Differentially methylated regions with at least five CpGs, and a mean difference of greater than 20% between day 14 and baseline white blood cells

Fusion-positive RMS enhancer sites; Universal DNAase-hypersensitivity sites; YES1 and IGF1R region sets

Adverse events possibly, probably, or definitely related to ganitumab across all 28 cycles (maximum grade per patient)

Supplemental methods and figures

Supplemental Protocol Information. A: Study Eligibility; B: Dasatinib dosing nomogram; C: Dasatinib dose modifications

Serial samples demonstrate recurrent loci with copy number alterations for each patient.

Representativeness of Study Participants

Adverse events possibly probably or definitely related to dasatinib across all 28 cycles (maximum grade per patient)

Progression-free survival for full cohort of patients (A) and by dose level (B).

Tumor fractions from plasma cfDNA.

Abstract Purpose: Antibodies against IGF-1R have shown meaningful but transient tumor responses in patients with rhabdomyosarcoma (RMS). The SRC family member YES has been shown to mediate IGF-1R antibody acquired resistance, and cotargeting IGF-1R and YES resulted in sustained responses in murine RMS models. We conducted a phase I trial of the anti-IGF-1R antibody ganitumab combined with dasatinib, a multi-kinase inhibitor targeting YES, in RMS patients (NCT03041701). Patients and Methods: Patients with relapsed/refractory alveolar or embryonal RMS and measurable disease were eligible. All patients received ganitumab 18 mg/kg intravenously every 2 weeks. Dasatinib dose was 60 mg/m2/dose (max 100 mg) oral once daily [dose level (DL)1] or 60 mg/m2/dose (max 70 mg) twice daily (DL2). A 3+3 dose escalation design was used, and maximum tolerated dose (MTD) was determined based on cycle 1 dose-limiting toxicities (DLTs). Results: Thirteen eligible patients, median age 18 years (range 8-29) enrolled. Median number of prior systemic therapies was 3; all had received prior radiation. Of 11 toxicity-evaluable patients, 1/6 had a DLT at DL1 (diarrhea) and 2/5 had a DLT at DL2 (pneumonitis, hematuria) confirming DL1 as MTD. Of nine response-evaluable patients, one had a confirmed partial response (PR) for four cycles, and one had stable disease (SD) for six cycles. Genomic studies from cell-free DNA correlated with disease response. Conclusions: The combination of dasatinib 60 mg/m2/dose daily and ganitumab 18 mg/kg every two weeks was safe and tolerable. This combination had a disease control rate of 22% at five months.

Ingenuity Pathway Analysis of RNAseq data.

Supplementary figure 1. The protein levels of SLFN11 in 25 EWS-FLI1-expressing cells (black) and 4 EWS-ERG-expressing cells (red) were detected by Western blotting using antibodies against SLFN11 (98 kDa) and actin (42 kDa, loading control). The relative SLFN11 levels of each cell line were normalized to actin levels and the SLFN11/actin ratio of TC-106 was set as 1.

Supplementary Tables 1-3 from Genome-Wide Identification of PAX3-FKHR Binding Sites in Rhabdomyosarcoma Reveals Candidate Target Genes Important for Development and Cancer

Supplementary Tables S1-S3 from A Pilot Study of Consolidative Immunotherapy in Patients with High-Risk Pediatric Sarcomas

Supplementary Methods and Supplementary Figures

Primary screening data, Lead candidates and GO analysis

AbstractPurpose: Succinate dehydrogenase (dSDH)-deficient tumors, including pheochromocytoma/paraganglioma, hereditary leiomyomatosis and renal cell cancer–associated renal cell carcinoma (HLRCC-RCC), and gastrointestinal stromal tumors (GIST) without KIT or platelet-derived growth factor receptor alpha mutations are often resistant to cytotoxic chemotherapy, radiotherapy, and many targeted therapies. We evaluated guadecitabine, a dinucleotide containing the DNA methyltransferase inhibitor decitabine, in these patient populations. Patients and Methods: Phase II study of guadecitabine (subcutaneously, 45 mg/m2/day for 5 consecutive days, planned 28-day cycle) to assess clinical activity (according to RECISTv.1.1) across three strata of patients with dSDH GIST, pheochromocytoma/paraganglioma, or HLRCC-RCC. A Simon optimal two-stage design (target response rate 30% rule out 5%) was used. Biologic correlates (methylation and metabolites) from peripheral blood mononuclear cells (PBMC), serum, and urine were analyzed. Results: Nine patients (7 with dSDH GIST, 1 each with paraganglioma and HLRCC-RCC, 6 females and 3 males, age range 18–57 years) were enrolled. Two patients developed treatment-limiting neutropenia. No partial or complete responses were observed (range 1–17 cycles of therapy). Biologic activity assessed as global demethylation in PBMCs was observed. No clear changes in metabolite concentrations were observed. Conclusions: Guadecitabine was tolerated in patients with dSDH tumors with manageable toxicity. Although 4 of 9 patients had prolonged stable disease, there were no objective responses. Thus, guadecitabine did not meet the target of 30% response rate across dSDH tumors at this dose, although signs of biologic activity were noted.

YEST348I expression rescues Dasatinib treatment in aRMS cells.

Supplementary Table S1. Evaluation of drug combinations in TC32 and TC71 Ewing sarcoma cells; Supplementary Table S2. Evaluation of drug combinations in EW8 Ewing sarcoma cells.