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VAF concordance

Analysis of Beat AML data.

Supplementary Data file including supplementary methods and clinical case vignettes.

Reasons for not using recommended targeted therapy.

combination of MEK inhibitor with venetoclax is synergistic.

MTT recommendation tiering system.

Compound sensitivity data for primary patient samples.

Inhibitor Recommendation Usage Summary.

Correlation between Ras pathway mutation VAF and in vitro sensitivity to MEK inhibitors.

Patient sequencing data, by patient number and diagnosis.

Neuroblastoma is a childhood cancer originating from embryonic neuronal progenitor cells and is the most common cancer diagnosed in infants. Although the majority of patients respond to initial chemotherapy, most high-risk patients suffer relapse due to therapy resistance. Here, we generated single-cell transcriptome and bulk whole-genome sequencing data of diagnosis and post-therapy samples from 23 patients diagnosed with high-risk neuroblastoma. We found two distinct adrenergic populations in the patient samples. Most tumor cells showed a mature sympathoblast phenotype whereas a small fraction was in an undifferentiated state with activation of protein translation, unfolded protein, and oxidative phosphorylation pathways. We found that therapy-resistant tumor cells in these two subpopulations had distinct characteristics. The more mature resistant subpopulation upregulated genes associated with epithelial-to-mesenchymal transition, including TWIST1, PLCB1 and CD276. The undifferentiated resistant subpopulation upregulated Ras signal transduction and TP53 pathway genes. Analysis of the immune microenvironment revealed that most tumor-associated macrophages became more immunosuppressive post-therapy via multiple newly gained signaling interactions including the complement signaling pathway. We discovered a limited infiltration of T lymphocytes in the tumor microenvironment, and chemotherapy induced an effector state with upregulated mTOR signaling and metabolism. Overall, our study revealed subpopulations of tumor cells in neuroblastoma that responded differently to induction chemotherapy. Our findings uncovered distinct molecular signatures of the resistant cells and their interactions with the immune microenvironment, paving the way for developing novel therapies for high-risk neuroblastoma. Citation Format: Yasin Uzun, Liron D. Grossmann, Chia-Hui Chen, Anusha Thadi, Chi-Yun Wu, Peng Gao, Dinh Diep, Lea Surrey, Daniel Martinez, Tasleema Patel, Qi Qiu, Sarah Johnson, Wenbao Yu, Shane Drabings, Changya Chen, Yuxuan Hu, Gregory Chen, Derek A. Oldridge, Kun Zhang, Hao Wu, Kathrin Bernt, Nancy Zhang, John M. Maris, Kai Tan. Longitudinal single-cell sequencing of high-risk neuroblastoma tumors reveals intrinsic and extrinsic mechanisms of therapy resistance [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 6051.

BACKGROUND High-risk neuroblastoma is a pediatric cancer arising from the developing sympathetic nervous system with a 50% relapse rate that is typically fatal. At least two subpopulations of neuroblastoma cells exist that can transdifferentiate, adrenergic and mesenchymal, the latter being more resistant to chemotherapy. Mechanisms of therapy resistance are largely unknown and the cells responsible for relapse have not been identified. METHODS We used single nucleus RNA and ATAC sequencing to identify and characterize the cells that survive chemotherapy, termed here “persister cells”, from a cohort of 20 matched diagnostic and post induction chemotherapyhigh-risk neuroblastoma patients and two patient derived xenograft (PDX) models from diagnostic tumors. Eight representative cell lines derived from neuroblastomas at diagnosis were treated with standard-of-care chemotherapy, and flow cytometry was used to sort for live cells. ML120B and CRISPR-CAS9 were used to modulate NF-kB signaling. An RNA-seq dataset of 153 high-risk neuroblastoma patients was used to determine differentially activated pathways between adrenergic and mesenchymal tumors. RESULTS Residual malignant cells in the post-chemotherapy tumor samples clustered into three main groups separated by the response to therapy. The most prevalent group of persister cells in responders (N=16/20) displayed low MYC(N) activity even in the presence of MYCN amplification. This group also demonstrated decreased expression of the adrenergic core regulatory circuit genes including PHOX2B, ISL1, HAND2, along with marked activation of TNF-alpha via NF-kB signaling. High NF-kB activity was found in a subpopulation of diagnostic cells in two chemo-refractory patients. We validated decreased expression of MYCN (2-fold decrease, p CONCLUSIONS NF-kB activation is a major mediator of de novo and acquired chemotherapy resistance in high-risk neuroblastoma. We postulate that concomitant silencing of this pathway could eliminate persister cells and prevent disease relapse. Citation Format: Liron D. Grossmann, Yasin Uzun, Jarrett Lindsay, Chia-Hui Chen, Catherine Wingrove, Peng Gao, Anusha Thadi, Quinlen Marshall, Nathan M. Kendsersky, Lea Surrey, Daniel Martinez, Emily Mycek, Colleen Casey, Kateryna Krytska, Matthew Tsang, Adam Wolpaw, David N. Groff, Erin Runbeck, Jayne McDevitt, Dinh Diep, Tasleema Patel, Kathrin M. Bernt, Chi Dang, Kun Zhang, Yael P. Mosse, Kai Tan, John M. Maris. NF-kB is a master regulator of resistance to therapy in high-risk neuroblastoma [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 699.

Tumor phenotypes are dictated not only by the neoplastic cell component, but also by the tumor microenvironment (TME), which includes immune and inflammatory cells. Acute myeloid leukemia (AML) is the second most common leukemia of childhood. Although intensive multi-agent chemotherapy in conjunction with improved supportive care has increased survival rates to 70%, 30-40% of children with AML relapse and only one-third of them will survive to adulthood. Investigation of new therapeutic strategies for high-risk AML, including immunotherapy, remains a priority and is being actively pursued. Importantly, AML-induced immune suppression poses a fundamental barrier to successful immune-based interventions. We previously showed that in vitro treatment of primary AML cells with interferon (IFN)-γ induces functional indoleamine 2,3-dioxygenase-1 (IDO1), a molecule with potent immunosuppressive properties, in 50% of unselected cases (IFN-γ responders). With a median follow-up of 8 years, IFN-γ responders experienced a significantly shorter event-free survival and overall survival (OS). Herein, we aimed to get insights into the immune landscape of childhood AML using multi-scale immune profiling strategies with the aim to identify molecular circuits that can be targeted to revert leukemia-induced immune dysfunction and improve clinical outcome. We employed a novel high-throughput digital platform, the nCounter system (nanoString Technologies, Seattle, USA), and Optimized Multi-color Immuno-phenotyping Panels (OMIPs) to comprehensively characterize the bone marrow immune infiltrate in 34 children diagnosed with non-promyelocytic AML (17 males, 17 females; median age at diagnosis=10 years; 28 de novo AML, 4 infant leukemia, 1 secondary AML, 1 congenital leukemia; 7 patients with favorable-risk cytogenetics, 21 patients with intermediate-risk cytogenetics and 6 patients with unfavorable-risk cytogenetics). The RNA Pan-Cancer Immune Profiling Panel, which includes 109 cell surface markers for 24 immune cell types, 30 cancer testis antigens, and >500 immune response genes, allowed us to measure immune gene expression levels on the clinic-ready nCounter® FLEX platform (nanoString Technologies). Transcriptomic data were normalized and analyzed using the nSolver software package. Relapse-free survival (RFS) and OS were selected as covariates. For immune phenotyping studies, viable bone marrow mononuclear cells were labeled with fluorochrome-conjugated antibodies and then analyzed on a 10-color Gallios flow cytometer (Beckman Coulter Life Sciences, Buckinghamshire, UK) with standard settings. Hierarchical clustering of immune gene expression data highlighted patient subgroups with heightened expression of T-cell and natural killer (NK)-cell function genes, as well as Toll-like receptor (TLR) genes, interleukin genes and tumor necrosis factor (TNF) family genes. Patients with high levels of CD8A mRNA also expressed IFNG, CXCL9, CXCL10, FOXP3 and negative checkpoints, including LAG3, CTLA4, IDO1 and CD279 (PD-L1), consistent with T-cell inflamed phenotypes that might underpin the establishment of adaptive immune resistance mechanisms of immune escape. In-depth phenotyping studies showed higher percentages of bone marrow-resident naïve B cells, plasmablasts, intermediate and non-conventional monocytes, plasmacytoid dendritic cells (DCs) and CXCR3-expressing Th1 cells at diagnosis compared with complete remission (CR). By contrast, both type 1 and type 2 myeloid DCs were more represented in the TME of patients with AML in CR. The frequencies of innate lymphoid cells (ILCs) and Vγ9+Vδ2+ T cells were not significantly different when comparing diagnosis and CR samples. Relapses occurred in 71.4% of children with “inflamed” AML compared with 28.6% of patients with “non-inflamed” AML (p=0.012; two-sided Fisher’s exact test). Importantly, RFS was remarkably shorter in patients with inflamed compared with non-inflamed AML (median RFS=394 days vs. undefined; hazard ratio = 0.266; 95% CI=0.11-0.64; p=0.0039, log-rank test). A non-significant association with OS was also observed. In conclusion, inflamed or “hot” AMLs are associated with shorter RFS and might be amenable to immunotherapy approaches tailored to the bone marrow TME, including PD-1/PD-L1 blockade and/or small-molecule IDO1 inhibitors. Grant support: Roger Counter Foundation, Dorset, UK and Qatar National Research Fund (grant #NPRP8-2297-3-494). Citation Format: Jayakumar Vadakekolathu, Gemma A. Foulds, Tasleema Patel, Stephen Reeder, Alan Graham Pockley, Sarah K. Tasian, Sergio Rutella. Immune gene expression profiling identifies predictors of relapse in childhood acute myeloid leukemia [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2017 Oct 1-4; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2018;6(9 Suppl):Abstract nr B62.