompanied by increased T cell reactivity and a less suppressive microenvironment. Using phylogenetic analyses and mixing experiments of single-cell clones, we dissect two characteristics of ITH: the number of clones forming the tumor and their clonal diversity. Our analysis of melanoma patient tumor data recapitulates our results in terms of overall survival and response to immune checkpoint therapy. These findings highlight the importance of clonal mutations in robust immune surveillance and the need to quantify patient ITH to determine the response to checkpoint blockade.

Partial Rescue of Ocular Pigment Cells and Structure by Inducible Ectopic Expression of Mitf-M in MITF-Deficient Mice

Purpose

Complete deficiency of microphthalmia transcription factor (MITF) in Mitfmi-vga9/mi-vga9 mice is associated with microphthalmia, retinal dysplasia, and albinism. We investigated the ability of dopachrome tautomerase (DCT) promoter-mediated inducible ectopic expression of Mitf-M to rescue these phenotypic abnormalities.

Methods

A new mouse line was created with doxycycline-inducible ectopic Mitf-M expression on an Mitf-deficient Mitfmi-vga9 background (DMV mouse). Adult DMV mice were phenotypically characterized and tissues were collected for histology, immunohistochemistry, and evaluation of Mitf, pigmentary genes, and retinal pigment epithelium (RPE) gene expression.

Results

Ectopic Mitf-M expression was specifically induced in the eyes, but was not detected in the skin of DMV mice. Inducible expression of Mitf-M partially rescued the microphthalmia, RPE structure, and pigmentation as well as a subset of the choroidal and iris melanocytes but not cutaneous melanocytes. RPE function and vision were not restored in the DMV mice.

Conclusions

Ectopic expression of Mitf-M during development of Mitf-deficient mice is capable of partially rescuing ocular and retinal structures and uveal melanocytes. These findings provide novel information about the roles of Mitf isoforms in the development of mouse eyes.

Topical Application of a Dual ABC Transporter Substrate and NF-κB Inhibitor Blocks Multiple Sources of Cutaneous Inflammation in Mouse Skin

Among the molecular signals underlying cutaneous inflammation is the transcription complex NF-κB, its upstream modulators, and cytokines and chemokines that are the downstream proinflammatory effectors. Central to NF-κB activation is IκB kinase (IKK), which phosphorylates IκBα, releasing NF-κB to the nucleus. In a screening of a kinase inhibitor library, we identified two IKK inhibitors that were high-affinity substrates for p-glycoprotein (ABCB1), the multidrug resistance protein known to facilitate transdermal drug delivery. ACHP (2-amino-6-[2-(cyclopropylmethoxy)-6-hydroxyphenyl]-4-(4-piperidinyl)-3-pyridinecarbonitrile) and IKK 16 prevented both nuclear translocation of NF-κB and activation of a NF-κB reporter and reduced the induction of cytokine and chemokine transcripts in human or mouse keratinocytes by IL-1α, tumor necrosis factor-α, and phorbol myristate acetate. ACHP, but not IKK 16, was nontoxic to mouse or human keratinocytes at any dose tested. In mice, topical ACHP prevented the cutaneous inflammation induced by topical phorbol myristate acetate or imiquimod, reduced the inflammation from erythema doses of artificial sunlight, and lowered the tumor incidence of mice treated with 7,12-dimethyl benzanthracene when applied before phorbol myristate acetate. Topical ACHP also reduced the NF-κB and IL-17 inflammatory signature after multiple doses of imiquimod. Thus, ACHP and IKK 16 hit their NF-κB target in mouse and human keratinocytes, and ACHP is an effective topical nonsteroidal anti-inflammatory in mice.

Abstract 5720: Functional characterization of neoantigens determining immune checkpoint blockade response in mouse models of human melanoma

Melanoma is the deadliest form of skin cancer due to the lack of widely effective therapies for advanced disease. Recently FDA-approved immunotherapies, such as immune checkpoint blockade (ICB) by CTLA-4 and PD-1/PD-L1 antibodies, provide unprecedent durable responses but in less than 40% of late stage melanoma patients. While high mutational loads characteristic of responsive tumors has not shown predictive value of patient outcome, accumulating evidences suggest a key role for neoantigens in the response to ICB. Moreover, new T-cell transfer- and vaccine-based therapeutic strategies highlighted the relevance of an efficient identification and prioritization of highly immunogenic neoantigens to improve immunotherapies. However, mechanistic studies are not possible in humans, and the development of adequate predictive methods is still the center of intense debate in the field. Here we use two genetically engineered melanoma mouse models exhibiting distinct response to ICB. Melanomas induced by neonatal ultraviolet radiation (UV) in a HGF-transgenic mouse (HGF-tg) showed high sensitivity to anti-CTLA-4, whereas UV-induced melanomas in HGF-tg; BrafV600E; Cdkn2a+/- mouse (Braf/HGF) did not respond. We hypothesized these models will allow us to identify the neoantigen features required for ICB response including type, expression levels and allele frequency patterns. High tumor immunogenicity, assessed by in vivo vaccination assays, as well as increased T-cell infiltration upon anti-CTLA-4 treatment were correlated to greater response. Moreover, exome and RNA sequencing analyses revealed similar mutational and neoantigen load in both models, albeit with no common expressed mutations. Notably, both models expressed similar levels of antigen presentation related genes (e.g. B2m, H2-Kd, Tap1) suggesting that specific neoantigens in HGF-tg melanoma cells may contribute to their sensitivity to anti-CTLA-4. To test this, we predicted MHC-I/-II binding of HGF-tg melanoma mutated epitopes in silico and generated a “neo-epitope” library. Importantly, the expression and allele frequency of most of selected mutations were decreased in anti-CTLA-4 responder HGF melanomas. The “neo-epitope” library was transduced into Braf/HGF non-responder cells and future studies will identify the neo-epitopes lost upon ICB, representing determinants of therapeutic success. Additionally, in vivo vaccination assays using synthetic mutant peptides will be performed to validate each neoantigen candidate. We anticipate that our studies will provide insight into the role that neoantigens play in melanoma immunotherapy responses.

(EPG and CPD contribute to this abstract equally).

Citation Format: Eva Perez Guijarro, Chi-Ping Day, Zoe W. Ohler, Rajaa El Meskini, Howard Yang, Suman Vodnala, Cari Graff-Cherry, Sung Chin, Anyen Fon, Helen Michael, Maxwell Lee, Terry Van Dyke, Shyam Sharan, Glenn Merlino. Functional characterization of neoantigens determining immune checkpoint blockade response in mouse models of human melanoma [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 5720.

Abstract 5678: Developing a preclinical immunotherapy platform using syngeneic mouse models of human melanoma

Melanoma is an aggressive and lethal disease with no efficacious therapies for a broad subset of late stage patients. Current immunotherapies, including immune checkpoint blockade (ICB), may prolong survival in certain patients, but generate responses in less than 40% of the treated cohort. This demands a better understanding of molecular mechanisms underlying the lack of response and acquired resistance to ICB. However, functional studies are limited in patients, and current preclinical studies are handicapped by the absence of appropriate mouse models that recapitulate the pathological and immunological diversity of human melanomas. Here we develop four syngeneic melanoma mouse models with human-relevant genetic modifications and carcinogenic agents, which we hypothesize will mirror the spectrum of responses to ICB and offer a platform for future mechanistic studies in melanoma. The models are: 1) neonatal ultraviolet radiation (UV)-induced melanoma in a HGF-transgenic mouse, in which melanocyte localization at the epidermal-dermal junction mimics human distribution (HU); 2) 7,12-Dimethylbenz(a)anthracene (DMBA)-induced melanoma in a HGF-tg and Cdk4R24C mouse (HC4D); 3) UV-induced melanoma in a BrafCA/+; HGF-tg; Cdkn2aflox/+; Tyr-CreERT2-t mouse (BHCU); and 4) UV-induced melanoma in a BrafCA/+; Ptenflox/+; Cdkn2aflox/+; Tyr-CreERT2-tg mouse (BPCU). Exome sequencing of the four models reveals a high correlation with mutational subtypes previously described in human melanoma. BPCU and BHCU represent different Braf mutant patient populations and HU and HC4D represent triple wildtype melanoma (non-BRAF, -NRAS, -NF1). The four mouse models demonstrate distinct responses to ICB with anti-CTLA-4 treatment. While HU and HC4D melanomas show high or partial sensitivity to anti-CTLA-4, respectively, BPCU and BHCU do not respond to treatment. In vivo vaccination assays demonstrate that the anti-CTLA-4 response in our models is linked to increased tumor immunogenicity. However, the number of non-synonymous mutations and antigen presentation functionality do not correlate with ICB efficacy. Tumor infiltration by T cells was assessed by CD3 and FoxP3 immunostaining and gene expression analysis. Although clear differential gene expression profiles are noted among the four models and in those tumors responding to the treatment, we unexpectedly found that “hot” melanomas (e.g., showing upregulation of inflammatory pathways and high T-cell infiltration) do not necessarily predict ICB efficacy. These results suggest that additional mechanisms could help determine the response or intrinsic resistance to anti-CTLA-4 and open new avenues for future research and treatment. Overall, our study offers four genetically and phenotypically distinct mouse models representing diverse human melanoma subtypes as powerful tools for the mechanistic study of the response to immunotherapies in melanoma.

Citation Format: Corinne Rauck, Eva Perez-Guijarro, Zoe W. Ohler, Rajaa El E. Meskini, Howard Yang, Suman Vodnala, Cari Graff-Cherry, Sung Chin, Anyen Fon, Helen Michael, Maxwell Lee, Terry Van Dyke, Shyam Sharan, Glenn Merlino, Chi-Ping Day. Developing a preclinical immunotherapy platform using syngeneic mouse models of human melanoma [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 5678.

Genetically engineered mouse models of melanoma

Melanoma is a complex disease that exhibits highly heterogeneous etiological, histopathological, and genetic features, as well as therapeutic responses. Genetically engineered mouse (GEM) models provide powerful tools to unravel the molecular mechanisms critical for melanoma development and drug resistance. Here, we expound briefly the basis of the mouse modeling design, the available technology for genetic engineering, and the aspects influencing the use of GEMs to model melanoma. Furthermore, we describe in detail the currently available GEM models of melanoma. Cancer 2017;123:2089-103. © 2017 American Cancer Society.

Abstract 2623: Identification of neo-antigens driving melanoma response to immune checkpoint blockers via in vivo screening

Immune checkpoint blockers (ICBs) have rendered unprecedented, durable responses in metastatic melanoma, but the heterogeneous response among patients continues to be the major obstacle for their therapeutic development. It is generally hypothesized that neoantigens derived from mutated genes are involved in tumor response to ICBs, since the latter is correlated witt mutational loads of tumors. However, direct experimental evidence showing that threshold quantity or specific properties of neoantigens drive ICB response are mostly lacking. To identify and characterize neoantigens implicated in ICB response, we have generated two UV-induced melanoma models based on the BrafV600E/Pten-knockout (Braf/PKO) and Hgf-transgenic (Hgf-tg) mouse, which displayed intrinsic resistance and high sensitivity to an anti-CTLA-4 antibody, respectively. Exome sequencing identified 216 and 291 non-synonymous mutations in the Braf/PKO and UV-Hgf melanoma cell lines, respectively. By RNA sequencing, 74 (34%) and 121 (42%) of these mutated genes were found to be expressed in each model, respectively, and there were no overlapping mutations between them. The mutations found in the “sensitive” UV-Hgf melanoma were analyzed in silico for their binding affinity to MHC-I and/or MHC-II, thus characterizing putative neoantigens. A “neo-epitope” library was generated by cloning the DNA sequences flanking non-synonymous mutations in frame with the eGFP gene in a lentiviral vector. We further showed that such eGFP-fused epitopes can be presented by the cells to induce specific T cell responses. The library will be transduced into the “resistant” Braf/PKO melanoma, which will be treated with anti-CTLA-4 in mice to identify the neoantigens required for the response. To prevent immunity against eGFP expressed by tumors, the library-transduced melanoma cells will be transplanted into the eGFP-tolerant “glowing head mice”. The results will be used to determine if one, or more, of our candidate neo-epitopes can induce a response to anti-CTLA-4. We will also analyze if the response to this ICB is an epitope-specific reaction or require multiple epitopes, which will help to identify resistance mechanisms. We anticipate that our results will provide insight into the role of neoantigens in ICB response. Moreover, our models will serve as a platform to study the specific contribution and predictive value of neoantigens for melanoma response to immunotherapy, which could help improve therapeutic strategies involving ICBs.

Citation Format: Chi-Ping Day, Eva Perez-Guijarro, Rajaa El Meskini, Zoe Weaver Ohler, Maxwell Lee, Howard Yang, Suman Vodnala, Shyam Sharan, Glenn Merlino. Identification of neo-antigens driving melanoma response to immune checkpoint blockers via in vivo screening [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2623. doi:10.1158/1538-7445.AM2017-2623

Abstract 1037: Progression from melanocytic nevi to melanoma is associated with increased genomic mutations in a UV-induced mouse model of human melanoma

Melanoma is the deadliest form of skin cancer with approximately 132,000 cases worldwide each year. Benign melanocytic nevi are nearly universal, and although progression of nevi to melanoma is very rare, 20-50% of melanoma appear to arise from a pre-existing nevus. UV exposure, particularly childhood sunburn, is believed to play an important role in the development of melanocytic nevi and melanoma, but the exact mechanism is unknown. Alterations in MAPK pathway genes, especially NRAS and BRAF, are common in both benign nevi and melanoma, but approximately 1/3 of melanomas do not have an identified driver mutation. Studying nevus initiation and progression prospectively in the human population is impractical due to the long latency to progression and repeated UV exposures Our laboratory has developed a hepatocyte growth factor (HGF) genetically engineered mouse model with “humanized” junctional distribution of melanocytes on an iDCT-GFP background with melanocyte-specific GFP expression, allowing melanocytic lesions to be tracked through percutaneous GFP imaging. Following a single relevant dose of UV modeling childhood sunburn, HGF iDCT-GFP develop discrete, small melanocytic lesions consistent with nevi. Most nevi remain stable over the lifetime of the mouse, but around 1 in 30 progress to melanoma usually starting at 6-12 months. The melanocytic lesions are histologically similar to human nevi and melanoma, label with melanocyte markers and tumors are transplantable into syngeneic mice. Melanomas that arise in the model are heterogeneous and include radial growth phase and vertical growth phase tumors and sometimes metastasize to liver and lung. Exome sequencing of 28 nevi and melanomas show that vertical growth phase melanomas have approximately 3x more mutations than radial growth phase melanomas or nevi. The increased number of mutations in vertical growth phase tumors is due to an increase in C&gt;T transitions despite the lack of additional UV exposure. Interestingly, melanocytic nevi and melanomas with DNA repair pathway mutations average 3x more mutations than lesions without mutations in these pathways. Melanomas sometime contain mutations in hotspot locations from human melanomas, including GNAQ, but most do not have a previously identified dominant driver. Genes potentially involved in the initiation of melanocytic lesions or progression to aggressive melanomas and relevant to human melanoma have been identified and are being functionally tested using CRISPR to introduce point mutations or knock out genes and in vitro skin reconstitution assays. Identification of novel drivers and pathways involved in non-BRAF, non-NRAS melanoma has the potential to uncover biomarkers and new therapeutic targets to improve clinical outcomes for melanoma patients.

Citation Format: Helen Michael, Chi-Ping Day, Howard Yang, Aleksandra Michalowski, Maxwell Lee, Glenn Merlino. Progression from melanocytic nevi to melanoma is associated with increased genomic mutations in a UV-induced mouse model of human melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1037. doi:10.1158/1538-7445.AM2017-1037

Concepts in Cancer Modeling: A Brief History

Modeling, an experimental approach to investigate complex biological systems, has significantly contributed to our understanding of cancer. Although extensive cancer research has been conducted utilizing animal models for elucidating mechanisms and developing therapeutics, the concepts in a good model design and its application have not been well elaborated. In this review, we discuss the theory underlying biological modeling and the process of producing a valuable and relevant animal model. Several renowned examples in the history of cancer research will be used to illustrate how modeling can be translatable to clinical applications. Finally, we will also discuss how the advances in cancer genomics and cancer modeling will influence each other going forward. Cancer Res; 76(20); 5921-5. ©2016 AACR.

Abstract 1479: Preclinical model of human melanoma for evaluation of targeted drug treatment and for immunotherapy validation

Malignant melanoma accounts for less than 5% of skin cancer cases, yet it represents 75% of deaths from skin cancer. The high mortality rate is due to the malignant, metastatic nature of the disease and resistance to chemotherapeutic treatments. Most mouse melanoma models have not fully recapitulated the histopathology of the disease and its metastatic nature. At NCI's Center for Advanced Preclinical Research (CAPR), we have adapted the HGF/SF; CDK4R24C transgenic mouse model to an optimized allograft transplant model for preclinical therapeutic studies in primary and metastatic melanoma. This genetically engineered mouse-derived Allograft (GDA) model recapitulates the features of the original GEM, including the epithelioid histopathology and key marker expression of human melanoma. It is an efficient and tractable tool for monitoring of both tumor growth and therapeutic responses in primary and metastatic melanoma in the context of a normal immune system. Additionally, aberrant expression of c-Met and upregulation of the downstream signaling pathway in HGF-GDA tumors is relevant for targeted therapeutics in melanoma. Thus, the model is a useful platform for evaluating therapies that target tumor cells and/or immunomodulatory pathways in intervention or adjuvant settings. Although drugs such as the c-Met inhibitor crizotinib and the MEK inhibitor trametinib were potent in cell culture, PD analyses of short-term (4-6 hour) treatment with small molecule therapies indicated that treatment incompletely suppresses the pathway in vivo compared to the corresponding primary cell line, and does not inhibit tumor growth. Therefore the HGF-GDA can be exploited to examine combination treatments that either prevent feedback activation of downstream pathway nodes in vivo, or modify alternate pathways, such as immunomodulatory targets. Hence, we are currently exploring rational combinations of oncogene-targeted therapy with immune-targeted therapy, for example, combined trametinib and anti-CTLA4 antibody treatment. In the HGF-GDA, complete response was observed in a subgroup of mice treated with anti-CTLA-4, i.e. established tumors fully regressed, yet the durable response and increased survival time (based on tumor volume) was not enhanced by concurrent treatment with trametinib. Future treatment studies will involve alternative regimens. Additionally, since metastasis, not the primary tumor, leads to progression of melanoma in patients, we have characterized a primary tumor resection model in which only metastatic disease is treated. Lung metastases develop after resection of the HGF-GDA primary tumor, which

may be treated in an intervention or adjuvant setting. Therefore we evaluated the effect on survival of the same combination therapy (trametinib and anti-CTLA-4) we previously used to treat the primary tumor, but as adjuvant treatment for the metastatic melanoma model.

Citation Format: Rajaa El Meskini, Michelle Gumprecht, Alan Kulaga, Anthony Iacovelli, Terry Van Dyke, Chi-Ping Day, Glenn Merlino, Zoe Weaver Ohler. Preclinical model of human melanoma for evaluation of targeted drug treatment and for immunotherapy validation. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1479.

Abstract 4388: The role of neoantigens in immunotherapy of cutaneous melanoma

Melanoma is increasing in incidence by up to 3% annually, and metastatic melanoma, which is resistant to most conventional therapies, has a poor prognosis with a 5-year survival rate of less than 20%. Immunotherapy is able to yield durable response in melanoma; however, the response rate is limited (20-30%). It has been shown that tumor immunogenicity is highly correlated to the response to immunotherapy. The mutational load and the characteristics of the neoantigens displayed by the tumor cells are theorized to play an important role in the immunogenicity of the tumor. We used genetically engineered preclinical mouse models to study the role of these neoantigens in melanoma response to immune therapy. Three syngeneic C57BL/6 mouse melanoma models were developed: UV induced melanoma in albino BRAF(V600E);PTEN-/- mice (1), DMBA induced melanoma in pigmented HGF-tg;CDK4(R24C) mice (2), and UV induced melanoma in pigmented HGF-tg mice. These three models were found to have varying degrees of tumor immunogenicity based on vaccination studies. The UV induced BRAF(V600E);PTEN-/- model displayed poor immunogenicity, while the DMBA induced HGF-tg;CDK4(R24C) model exhibited moderate immunogenicity and the UV induced HGF-tg model showed the highest immunogenicity. Exome sequencing results showed that high immunogenicity is associated with mutations of genes in DNA damage responses and frameshift mutations. To test the role of neoantigens, RNA from each of the melanoma models was sequenced and analyzed for mutational and expression profiles. We will be comparing the response of these three mouse models to correlate immunogenicity with response to anti-CTLA-4 therapy. We plan to analyze the pathways in which mutated genes were enriched, allowing the identification of “druggable” targets to enhance therapeutic efficacy of immune checkpoint inhibitors. CRISPR/Cas9-based screening approaches will be used to identify specific neoantigens able to influence response to immune therapy. In conclusion, our preclinical mouse models show that tumor immunogenicity may be correlated to the carcinogenic mechanisms, and RNA sequence has provided further insight into the role of mutational load and neo-epitopes on immune-based therapeutic response.

(1) Provided by Marcus Bosenberg (Yale School of Medicine, New Heaven, CT), Martin McMahon (Huntsman Cancer Institute, Salt Lake City, UT).

(2) Provided by Thomas Tueting (University Hospital Bonn, Bonn, Germany).

Citation Format: Renee M. Thomas, Chi-Ping Day, Zoe Weaver Ohler, Rajaa El Meskini, Carri Graff-Cherry, Sung Chin, Aleksandra Michalowski, Ji Luo, Terry Van Dyke, Glenn Merlino. The role of neoantigens in immunotherapy of cutaneous melanoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4388.

Abstract B112: Identifying determinants of melanoma response to immune checkpoint inhibitors via preclinical modeling

Immune checkpoint inhibitors (ICPi; e.g. anti-CTLA-4, anti-PD-1, anti-PD-L1) have shown great promise for melanoma treatment; however, sustained responses are achieved only in a fraction of patients, while the majority does not respond at all. Though load and patterns of mutations have been shown to be associated with IMT responses, the determinants have never been well characterized. In this study we aimed to identify predictive markers of melanoma response to ICPi by preclinical modeling. Three genetically engineered mice (GEM) were built to model melanomagenesis driven by different carcinogenic processes: (1) UV in albino BRAF(V600E); PTEN-knockout C57BL/6 mice, (2) carcinogen DMBA in pigmented Hgf-tg; CDK4(R24C) C57BL/6 mice, and (3) UV in pigmented Hgf-tg C57BL/6 mice. Melanoma cells derived from these models were subjected for exome sequencing and immunogenicity test by vaccination and challenge. Their responses to anti-CTLA-4 antibody were then tested in preclinical settings. Model (1), (2) and (3) are non-, medium-, and high-immunogenic, respectively. Consistent with published data, responses to anti-CTLA-4 are well correlated with the immunogenicity of individual melanoma models. Moreover, co-administration of BRAF or MEK inhibitors with immunotherapy did not enhance therapeutic efficacy. Based on exome sequencing, all the models exhibit coding mutations in genes of neuronal development, MAPK pathways, and G protein-coupled pathways, but UV-type mutations (C to T and G to A) were enriched only in model (1). Interestingly, deleterious mutations in DNA damage response (DDR) genes existed only in immunogenic models (2) and (3). These results suggested that carcinogenic mechanisms determine tumor immunogenicity and therefore response to IMT. Consistent with recent data from clinical studies, mutations in DDR genes may be predictive of IMT response. Currently we are evaluating the functions of specific DDR genes in melanoma, and the possibility they may serve as therapeutic targets in combination therapies with ICPi.

Citation Format: Chi-Ping Day, Rajaa El Meskini, Cari Graff-Cherry, Aleksandra Michalowski, Zoe Weaver Ohler, Terry Van Dyke, Glenn Merlino. Identifying determinants of melanoma response to immune checkpoint inhibitors via preclinical modeling. [abstract]. In: Proceedings of the CRI-CIMT-EATI-AACR Inaugural International Cancer Immunotherapy Conference: Translating Science into Survival; September 16-19, 2015; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(1 Suppl):Abstract nr B112.

Preclinical mouse cancer models: a maze of opportunities and challenges

Significant advances have been made in developing novel therapeutics for cancer treatment, and targeted therapies have revolutionized the treatment of some cancers. Despite the promise, only about five percent of new cancer drugs are approved, and most fail due to lack of efficacy. The indication is that current preclinical methods are limited in predicting successful outcomes. Such failure exacts enormous cost, both financial and in the quality of human life. This Primer explores the current status, promise, and challenges of preclinical evaluation in advanced mouse cancer models and briefly addresses emerging models for early-stage preclinical development.

"Glowing head" mice: a genetic tool enabling reliable preclinical image-based evaluation of cancers in immunocompetent allografts

Preclinical therapeutic assessment currently relies on the growth response of established human cell lines xenografted into immunocompromised mice, a strategy that is generally not predictive of clinical outcomes. Immunocompetent genetically engineered mouse (GEM)-derived tumor allograft models offer highly tractable preclinical alternatives and facilitate analysis of clinically promising immunomodulatory agents. Imageable reporters are essential for accurately tracking tumor growth and response, particularly for metastases. Unfortunately, reporters such as luciferase and GFP are foreign antigens in immunocompetent mice, potentially hindering tumor growth and confounding therapeutic responses. Here we assessed the value of reporter-tolerized GEMs as allograft recipients by targeting minimal expression of a luciferase-GFP fusion reporter to the anterior pituitary gland (dubbed the “Glowing Head” or GH mouse). The luciferase-GFP reporter expressed in tumor cells induced adverse immune responses in wildtype mouse, but not in GH mouse, as transplantation hosts. The antigenicity of optical reporters resulted in a decrease in both the growth and metastatic potential of the labeled tumor in wildtype mice as compared to the GH mice. Moreover, reporter expression can also alter the tumor response to chemotherapy or targeted therapy in a context-dependent manner. Thus the GH mice and experimental approaches vetted herein provide concept validation and a strategy for effective, reproducible preclinical evaluation of growth and response kinetics for traceable tumors.

Abstract IA22: Modeling recurrent metastatic melanoma in the mouse

Recurrence and metastasis following resection and therapy are the most critical problems in progressive cancers and the main causes of cancer-related death. This problem is magnified in cutaneous malignant melanoma, which is highly metastatic in advanced stages and generally resistant to chemotherapy. Although new drugs such as Vemurafenib successfully target BRAFV600E and typically demonstrate a significant clinical response, progressive melanomas recur resulting in near uniform patient mortality. Dissection of processes underpinning recurrent and metastatic melanoma is certain to identify new therapeutic targets for more efficacious treatment. However, current preclinical studies do not model progressive recurrent disease, but rather rely on the growth response of human melanoma cell lines subcutaneously xenografted into immunocompromised mice as the efficacy endpoint; these studies have shown poor predictive power for clinical activity. Therefore we have designed new and improved genetically engineered mouse (GEM) models of progressive melanoma. These are being used to test targeted and immune-based therapies singly and in combination, and to study mechanisms associated with the resistance of recurrent/metastatic melanoma to promising clinical drugs.

To identify novel targets for advanced disease we hypothesized that metastatic melanomas can exploit hard-wired pathways employed by migratory embryonic melanocytes, but not mature melanocytes, to achieve a more aggressive malignant phenotype. We had previously generated a GEM model (iDCT-GFP) that expresses Green Fluorescent Protein specifically in all melanocytic cells in a doxycycline-regulatable manner. The iDCT-GFP mouse was used in concert with FACS to isolate melanoblasts from key developmental stages, sequence their transcriptomes using RNA-Seq, and identify genes/pathways common to metastatic melanoma cells. We have thus generated a full library of the genes expressed during embryonic development of the melanocyte. A detailed comparative analysis of mouse melanoblast gene expression profiles with human metastatic melanoma cells was then performed, identifying what we believe to be a small number of critical genes common to both. We anticipate that this approach will enhance our understanding of this fatal disease at both mechanistic and prognostic levels, and facilitate the identification of novel therapeutic targets for the treatment of metastatic melanoma.

Citation Format: Glenn T. Merlino, Chi-Ping Day, Pravin Mishra, Theresa Guo, Raza Zaida, Sean Davis, Paul Meltzer, Frances Noonan, Edward De Fabo, Zoe Ohler-Weaver, Terry Van Dyke. Modeling recurrent metastatic melanoma in the mouse. [abstract]. In: Proceedings of the AACR Special Conference: The Translational Impact of Model Organisms in Cancer; Nov 5-8, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2014;12(11 Suppl):Abstract nr IA22.

Carriage of the PNPLA3 rs738409 C >G polymorphism confers an increased risk of non-alcoholic fatty liver disease associated hepatocellular carcinoma

BACKGROUND & AIMS

Subtle inter-patient genetic variation and environmental factors combine to determine disease progression in non-alcoholic fatty liver disease (NAFLD). Carriage of the PNPLA3 rs738409 c.444C >G minor allele (encoding the I148M variant) has been robustly associated with advanced NAFLD. Although most hepatocellular carcinoma (HCC) is related to chronic viral hepatitis or alcoholic liver disease, the incidence of NAFLD-related HCC is increasing. We examined whether rs738409 C >G was associated with HCC-risk in patients with NAFLD.

METHODS

PNPLA3 rs738409 genotype was determined by allelic discrimination in 100 European Caucasians with NAFLD-related HCC and 275 controls with histologically characterised NAFLD.

RESULTS

Genotype frequencies were significantly different between NAFLD-HCC cases (CC=28, CG=43, GG=29) and NAFLD-controls (CC=125, CG=117, GG=33) (p=0.0001). In multivariate analysis adjusted for age, gender, diabetes, BMI, and presence of cirrhosis, carriage of each copy of the rs738409 minor (G) allele conferred an additive risk for HCC (adjusted OR 2.26 [95% CI 1.23-4.14], p=0.0082), with GG homozygotes exhibiting a 5-fold [1.47-17.29], p=0.01 increased risk over CC. When compared to the UK general population (1958 British Birth Cohort, n=1476), the risk-effect was more pronounced (GC vs. CC: unadjusted OR 2.52 [1.55-4.10], p=0.0002; GG vs. CC: OR 12.19 [6.89-21.58], p<0.0001).

CONCLUSIONS

Carriage of the PNPLA3 rs738409 C >G polymorphism is not only associated with greater risk of progressive steatohepatitis and fibrosis but also of HCC. If validated, these findings suggest that PNPLA3 genotyping has the potential to contribute to multi-factorial patient-risk stratification, identifying those to whom HCC surveillance may be targeted.

TGF-β signaling in myeloid cells is required for tumor metastasis

TGF-β is overexpressed in advanced human cancers. It correlates with metastasis and poor prognosis. However, TGF-β functions as both a tumor suppressor and a tumor promoter. Here, we report for the first time that genetic deletion of Tgfbr2 specifically in myeloid cells (Tgfbr2(MyeKO)) significantly inhibited tumor metastasis. Reconstitution of tumor-bearing mice with Tgfbr2(MyeKO) bone marrow recapitulated the inhibited metastasis phenotype. This effect is mediated through decreased production of type II cytokines, TGF-β1, arginase 1, and inducible nitric oxide synthase, which promoted IFN-γ production and improved systemic immunity. Depletion of CD8 T cells diminished the metastasis defect in the Tgfbr2(MyeKO) mice. Consistent with animal studies, myeloid cells from patients with advanced-stage cancer showed increased TGF-β receptor II expression. Our studies show that myeloid-specific TGF-β signaling is an essential component of the metastasis-promoting puzzle of TGF-β. This is in contrast to the previously reported tumor-suppressing phenotypes in fibroblasts, epithelial cells, and T cells.