Pediatric solid tumors arise from endodermal, ectodermal, or mesodermal lineages1. Although the overall survival of children with solid tumors is 75%, that of children with recurrent disease is below 30%2. To capture the complexity and diversity of pediatric solid tumors and establish new models of recurrent disease, we developed a protocol to produce orthotopic patient-derived xenografts (O-PDXs) at diagnosis, recurrence, and autopsy. Tumor specimens were received from 168 patients, and 67 O-PDXs were established for 12 types of cancer. The origins of the O-PDX tumors were reflected in their gene-expression profiles and epigenomes. Genomic profiling of the tumors, including detailed clonal analysis, was performed to determine whether the clonal population in the xenograft recapitulated the patient’s tumor. We identified several drug vulnerabilities and showed that the combination of a WEE1 inhibitor (AZD1775), irinotecan, and vincristine can lead to complete response in multiple rhabdomyosarcoma O-PDX tumors in vivo.

Genomic studies of pediatric cancer have primarily focused on specific tumor types or high-risk disease. Here, we used a three-platform sequencing approach, including whole genome (WGS), exome, and RNA sequencing, to examine tumor and germline genomes from 309 prospectively identified children with newly diagnosed (85%) or relapsed/refractory (15%) cancers, unselected for tumor type. Eighty-six percent of patients harbored diagnostic (53%), prognostic (57%), therapeutically-relevant (25%), and/or cancer predisposing (18%) variants. Inclusion of WGS enabled detection of activating gene fusions and enhancer hijacks (36% and 8% of tumors, respectively), small intragenic deletions (15% of tumors) and mutational signatures revealing of pathogenic variant effects. Evaluation of paired tumor-normal data revealed relevance to tumor development for 55% of pathogenic germline variants. This study demonstrates the power of a three-platform approach that incorporates WGS to interrogate and interpret the full range of genomic variants across newly diagnosed as well as relapsed/refractory pediatric cancers. STATEMENT OF SIGNIFICANCEPediatric cancers are driven by diverse genomic lesions and sequencing has proven useful in evaluating high risk and relapsed/refractory cases. We show that combined whole genome, exome, and RNA-sequencing of tumor and paired normal tissues enables identification and characterization of genetic drivers across the full spectrum of pediatric cancers.Research.

Primitive myxoid mesenchymal tumor of infancy is a rare sarcoma that preferentially affects infants. It can be locally aggressive and rarely metastasizes, but the long-term outcome of children with this tumor is mostly unknown. Histologically, it is characterized by primitive cells with abundant myxoid stroma. Internal tandem duplication of B-cell CLL/lymphoma 6 (BCL6)-interacting co-repressor (BCOR) exon 15 has recently been described in clear cell sarcoma of kidney, central nervous system high-grade neuroepithelial tumor with BCOR alteration, and primitive myxoid mesenchymal tumor of infancy. Herein, we report 5 cases of primitive myxoid mesenchymal tumor of infancy: 3 girls and 2 boys with mean age of 6.5 months. Tumors were located in the paraspinal region (n=3), back (n=1), or foot (n=1) and ranged in size from 2.5 to 10.2 cm. BCOR-internal tandem duplication was confirmed by PCR and sequencing in all 5 cases. The minimally duplicated region consisted of 9 residues, which is shorter than was previously reported in others BCOR-associated tumors. To assess the clinical value and specificity of the BCOR-internal tandem duplication, a group of 11 ETV6-rearranged congenital infantile fibrosarcomas were evaluated and no BCOR-internal tandem duplication was identified in any case. Though not detected in congenital infantile fibrosarcomas, BCOR and BCL6 immunoreactivity was present in >90% of the nuclei of tumor cells in each of the 5 primitive myxoid mesenchymal tumor of infancy. The presence of BCOR-internal tandem duplication in all 5 primitive myxoid mesenchymal tumors of infancy provides evidence it is a recurrent somatic abnormality and substantiates the concept that indeed this tumor is a unique sarcoma of infancy. Our findings indicate that identification of BCOR-internal tandem duplication and/or nuclear immunoreactivity for BCOR or BCL6 can aid in the diagnosis of primitive myxoid mesenchymal tumor of infancy and help to differentiate it from congenital infantile fibrosarcoma.

To discriminate lipomas from atypical lipomatous tumor/well-differentiated liposarcoma (ALT/WDL) we perform fluorescence in situ hybridization (FISH) for MDM2 amplification in several problematic situations: "lipomas" >10 cm, lesions with equivocal atypia, recurrent "lipomas," all retroperitoneal/pelvic/abdominal "lipomas", and in cases not fitting the above criteria but having worrisome clinical or radiologic features. To ascertain the validity of these criteria, we have reviewed our experience with 301 consecutive differentiated lipomatous tumors in which the diagnosis of ALT could not be established on the basis of histologic sections and in which FISH was performed on the basis of the above criteria. The final diagnosis was based on MDM2 amplification status. Given the nature of this study to evaluate difficult lesions, most cases included (74%) were received in consultation. This enhanced our study series for borderline cases, and the data presented may not be generalizable to adipocytic tumors seen outside a subspecialty setting. Of 301 cases, 108 proved to be ALT/WDL (36%). The most common test indication was size >10 cm (n=187), followed by equivocal atypia (n=145), retroperitoneal/pelvic/abdominal location (n=86), recurrence (n=33), and clinical concern (n=12). Of the tumors >10 cm, 68 (36%) proved to be ALT/WDL, whereas the remainder were interpreted as lipoma or its variants (eg, spindle cell or pleomorphic lipoma). The 2 groups did not differ statistically in size, although ALTs consistently occurred in patients above 50 years of age. Of the cases with equivocal atypia, 72 (50%) proved to be ALT/WDL. Those in the retroperitoneum/abdomen/pelvis were ALT/WDL in 30 cases (35%), and those that had recurred were ALT in 18 cases (55%). Recurrence, atypia, and having multiple indications for testing were more common in ALT than in benign lesions (P=0.02, 0.0001, 0.0012, respectively). No ALT/WDL occurred in the hands and feet, and only a single ALT/WDL was superficial (1 ALT/WDL vs. 60 lipoma/spindle cell or pleomorphic lipoma). Small (<10 cm) retroperitoneal tumors without additional features were always benign (n=9). On the basis of our results, FISH testing is recommended for: (1) recurrent lesions; (2) deep extremity lesions that are >10 cm in patients over 50 years of age; (3) in cases with equivocal atypia; (4) in lesions of the retroperitoneum/pelvis/abdomen, and in special clinical situations as directed by treating clinicians. Testing is low yield in superficial lesions, in small extremity lesions without additional indicators for testing, in large extremity lesions without additional features in patients under the age of 50, and in lesions arising in the hands/feet. More evidence is needed regarding testing in small retroperitoneal lesions without additional features. By adopting these criteria, we could have avoided testing 74 cases, missing a single superficial ALT/WDL.

Purpose The clinical features, pathogenesis, and outcomes in children with adrenocortical tumors (ACTs) without germline TP53 mutations have not been systematically studied. Herein, we describe these correlates and analyze their association with outcome. Patients and Methods Genomic DNA was analyzed for TP53, CTNNB1, CDKN1C, ATRX, and chromosome 11p15 abnormalities. β-catenin expression and Ki-67 labeling index (LI) were evaluated by immunostaining. Primary end points were progression-free (PFS) and overall survival. Results Median age of 42 girls and 18 boys was 3.3 years (range, 0.25 to 21.7 years). Complete resection (stages I and II) was achieved in 32 patients, and 28 patients had stage III or IV disease. Constitutional abnormalities of chromosome 11p15 occurred in nine of 40 patients, with six patients not showing phenotype of Beckwith-Wiedemann syndrome. Three-year PFS and overall survival for all patients were 71.4% and 80.5%, respectively. In single-predictor Cox regression analysis, age, disease stage, tumor weight, somatic TP53 mutations, and Ki-67 LI were associated with prognosis. Ki-67 LI and age remained significantly associated with PFS after adjusting for stage and tumor weight. Three-year PFS for 27 patients with Ki-67 LI ≥ 15% was 48.5% compared with 96.2% for 29 patients with Ki-67 LI < 15% (log-rank P = .002), and the rate of relapse increased by 24% with each 1-year increase in age at diagnosis (hazard ratio, 1.24; P = .0057). Conclusion Clinicopathologic features and outcomes of children with ACTs without germline TP53 mutations overlapped those reported for children with germline TP53 mutations. Our findings highlight the central role of genetic or epigenetic alterations on chromosome 11p15 in pediatric ACTs. Ki-67 LI is a strong prognostic indicator and should be investigated to improve the histologic classification of pediatric ACTs.