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Background: Sarcomas are a heterogeneous group of mesenchymal tumors frequently diagnosed in pediatric and young adult patients. These tumors respond poorly to conventional immunotherapy, although the precise reason for this is not known. We sought to characterize the systemic immune response to sarcomas by measuring the levels of circulating cytokines in the plasma of newly diagnosed sarcoma patients, testing the hypothesis that the nature of a patient’s immune response to their tumor directly affects outcome. Methods: Plasma was collected from newly diagnosed, treatment-naive pediatric sarcoma patients participating in an ongoing clinical trial, MCC20320. A panel of 18 cytokines was selected, and cytokine levels were measured using the Luminex platform. Cytokine levels were analyzed based on clinicopathological parameters such as gender, age, stage, and survival. Results: We found that the cytokine profile in patients newly diagnosed with sarcoma is distinct from healthy controls, but different sarcomas were not distinguishable. Patients with osteosarcoma who had elevated levels of multiple cytokines had inferior overall survival compared to those with fewer or no elevated levels. Similarly, elevated levels of individual cytokines and chemokines, including IL-24, CXCL5, and CXCL10, were associated with inferior event-free or overall survival in patients with osteosarcoma. Perhaps most significantly, elevated IL-1β at diagnosis was associated with metastatic presentation and inferior event-free survival in patients with osteosarcoma. Conclusions: These findings suggest that pediatric sarcoma patients mount a systemic immune response that may affect event-free or overall survival. IL-1β in particular may be a valuable therapeutic target for osteosarcoma patients.

Background/Objectives: Osteosarcoma is the most common malignant bone tumor in children, characterized by a high degree of genomic instability, resulting in copy number alterations and genomic rearrangements without disease-defining recurrent mutations. Clinical trials based on molecular characterization have failed to find new effective therapies or improve outcomes over the last 40 years. Methods: To better understand the immune microenvironment of osteosarcoma, we performed single-cell RNA sequencing on six tumor biopsy samples, combined with a previously published cohort of six samples. Additional osteosarcoma samples were profiled using spatial transcriptomics for the validation of discovered subtypes and to add spatial context. Results: Analysis revealed immunosuppressive cells, including myeloid-derived suppressor cells (MDSCs), regulatory and exhausted T cells, and LAMP3+ dendritic cells. Conclusions: Using cell–cell communication modeling, we identified robust interactions between MDSCs and other cells, leading to NF-κB upregulation and an immunosuppressive microenvironment, as well as interactions involving regulatory T cells and osteosarcoma cells that promoted tumor progression and a proangiogenic niche.

Background Children with relapsed central nervous system (CNS tumors), neuroblastoma, sarcomas, and other rare solid tumors face poor outcomes. This prospective clinical trial examined the feasibility of combining genomic and transcriptomic profiling of tumor samples with a molecular tumor board (MTB) approach to make real‑time treatment decisions for children with relapsed/refractory solid tumors. Methods Subjects were divided into three strata: stratum 1—relapsed/refractory neuroblastoma; stratum 2—relapsed/refractory CNS tumors; and stratum 3—relapsed/refractory rare solid tumors. Tumor samples were sent for tumor/normal whole-exome (WES) and tumor whole-transcriptome (WTS) sequencing, and the genomic data were used in a multi-institutional MTB to make real‑time treatment decisions. The MTB recommended plan allowed for a combination of up to 4 agents. Feasibility was measured by time to completion of genomic sequencing, MTB review and initiation of treatment. Response was assessed after every two cycles using Response Evaluation Criteria in Solid Tumors (RECIST). Patient clinical benefit was calculated by the sum of the CR, PR, SD, and NED subjects divided by the sum of complete response (CR), partial response (PR), stable disease (SD), no evidence of disease (NED), and progressive disease (PD) subjects. Grade 3 and higher related and unexpected adverse events (AEs) were tabulated for safety evaluation. Results A total of 186 eligible patients were enrolled with 144 evaluable for safety and 124 evaluable for response. The average number of days from biopsy to initiation of the MTB-recommended combination therapy was 38 days. Patient benefit was exhibited in 65% of all subjects, 67% of neuroblastoma subjects, 73% of CNS tumor subjects, and 60% of rare tumor subjects. There was little associated toxicity above that expected for the MGT drugs used during this trial, suggestive of the safety of utilizing this method of selecting combination targeted therapy. Conclusions This trial demonstrated the feasibility, safety, and efficacy of a comprehensive sequencing model to guide personalized therapy for patients with any relapsed/refractory solid malignancy. Personalized therapy was well tolerated, and the clinical benefit rate of 65% in these heavily pretreated populations suggests that this treatment strategy could be an effective option for relapsed and refractory pediatric cancers. Trial registration ClinicalTrials.gov, NCT02162732. Prospectively registered on June 11, 2014.

Snf5 (Ini1/Baf47/Smarcb1), a core member of the Swi/Snf chromatin remodeling complex, is a potent tumor suppressor whose mechanism of action is largely unknown. Biallelic loss of Snf5 leads to the onset of aggressive cancers in both humans and mice. We have developed an innovative and widely applicable analytical technique for cross-species validation of cancer models and show that the gene expression profiles of our Snf 5 murine models closely resemble those of human Snf5-deficient rhabdoid tumors. We exploit this system to produce what we believe to be the first report documenting the effects on gene expression of inactivating a Swi/Snf subunit in normal mammalian cells and to identify the transcriptional pathways regulated by Snf5. We demonstrate that the tumor suppressor activity of Snf5 depends on its regulation of cell cycle progression; Snf5 inactivation leads to aberrant upregulation of E2F targets and increased levels of p53 that are accompanied by apoptosis, polyploidy, and growth arrest. Further, conditional mouse models demonstrate that inactivation of p16lnk4a or Rb (retinoblastoma) does not accelerate tumor formation in Snf5 conditional mice, whereas mutation of p53 leads to a dramatic acceleration of tumor formation.

Background Survival for patients with high‐risk neuroblastoma (HRNB) remains poor despite aggressive multimodal therapies. Aims To study the feasibility and safety of incorporating a genomic‐based targeted agent to induction therapy for HRNB as well as the feasibility and safety of adding difluoromethylornithine (DFMO) to anti‐GD2 immunotherapy. Methods Twenty newly diagnosed HRNB patients were treated on this multicenter pilot trial. Molecular tumor boards selected one of six targeted agents based on tumor‐normal whole exome sequencing and tumor RNA‐sequencing results. Treatment followed standard upfront HRNB chemotherapy with the addition of the selected targeted agent to cycles 3–6 of induction. Following consolidation, DFMO (750 mg/m2 twice daily) was added to maintenance with dinutuximab and isotretinoin, followed by continuation of DFMO alone for 2 years. DNA methylation analysis was performed retrospectively and compared to RNA expression. Results Of the 20 subjects enrolled, 19 started targeted therapy during cycle 3 and 1 started during cycle 5. Eighty‐five percent of subjects met feasibility criteria (receiving 75% of targeted agent doses). Addition of targeted agents did not result in toxicities requiring dose reduction of chemotherapy or permanent discontinuation of targeted agent. Following standard consolidation, 15 subjects continued onto immunotherapy with DFMO. This combination was well‐tolerated and resulted in no unexpected adverse events related to DFMO. Conclusion This study demonstrates the safety and feasibility of adding targeted agents to standard induction therapy and adding DFMO to immunotherapy for HRNB. This treatment regimen has been expanded to a Phase II trial to evaluate efficacy.

Background The pelvis is an infrequent site of osteosarcoma and treatment requires surgery plus systemic chemotherapy. Poor survival has been reported, but has not been confirmed previously by the Children’s Oncology Group (COG). In addition, survival of patients with pelvic osteosarcomas has not been compared directly with that of patients with nonpelvic disease treated on the same clinical trials. Questions/purposes First, we assessed the event-free (EFS) and overall survival (OS) of patients with pelvic osteosarcoma treated on COG clinical trials. We then asked whether patient survival compared with that of patients treated on the same clinical trials with nonpelvic disease. Finally, we asked whether patients with metastatic disease at initial diagnosis had worse survival. Methods We retrospectively reviewed data from 1054 patients with osteosarcoma treated in four studies between 1993 and 2005. Twenty-six of the 1054 patients (2.5%) had a primary tumor of the pelvis. At diagnosis, nine patients had metastatic disease. The minimum followup was 2 months (mean, 34 months; range, 2–102 months). Results Two of the nine patients with metastatic disease at diagnosis and five of the 17 with localized disease were alive at last contact. Estimates of the 5-year EFS for localized versus metastatic disease of the pelvis were 22% versus 23%. OS for patients with localized versus metastatic disease was 47% versus 22%. Patients with osteosarcoma in all other locations had a 5-year EFS of 57% and OS of 69%. Conclusions Our analysis confirms poor survival for patients with pelvic osteosarcoma. Survival with metastatic disease in the absence of a pelvic primary tumor is similar to that for localized or metastatic pelvic osteosarcoma. Improved surgical or medical therapy is needed, and patients with pelvic osteosarcoma may warrant alternate or experimental therapy. Level of Evidence Level II, prognostic study. See Guidelines for Authors for a complete description of levels of evidence.

The survival rate for children with acute lymphoblastic leukemia (ALL) has dramatically improved over the last 50 years. However, for those in the adolescent and young adult (AYA) age-group of 15–30 years with ALL, there has not been the same degree of improvement. Historically, pediatric and adult providers have utilized different treatment approaches based on clinical trials. However, studies that have compared the outcome of AYA patients with ALL treated on pediatric or adult clinical trials have generally shown substantially better outcomes for this patient population treated with the pediatric trials. Additionally, hematopoietic stem cell transplantation has been considered as part of intensified therapy for AYA patients with ALL. Herein, we review the outcomes with chemotherapy alone and with hematopoietic stem cell transplantation, and explore the challenges faced in determining the ideal therapy for the AYA population of patients.

Targeted kinase inhibitors and camptothecins have shown preclinical and clinical activity in several cancers. This trial evaluated the maximum tolerated dose (MTD) and dose‐limiting toxicities of sorafenib and topotecan administered orally in pediatric patients with relapsed solid tumors. Sorafenib was administered twice daily and topotecan once daily on days 1–5 and 8–12 of each 28‐day course. The study utilized a standard 3 + 3 dose escalation design. Three dose levels (DL) were evaluated: (1) sorafenib 150 mg/m2 and topotecan 1 mg/m2; (2) sorafenib 150 mg/m2 and topotecan 1.4 mg/m2; and (3) sorafenib 200 mg/m2 and topotecan 1.4 mg/m2. Pharmacokinetics were ascertained and treatment response assessed. Thirteen patients were enrolled. DL2 was the determined MTD. Grade 4 thrombocytopenia delaying therapy for >7 days was observed in one of six patients on DL2, and grade 4 neutropenia that delayed therapy in two of three patients on DL3. A patient with preexisting cardiac failure controlled with medication developed a transient drop in the left ventricular ejection fraction that improved when sorafenib was withheld. Sorafenib exposure with or without topotecan was comparable, and the concentration‐time profiles for topotecan alone and in combination with sorafenib were similar. One objective response was noted in a patient with fibromatosis. We determined MTD to be sorafenib 150 mg/m2 twice daily orally on days 1–28 combined with topotecan 1.4 mg/m2 once daily on days 1–5 and 8–12. While these doses are 1 DL below the MTD of the agents individually, pharmacokinetic studies suggested adequate drug exposure without drug interactions. The combination had limited activity in the population studied. We completed a phase I trial of the combination of sorafenib and topotecan in pediatric patients. We found the combination to have similar pharmacokinetic exposure when compared to the single agent studies and all therapy was delivered by mouth. No objective responses were seen in the patients enrolled.

Background - Osteosarcoma (OS) is the most common malignant bone tumor in children. OS is characterized by a high degree of genomic instability, resulting in copy-number alterations and genomic rearrangements with no disease-defining recurrent mutations. Given the diverse genomic landscape of OS and the difficulty of identifying druggable therapeutic targets, use of immunotherapy techniques appears lucrative. However, clinical trials based on molecular characterization have failed to find new effective therapies, and outcomes have not improved over the last 40 years. Materials/Methods - We performed single-cell RNA sequencing (scRNA-seq) using the 10x Genomics Chromium platform on six fresh tumor biopsy samples from pediatric OS patients. Raw data was processed using 10x CellRanger to produce transcript read counts for each cell. After filtering low-quality cells and doublet removal, counts were normalized using Seurat, and cells were integrated across samples with Harmony. Data was combined with a previously-published OS scRNA-seq cohort of six samples (GSE162454). Two additional OS samples were profiled using 10x Genomics Visium spatial transcriptomics for validation of discovered subtypes and to add spatial context. Results - Clustering identified 16 major cell types based on expression of canonical cell markers. Several immunosuppressive cell types were identified via subclustering of major cell types, including neutrophil myeloid-derived suppressor cells (MDSCs), regulatory and exhausted T-cells, and LAMP3+ dendritic cells. Markers for the cell types found in OS were identified for further validation using imaging techniques, including Visium spatial transcriptomics. We performed deconvolution using the scRNA-seq cell identities to examine colocalization of discovered cell types. Overall, the discovered clusters were common between patients, showing consistent cell type proportions. However, we found patient-specific differences in the frequency of some cell types, with one sample showing a higher proportion of T-cells along with increased presence of colocalized IFN-stimulated macrophages, and the other with a greater presence of neutrophils/MDSCs. Conclusions - Using single-cell transcriptomics, we were able to discover the presence of multiple immunosuppressive cell subtypes of neutrophils, T-cells, and dendritic cells. Additionally, spatial transcriptomics revealed multiple similar clusters between samples, and common colocalization of the discovered cell types within those clusters. However, differences in T-cell presence and interferon induction may be indicative of patient-specific immunogenicity in osteosarcoma tumors.Competing Interest StatementThe authors have declared no competing interest.Footnotes* Authorship updated, additional funding sources noted.* https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE162454

A study of genome evolution in a metastatic breast cancer bearing an activating PIK3CA mutation, following treatment with the PI(3)Kα inhibitor BYL719, shows that all metastatic lesions, when compared to the pre-treatment tumour, had lost a copy of PTEN; parallel genetic evolution of separate sites with different PTEN genomic alterations had led to a convergent PTEN-null phenotype resistant to PI(3)Kα inhibition. Anticancer resistance due to PTEN loss The emergence and expansion of resistant clonal subpopulations is a major challenge facing the field of targeted therapeutics. Here, the authors study genome evolution in a metastatic breast cancer bearing an activating PIK3CA mutation, following treatment with the phosphatidylinositol-4,5-bisphosphate 3-kinase alpha subunit (PI(3)Kα) selective-inhibitor BYL719. Fourteen metastatic sites were sequenced to reveal that all metastatic lesions, when compared to the pre-treatment tumour, had lost a copy of the gene for the tumour suppressor phosphatase PTEN . Resistance to BYL719 was associated with additional and different PTEN genetic alterations, resulting in loss of PTEN expression. Based on these observations and additional functional characterization, the authors conclude that parallel genetic evolution of separate sites with different PTEN genomic alterations leads to a convergent PTEN-null phenotype resistant to PI(3)Kα inhibition. Broad and deep tumour genome sequencing has shed new light on tumour heterogeneity and provided important insights into the evolution of metastases arising from different clones 1 , 2 . There is an additional layer of complexity, in that tumour evolution may be influenced by selective pressure provided by therapy, in a similar fashion to that occurring in infectious diseases. Here we studied tumour genomic evolution in a patient (index patient) with metastatic breast cancer bearing an activating PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha, PI(3)Kα) mutation. The patient was treated with the PI(3)Kα inhibitor BYL719, which achieved a lasting clinical response, but the patient eventually became resistant to this drug (emergence of lung metastases) and died shortly thereafter. A rapid autopsy was performed and material from a total of 14 metastatic sites was collected and sequenced. All metastatic lesions, when compared to the pre-treatment tumour, had a copy loss of PTEN (phosphatase and tensin homolog) and those lesions that became refractory to BYL719 had additional and different PTEN genetic alterations, resulting in the loss of PTEN expression. To put these results in context, we examined six other patients also treated with BYL719. Acquired bi-allelic loss of PTEN was found in one of these patients, whereas in two others PIK3CA mutations present in the primary tumour were no longer detected at the time of progression. To characterize our findings functionally, we examined the effects of PTEN knockdown in several preclinical models (both in cell lines intrinsically sensitive to BYL719 and in PTEN -null xenografts derived from our index patient), which we found resulted in resistance to BYL719, whereas simultaneous PI(3)K p110β blockade reverted this resistance phenotype. We conclude that parallel genetic evolution of separate metastatic sites with different PTEN genomic alterations leads to a convergent PTEN-null phenotype resistant to PI(3)Kα inhibition.