Multi-institutional Characterization of Outcomes for Pediatric and Young Adult Patients With High-Risk Myxopapillary Ependymoma After Radiation Therapy

PURPOSE

Myxopapillary ependymoma (MPE) is a rare, typically slow-growing subtype of spinal ependymomas. There are no standard guidelines for radiotherapy and long-term outcomes after radiation, particularly patterns of relapse, for pediatric and young adult (YA) patients with MPE remain under-characterized.

METHODS AND MATERIALS

This is an Institutional Review Board-approved multi-institutional retrospective cohort study of 60 pediatric and YA patients diagnosed with MPE and received radiotherapy between 2000-2020. Clinical and treatment characteristics, and long-term outcomes were recorded. Site(s) of progression was compared to radiation fields. Survival outcomes were analyzed using Kaplan-Meier method. Cumulative incidence of local in-field progression (CILP) after initial radiotherapy was analyzed using Gray's method with out-of-field-only progression as a competing risk. Univariate analyses were performed using Cox proportional hazard's model.

RESULTS

The median age at radiation was 14.8 years (range: 7.1-26.5). At time of radiotherapy, 45 (75.0%) and 35 (58.3%) patients had gross residual and multifocal disease, respectively. Forty-eight (80.0%), seven (11.7%) and five (8.3%) patients received involved field radiotherapy, craniospinal irradiation, and whole spine radiation, respectively. Median follow-up from end of radiotherapy was 6.2 years (range: 0.6-21.0). Five-year overall survival, progression-free survival, and CILP were 100%, 60.8% and 4.1%, respectively. Both local recurrences were at sites of gross residual disease. Of the eighteen out-of-field first recurrences after radiotherapy, all were superior to the initial treatment field and nine had intracranial relapse. On univariate analyses, distant-only recurrence before radiation (HR: 4.00, 95% CI: 1.54-10.43, p = 0.005) was significantly associated with shorter time to progression.

CONCLUSIONS

While the risk of recurrence within the radiation field is low, pediatric and YA patients with high-risk MPE remain at risk for recurrences in the spine above the radiation field and intracranially after radiotherapy. Future prospective studies are needed to investigate the appropriate radiation field and dose based on the extent of metastases.

Genetic susceptibility to cognitive decline following craniospinal irradiation for pediatric central nervous system tumors

BACKGROUND

Survivors of pediatric central nervous system (CNS) tumors treated with craniospinal irradiation (CSI) exhibit long-term cognitive difficulties. Goals of this study were to evaluate longitudinal effects of candidate and novel genetic variants on cognitive decline following CSI.

METHODS

Intelligence quotient (IQ), working memory (WM), and processing speed (PS) were longitudinally collected from patients treated with CSI (n = 241). Genotype-by-time interactions were evaluated using mixed-effects linear regression to identify common variants (minor allele frequency > 1%) associated with cognitive performance change. Novel variants associated with cognitive decline (P < 5 × 10-5) in individuals of European ancestry (n = 163) were considered replicated if they demonstrated consistent genotype-by-time interactions (P < .05) in individuals of non-European ancestries (n = 78) and achieved genome-wide statistical significance (P < 5 × 10-8) in a meta-analysis across ancestry groups.

RESULTS

Participants were mostly males (65%) diagnosed with embryonal tumors (98%) at a median age of 8.3 years. Overall, 1150 neurocognitive evaluations were obtained (median = 5, range: 2-10 per participant). One of the five loci previously associated with cognitive outcomes in pediatric CNS tumors survivors demonstrated significant time-dependent IQ declines (PPARA rs6008197, P = .004). Two variants associated with IQ in the general population were associated with declines in IQ after Bonferroni correction (rs9348721, P = 1.7 × 10-5; rs31771, P = 7.8 × 10-4). In genome-wide analyses, we identified novel loci associated with accelerated declines in IQ (rs116595313, meta-P = 9.4 × 10-9), WM (rs17774009, meta-P = 4.2 × 10-9), and PS (rs77467524, meta-P = 1.5 × 10-8; rs17630683, meta-P = 2.0 × 10-8; rs73249323, meta-P = 3.1 × 10-8).

CONCLUSIONS

Inherited genetic variants involved in baseline cognitive functioning and novel susceptibility loci jointly influence the degree of treatment-associated cognitive decline in pediatric CNS tumor survivors.

Prognostic factors for pediatric, adolescent, and young adult patients with non-DIPG grade 4 gliomas: a contemporary pooled institutional experience

PURPOSE

WHO grade 4 gliomas are rare in the pediatric and adolescent and young adult (AYA) population. We evaluated prognostic factors and outcomes in the pediatric versus AYA population.

METHODS

This retrospective pooled study included patients less than 30 years old (yo) with grade 4 gliomas treated with modern surgery and radiotherapy. Overall survival (OS) and progression-free survival (PFS) were characterized using Kaplan-Meier and Cox regression analysis.

RESULTS

Ninety-seven patients met criteria with median age 23.9 yo at diagnosis. Seventy-seven patients were ≥ 15 yo (79%) and 20 patients were < 15 yo (21%). Most had biopsy-proven glioblastoma (91%); the remainder had H3 K27M-altered diffuse midline glioma (DMG; 9%). All patients received surgery and radiotherapy. Median PFS and OS were 20.9 months and 79.4 months, respectively. Gross total resection (GTR) was associated with better PFS in multivariate analysis [HR 2.00 (1.01-3.62), p = 0.023]. Age ≥ 15 yo was associated with improved OS [HR 0.36 (0.16-0.81), p = 0.014] while female gender [HR 2.12 (1.08-4.16), p = 0.03] and DMG histology [HR 2.79 (1.11-7.02), p = 0.029] were associated with worse OS. Only 7% of patients experienced grade 2 toxicity. 62% of patients experienced tumor progression (28% local, 34% distant). Analysis of salvage treatment found that second surgery and systemic therapy significantly improved survival.

CONCLUSION

Age is a significant prognostic factor in WHO grade 4 glioma, which may reflect age-related molecular alterations in the tumor. DMG was associated with worse OS than glioblastoma. Reoperation and systemic therapy significantly increased survival after disease progression. Prospective studies in this population are warranted.

Circulating tumor DNA sequencing of pediatric solid and brain tumor patients: An institutional feasibility study

The potential of circulating tumor DNA (ctDNA) analysis to serve as a real-time "liquid biopsy" for children with central nervous system (CNS) and non-CNS solid tumors remains to be fully elucidated. We conducted a study to investigate the feasibility and potential clinical utility of ctDNA sequencing in pediatric patients enrolled on an institutional clinical genomics trial. A total of 240 patients had tumor DNA profiling performed during the study period. Plasma samples were collected at study enrollment from 217 patients and then longitudinally from a subset of patients. Successful cell-free DNA extraction and quantification occurred in 216 of 217 (99.5%) of these initial samples. Twenty-four patients were identified whose tumors harbored 30 unique variants that were potentially detectable on a commercially-available ctDNA panel. Twenty of these 30 mutations (67%) were successfully detected by next-generation sequencing in the ctDNA from at least one plasma sample. The rate of ctDNA mutation detection was higher in patients with non-CNS solid tumors (7/9, 78%) compared to those with CNS tumors (9/15, 60%). A higher ctDNA mutation detection rate was also observed in patients with metastatic disease (9/10, 90%) compared to non-metastatic disease (7/14, 50%), although tumor-specific variants were detected in a few patients in the absence of radiographic evidence of disease. This study illustrates the feasibility of incorporating longitudinal ctDNA analysis into the management of relapsed or refractory patients with childhood CNS or non-CNS solid tumors.

Intensive Multimodality Therapy for Extraocular Retinoblastoma: A Children's Oncology Group Trial (ARET0321)

PURPOSE

Metastatic retinoblastoma has a poor prognosis when treated with conventional chemotherapy and radiation therapy (RT). Intensified therapy may improve the outcome.

METHODS

A prospective, international trial enrolled patients with extraocular retinoblastoma. Patients with stage II or III (locoregional) retinoblastoma received four cycles of chemotherapy, followed by involved field RT (45 Gy). Patients with stage IVa or IVb (metastatic or trilateral) retinoblastoma also received four cycles of chemotherapy and those with ≥ partial response then received one cycle of high-dose carboplatin, thiotepa, and etoposide with autologous hematopoietic stem-cell support. Patients with stage IVa or IVb with residual tumor postchemotherapy received RT. The proportion of patients who achieved event-free survival would be reported and compared with historical controls separately for each of the three groups of patients.

RESULTS

Fifty-seven eligible patients were included in the analyses. Event-free survival at 1 year was 88.1% (90% CI, 66.6 to 96.2) for stage II-III, 82.6% (90% CI, 61.0 to 92.9) for stage IVa, and 28.3% (90% CI, 12.7 to 46.2) for stage IVb/trilateral. Toxicity was significant as expected and included two therapy-related deaths.

CONCLUSION

Intensive multimodality therapy is highly effective for patients with regional extraocular retinoblastoma and stage IVa metastatic retinoblastoma. Although the study met its aim for stage IVb, more effective therapy is still required for patients with CNS involvement (ClinicalTrials.gov identifier: NCT00554788).

Cerebellar Mutism Syndrome in Pediatric Neuro-oncology: A Multidisciplinary Perspective and Call for Research Priorities

Cerebellar mutism syndrome (CMS), also known as posterior fossa syndrome, occurs in a subset of children after posterior fossa tumor resection, most commonly medulloblastoma. Patients with this syndrome exhibit often transient, although protracted, symptoms of language impairment, emotional lability, cerebellar, and brainstem dysfunction. However, many patients experience persistent neurological deficits and lasting neurocognitive impairment. Historically, research and clinical care were hindered by inconsistent nomenclature, poorly defined diagnostic criteria, and uncertainty surrounding risk factors and etiology. Proposed diagnostic criteria include two major symptoms, language impairment and emotional lability, as proposed by the international Board of the Posterior Fossa Society in their consensus statement as well as other experts in this field. Risk factors most commonly associated with development of CMS include midline tumor location, diagnosis of medulloblastoma and specific tumor subtype, younger age at diagnosis, and preoperative language impairment. A proposed etiology of CMS includes disruption of the cerebellar outflow tracts, the cerebellar nuclei, and their efferent projections through the superior cerebellar peduncle. Treatment for CMS remains supportive. Herein, we present a comprehensive overview of CMS etiology, diagnosis, risk factors, clinical presentation, and clinical management. In addition, we identify essential multidisciplinary research priorities to advance diagnostics, prevention, and intervention efforts for patients with, or at risk for, development of CMS.

Outcomes of patients with bilateral retinoblastoma: A report from the RIVERBOAT Consortium

10045

Background: Retinoblastoma (RB) is the most common tumor of the eye in childhood. Intraocular RB cure rates approach 100%. Therefore, treatment advances have focused on globe salvage preserving functional vision. The Research Into Visual Endpoints and RB Health Outcomes After Treatment (RIVERBOAT) consortium was established to examine patient health outcomes, including vision, in the contemporary therapy era. Methods: Patients with RB treated at consortium centers from 2007 to the present were identified. Medical record abstraction was performed for disease presentation, treatment, and outcomes. A subset of the patients returned to centers and completed functional vision questionnaires (Child Vision Function Questionnaire for ages 0 – 7 and Cardiff Visual Ability Questionnaire for Children for ages >8) and had visual acuity assessed. For participants who could not yet return for a study evaluation, medical record abstraction alone was performed. Results: Among 463 participants enrolled to date, 193 (42%) had bilateral disease. Two each had metastatic RB, trilateral RB, and secondary osteosarcoma. One patient each with metastatic RB and trilateral RB is deceased, with overall survival for the cohort of 99%. The eye group distribution (International Intraocular Retinoblastoma Classification) was 14% A, 22% B, 14% C, 28% D, 19% E and 3% not classified. Primary enucleation was performed in 43 (22%), secondary enucleation in 48 (25%) and bilateral enucleation in 1(0.5%). Intravenous chemotherapy (IV) alone was administered in 58%, intra-arterial chemotherapy (IAC) alone in 4%, with 31% receiving both. Among 145 patients who did not require secondary or bilateral enucleation, the distribution was 16% A, 21% B, 16% C, 28% D, 15% E, and 4% non-classified eyes. This salvage was achieved with IV alone, IAC alone, or both in 55%, 5% and 30% respectively and with ophthalmic therapy only in 10%. The mean percentage of patients receiving IAC per year increased from 6% in 2008 – 2013 to 11% in 2014 – 2022 and was stable at 11% in 2018 – 2022. Among 53 patients who have reported functional vision to date, the mean scores were 0.81 for < 3 years 0.80 for 3-7 years and -1.31 for those >8 years, all considered to be good functional vision. Among 50 eyes in 37 of these 53 patients, 33 had normal vision (20/20-20/40) across A to E groups. Moderate vision loss (> 20/40 – 20/70) was noted in 1 C and 1 B eye and low vision (> 20/70 - < 20/200) in 6 group B, C or D eyes. Nine B or D eyes were legally blind (>20/200). No patients had two legally blind eyes. Conclusions: In this cohort of RB patients with bilateral disease treated between 2007 and 2022, 52% have been successfully treated without enucleation. Self-reported functional vision in 53 of these patients with all group eyes was good. Only 6 of 50 eyes in 37 patients met criteria for legal blindness and 66% of eyes had normal vision. With cohort accrual ongoing, we will determine if these promising outcomes continue.

Outcomes of patients with unilateral retinoblastoma: A report from the RIVERBOAT Consortium

10046

Background: Retinoblastoma (RB) is the most common tumor of the eye in childhood. Intraocular RB cure rates approach 100%. Therefore, treatment now focuses on globe salvage preserving functional vision. The Research Into Visual Endpoints and RB Health Outcomes After Treatment (RIVERBOAT) consortium was established to examine patient health outcomes, including vision, in the contemporary therapy era. Methods: Patients with RB treated at consortium centers from 2007 to present were identified. Medical record abstraction was performed for disease presentation, treatment, and outcomes. A subset of the patients returned to centers and completed functional vision questionnaires (Child Vision Function Questionnaire - ages 0 – 7 and Cardiff Visual Ability Questionnaire for Children - ages > 8) and had visual acuity assessed. For participants who could not yet return for a study evaluation, medical record abstraction alone was performed. Results: Among 463 participants enrolled to date, 270 (58%) had unilateral disease. One patient with metastatic RB did not survive, resulting in overall survival of 99.6. There was one case of secondary leukemia. The eye group distribution (International Intraocular Retinoblastoma Classification) was 0.4% A, 5.6% B, 7.0% C, 36.0% D, 49.0% E and 2.0% not classified. 131 (49%) patients underwent primary enucleation and are not included in further analyses. Among the remaining 139 patients, 3% were treated with local ophthalmic therapy only, 22% with intravenous chemotherapy (IV) only, 53% with intra-arterial chemotherapy (IAC) only, 22% with IV and IAC, and 35% required secondary enucleation. Globe salvage after chemotherapy was successful in 100% A, 93% B, 82% C, 72% D, and 48% E eyes. This salvage was achieved with IV only, IAC only, or both in 22%, 58% and 20% respectively. The mean percentage of patients receiving IAC per year increased from 13% (2008 – 2013) to 21% (2014 – 2017) to 28% (2018 – 2022). In 29 patients without enucleation who reported functional vision to date, the mean scores (survey theoretical ranges) were 0.72 for < 3 years (0.57 to 0.87), 0.82 for 3 -7 years (0.56 to 0.94) and -2.72 for > 8 years (-2.53 to -0.51), all considered good functional vision. In 20 of these 29 patients, 4 eyes had normal vision (20/20-20/40) across A to D groups. Moderate vision loss (> 20/40 – 20/70) was noted in 3 D eyes and low vision (> 20/70 - < 20/200) in 1 D eye. Twelve B through E eyes met criteria for a legally blind eye (>20/200). Conclusions: In this cohort of RB patients with unilateral disease treated from 2007 - 2022, 66% required primary or secondary enucleation. Among 29 patients with globe salvage, self-reported functional vision was good, but 12 eyes in 20 of the patients were legally blind. IAC only or IV plus IAC was most used in those who avoided secondary enucleation. With ongoing cohort accrual and increased IAC use, it will remain to be determined if globe salvage with functional vision will improve.

Outcomes based on histopathologic response to preoperative chemotherapy in children with bilateral Wilms tumor: A prospective study (COG AREN0534)

BACKGROUND

An objective of the Children's Oncology Group AREN0534 Study was to improve the survival of patients with bilateral Wilms tumors (BWT) by using preoperative chemotherapy of limited duration and tailoring postoperative therapy based on histopathologic response. The authors report outcomes based on postoperative histopathologic responses.

METHODS

Patients with BWT received treatment with vincristine, dactinomycin, and doxorubicin for 6 or 12 weeks followed by surgery. Postoperative therapy was prescribed based on the highest risk tumor according to the International Society of Pediatric Oncology classification and the Children's Oncology Group staging system.

RESULTS

Analyses were performed on data from 180 evaluable children. The 4-year event-free survival (EFS) and overall survival (OS) rates were 81% (95% CI, 74%-87%) and 95% (95% CI, 91%-99%), respectively. Seven patients who had completely necrotic tumors had a 4-year EFS rate of 100%. Of 118 patients who had tumors with intermediate-risk histopathology, the 4-year EFS and OS rates were 82% (95% CI, 74%-90%) and 97% (95% CI, 94%-100%), respectively. Fourteen patients who had blastemal-type tumors had 4-year EFS and OS rates of 79% (95% CI, 56%-100%) and 93% (95% CI, 79%-100%), respectively. Eighteen patients who had diffuse anaplasia had 4-year EFS and OS rates of 61% (95% CI, 35%-88%) and 72% (95% CI, 47%-97%), respectively; and the 4-year EFS and OS rates of 7 patients who had focal anaplasia were 71% (95% CI, 38%-100%) and 100%, respectively. There was no difference in the outcomes of patients who had different histopathologic subtypes within the intermediate-risk group (P = .54).

CONCLUSIONS

A risk-adapted treatment approach for BWT results in excellent outcomes. This approach was not successful in improving the outcome of patients who had diffuse anaplasia.

Quantifying the risk and dosimetric variables of symptomatic brainstem injury after proton beam radiation in pediatric brain tumors

BACKGROUND

Brainstem toxicity after radiation therapy (RT) is a devastating complication and a particular concern with proton radiation (PBT). We investigated the incidence and clinical correlates of brainstem injury in pediatric brain tumors treated with PBT.

METHODS

All patients <21 years with brain tumors treated with PBT at our institution from 2007-2019, with a brainstem Dmean >30 Gy and/or Dmax >50.4 Gy were included. Symptomatic brainstem injury (SBI) was defined as any new or progressive cranial neuropathy, ataxia, and/or motor weakness with corresponding radiographic abnormality within brainstem.

RESULTS

A total of 595 patients were reviewed and 468 (medulloblastoma = 200, gliomas = 114, ependymoma = 87, ATRT = 43) met our inclusion criteria. Median age at RT was 6.3 years and median prescribed RT dose was 54Gy [RBE]. Fifteen patients (3.2%) developed SBI, at a median of 4 months after RT. Grades 2, 3, 4, and 5 brainstem injuries were seen in 7, 5, 1, and 2 patients respectively. Asymptomatic radiographic changes were seen in 51 patients (10.9%). SBI was significantly higher in patients with age ≤3 years, female gender, ATRT histology, patients receiving high-dose chemotherapy with stem cell rescue, and those not receiving craniospinal irradiation. Patients with SBI had a significantly higher V50-52. In 2014, our institution started using strict brainstem dose constraints (Dmax ≤57 Gy, Dmean ≤52.4 Gy, and V54≤10%). There was a trend towards decrease in SBI from 4.4% (2007-2013) to 1.5% (2014-2019) (P = .089) without affecting survival.

CONCLUSION

Our results suggest a low risk of SBI after PBT for pediatric brain tumors, comparable to photon therapy. A lower risk was seen after adopting strict brainstem dose constraints.

Kidney Preservation and Wilms Tumor Development in Children with Diffuse Hyperplastic Perilobar Nephroblastomatosis: A Report from the Children’s Oncology Group Study AREN0534

INTRODUCTION

Diffuse hyperplastic perilobar nephroblastomatosis (DHPLN) represents a unique category of nephroblastomatosis. Treatment has ranged from observation to multiple regimens of chemotherapy. Wilms tumors (WTs) develop in 100% of untreated patients and between 32 and 52% of treated patients. Renal preservation rates have not been previously reported. An aim of the Children's Oncology Group (COG) study AREN0534 was to prospectively evaluate the efficacy of chemotherapy in preserving renal units and preventing WT development in children with DHPLN.

METHODS

Patients were enrolled through the COG protocol AREN03B2 with central radiological review. DHPLN was defined as the cortical surface of the kidney being composed of hyperplastic rests, with the entire nephrogenic zone involved, and with a thick rind capping all of one or both kidneys. Treatment was with vincristine and dactinomycin (regimen EE4A), with cross-sectional imaging at weeks 6 and 12. If the patient's disease was stable or decreasing, treatment was continued for 19 weeks. Renal preservation, WT development rates at 1 year, and overall survival (OS) are reported.

RESULTS

Nine patients were enrolled (five females and four males), with a median age at enrollment of 10.22 months (range 2.92-29.11). One patient who was enrolled was deemed unevaluable because they did not meet the radiological criteria for DHPLN, resulting in eight evaluable patients. These eight patients had DHPLN confirmed via radiological criteria (all bilateral). Initial chemotherapy was EE4A for all eight patients, with seven of eight patients starting chemotherapy without tissue diagnosis.One patient who had an upfront partial nephrectomy was found to have DHPLN in the specimen and was subsequently treated with EE4A. All patients remained alive, with a median follow-up of 6.6 years (range 4.5-9.1). No patients were anephric; 14 of 16 kidneys were functioning (87.5%). Six of eight patients (75%) did not have WT on therapy, but two of these patients relapsed within 6 months of stopping therapy; both had favorable histology WT. One patient who was diagnosed with WT on therapy relapsed at 12 months (one of eight [12.5%]) and developed anaplastic histology.

CONCLUSIONS

Chemotherapy for patients with DHPLN was effective in preserving kidney function. Five-year OS is excellent, however the ideal type and duration of chemotherapy to prevent WT development remains elusive.

Gadolinium is not necessary for surveillance MR imaging in children with chiasmatic-hypothalamic low-grade glioma

BACKGROUND

Patients with chiasmatic-hypothalamic low-grade glioma (CHLGG) have frequent MRIs with gadolinium-based contrast agents (GBCA) for disease monitoring. Cumulative gadolinium deposition in the brains of children is a potential concern. The purpose of this study is to evaluate whether MRI with GBCA is necessary for determining radiographic tumor progression in children with CHLGG.

METHODS

Children who were treated for progressive CHLGG from 2005 to 2019 at Texas Children's Cancer Center were identified. Pre- and post-contrast MRI sequences were separately reviewed by one neuroradiologist who was blinded to the clinical course. Three dimensional measurements and tumor characteristics were evaluated. Radiographic progression was defined as a 25% increase in size (product of two largest dimensions) compared with baseline or best response after initiation of therapy.

RESULTS

A total of 28 patients with progressive CHLGG were identified with a total of 683 MRIs with GBCA reviewed (mean 24 MRIs/patient; range, 11-43 MRIs). Radiographic progression was observed 92 times, 91 (99%) on noncontrast and 90 (98%) on contrast imaging. Sixty-seven progressions necessitating management changes were identified in all (100%) noncontrast sequences and 66 (99%) contrast sequences. Tumor growth > 2 mm in any dimension was identified in 184/187 (98%) noncontrast and 181/187 (97%) with contrast imaging. Metastatic tumors were better visualized on contrast imaging in 4/7 (57%).

CONCLUSION

MRI without GBCA effectively identifies patients with progressive disease. When imaging children with CHLGG, eliminating GBCA should be considered unless monitoring patients with metastatic disease.

ZFTA-RELA Dictates Oncogenic Transcriptional Programs to Drive Aggressive Supratentorial Ependymoma

More than 60% of supratentorial ependymomas harbor a ZFTA-RELA (ZRfus) gene fusion (formerly C11orf95-RELA). To study the biology of ZRfus, we developed an autochthonous mouse tumor model using in utero electroporation (IUE) of the embryonic mouse brain. Integrative epigenomic and transcriptomic mapping was performed on IUE-driven ZRfus tumors by CUT&RUN, chromatin immunoprecipitation sequencing, assay for transposase-accessible chromatin sequencing, and RNA sequencing and compared with human ZRfus-driven ependymoma. In addition to direct canonical NFκB pathway activation, ZRfus dictates a neoplastic transcriptional program and binds to thousands of unique sites across the genome that are enriched with PLAGL family transcription factor (TF) motifs. ZRfus activates gene expression programs through recruitment of transcriptional coactivators (Brd4, Ep300, Cbp, Pol2) that are amenable to pharmacologic inhibition. Downstream ZRfus target genes converge on developmental programs marked by PLAGL TF proteins, and activate neoplastic programs enriched in Mapk, focal adhesion, and gene imprinting networks. SIGNIFICANCE: Ependymomas are aggressive brain tumors. Although drivers of supratentorial ependymoma (ZFTA- and YAP1-associated gene fusions) have been discovered, their functions remain unclear. Our study investigates the biology of ZFTA-RELA-driven ependymoma, specifically mechanisms of transcriptional deregulation and direct downstream gene networks that may be leveraged for potential therapeutic testing.This article is highlighted in the In This Issue feature, p. 2113.

Disease Control and Patterns of Failure After Proton Beam Therapy for Rhabdomyosarcoma

PURPOSE

Pediatric patients with rhabdomyosarcoma (RMS) are treated with multimodal therapy, often with radiation therapy (RT) as part of local therapy. We report on the efficacy and patterns of failure after proton beam therapy (PBT) for RMS.

METHODS AND MATERIALS

Between January 2006 and February 2017, patients with RMS were enrolled in a prospective institutional review board-approved registry protocol for pediatric patients undergoing PBT. Demographics, clinical characteristics, and treatment related outcomes were reviewed.

RESULTS

Ninety-four RMS patients were treated with a combination of chemotherapy (CT) and PBT. The majority of patients had head and neck (49%) and genitourinary (30%) primaries. Median tumor size was 4.1 cm (range, 1.0-16.5 cm); 33 patients (35%) had primary tumors >5 cm. Median cyclophosphamide equivalent dose was 14.4 g/m² (range, 0-30.8 g/m²). Median time from CT initiation to RT initiation was 13 weeks (range, 1-58 weeks). With median follow-up of 4 years, 4-year overall survival (OS) was 71%, and 4-year progression-free survival (PFS) was 63%. Thirty patients (32%) experienced relapse (13% with local failure [LF]). Four-year local control (LC) was 85% overall; 4-year LC rates were 100% for low-risk, 85% for intermediate-risk, and 55% for high-risk patients (P = .02). Tumor size predicted LC (P = .007), with 7% versus 33% LF rate by tumor size (≤5 cm vs >5 cm). Delayed RT delivery (≥13 weeks from initiation of CT) predicted worse LC (P = .01). Increased tumor size predicted both inferior PFS (P = .02) and OS (P = .01). Delayed RT delivery predicted both inferior PFS (P = .04) and OS (P = .03).

CONCLUSIONS

PBT provides LC comparable to prior studies using photon RT. Inferior LC, PFS, and OS rates were observed for patients with larger tumors and those treated with delayed RT. This finding supports ongoing prospective efforts to dose-escalate treatment of tumors >5 cm; however, these data call into question the optimal timing of local therapy, particularly for patients treated with reduced-dose cyclophosphamide.

Overall survival and secondary malignant neoplasms in children receiving passively scattered proton or photon craniospinal irradiation for medulloblastoma

BACKGROUND

Both intensity-modulated radiotherapy (RT) and passively scattered proton therapy have a risk of secondary malignant neoplasm (SMN) in children. To determine the influence of RT modality on the incidence of SMN after craniospinal irradiation (CSI), the authors compared the incidence of SMN in children who had medulloblastoma treated with either photon CSI plus an intensity-modulated RT boost (group I) or passively scattered proton CSI plus a boost (group II).

METHODS

From 1996 to 2014, 115 children with medulloblastoma (group I, n = 63; group II, n = 52) received CSI followed by a boost to the tumor bed. Most patients had standard-risk disease (63.5%). The median follow-up was 12.8 years for group I and 8.7 years for group II.

RESULTS

The 5-year and 10-year overall survival (OS) rates were 88.8% and 85.1%, respectively, for standard-risk patients and 63.1% and 57.3%, respectively, for high-risk patients, with no OS difference by RT modality (P = .81). Six SMNs were identified (4 in group I, 2 in group II). The 5-year and 10-year SMN incidence rates were 1.0% and 6.9%, respectively (0.0% and 8.0%, respectively, in group I; 2.2% and 4.9%, respectively, in group II; P = .74). Two SMNs occurred in the clinical target volume in the brain, 2 occurred in the exit dose region from the photon spinal field, 1 occurred in the entrance path of a proton beam, and 1 occurred outside the radiation field. There were no reported cases of secondary leukemia.

CONCLUSIONS

This analysis demonstrates no difference in OS or SMN incidence between patients in groups I and II 10 years after RT.

LAY SUMMARY

One hundred fifteen children with medulloblastoma received radiotherapy (RT) with either photon craniospinal irradiation (CSI) and an intensity-modulated RT boost (group I; n = 63) or passively scattered proton CSI and a boost (group II;, n = 52). The majority of children had standard-risk disease (63.5%). The 5-year and 10-year overall survival rates were 88.8% and 85.1% for standard-risk patients, respectively, and 63.1% and 57.3% for high-risk patients, respectively, with no difference in overall survival by RT group (P = .81). The 5-year and 10-year second malignant neoplasm incidence rates were 1.0% and 6.9%, respectively, with no difference in second malignant neoplasm incidence according to RT group (P = .74).

Response criteria for intraocular retinoblastoma: RB-RECIST

Standardized guidelines for assessing tumor response to therapy are essential for designing and conducting clinical trials. The Response Evaluation Criteria In Solid Tumors (RECIST) provide radiological standards for assessment of solid tumors. However, no such guidelines exist for the evaluation of intraocular cancer, and ocular oncology clinical trials have largely relied on indirect measures of therapeutic response-such as progression-free survival-to evaluate the efficacy of treatment agents. Herein, we propose specific criteria for evaluating treatment response of retinoblastoma, the most common pediatric intraocular cancer, and emphasize a multimodal imaging approach for comprehensive assessment of retinoblastoma tumors in clinical trials.

Early radiotherapy preserves vision in sporadic optic pathway glioma

BACKGROUND

Sporadic optic pathway/hypothalamic gliomas represent a unique entity within pediatric low-grade glioma. Despite favorable survival, location makes treatment difficult and local progression debilitating. This study is a longitudinal assessment of visual acuity (VA) among children treated within the last 2 decades.

METHODS

Clinical characteristics were abstracted for patients treated from 2000 to 2018 at Texas Children's Cancer Center in Houston. Ophthalmologic data taken at 3- to 6-month intervals were examined with age-appropriate VA metrics converted to the LogMAR (logarithm of the minimum angle of resolution) scale. Kaplan-Meier blindness-free survival (BFS) curves, calculated as time-to-bilateral functional blindness (LogMAR ≥0.8 in both eyes), were calculated for patients receiving early radiation therapy (RT; upfront or as first-line salvage treatment) or chemotherapy (CT) and evaluated using the log-rank test.

RESULTS

Thirty-eight patients with a median follow-up of 8.5 years (range, 2-17 years) were identified. Median age at diagnosis was 3 years (interquartile range, <1-6 years). Early RT was administered in 11 patients (29%). Twenty-seven patients (71%) were treated primarily with CT, initiated at a median age of 3.5 years (range, <1-11 years). Eight patients in the CT group did eventually require RT secondary to VA loss and following multiple lines of CT. Median age at RT for all patients was 11 years (range, 3-17 years). BFS rates were 81% at 5 years and 60% at 8 years for CT and 100% at 5 and 8 years for early RT (P = .017).

CONCLUSIONS

In a contemporary cohort, early RT, defined as initial or first-line salvage therapy, was found to have superior BFS for appropriately selected patients with sporadic optic pathway/hypothalamic gliomas.

LAY SUMMARY

Children with low-grade brain tumors of the optic pathway generally have excellent long-term survival; however, given the location of these tumors, there can commonly be threatened vision if the tumor grows. Although radiation is generally deferred in children on the basis of legitimate concerns regarding the effects on the developing brain, it may represent a vision-preserving therapy for well-selected older patients.

Observed-to-expected incidence ratios of second malignant neoplasms after radiation therapy for medulloblastoma: A Surveillance, Epidemiology, and End Results analysis

BACKGROUND

The authors analyzed the incidence and types of second malignant neoplasms (SMNs) in patients treated for medulloblastoma.

METHODS

The authors compared the incidence of SMNs after radiotherapy (RT) for medulloblastoma in patients treated in 1973-2014 with the incidence in the general population with the multiple primary-standardized incidence ratio function of Surveillance, Epidemiology, and End Results 9. Observed-to-expected incidence (O/E) ratios and 95% confidence intervals (CIs) were reported for the entire cohort and by disease site according to age at diagnosis, treatment era, and receipt of chemotherapy. P values < .05 were considered statistically significant.

RESULTS

Of the 1294 patients with medulloblastoma who received RT, 68 developed 75 SMNs. The O/E ratio for SMNs among all patients was 4.49 (95% CI, 3.53-5.62; P < .05). The site at highest risk was the central nervous system (CNS; O/E, 40.62; 95% CI, 25.46-61.51), which was followed by the endocrine system (O/E, 15.95; 95% CI, 9.12-25.91), bone (O/E, 14.45; 95% CI, 1.75-52.21), soft tissues (O/E, 9.01; 95% CI, 1.09-32.56), the digestive system (O/E, 5.03; 95% CI, 2.51-9.00), and the lymphatic/hematopoietic system (O/E, 3.37; 95% CI, 1.35-6.94). The O/E ratio was higher for patients given chemotherapy and RT (O/E, 5.52; 95% CI, 3.75-7.83) than for those given RT only (O/E, 3.96; 95% CI, 2.88-5.32).

CONCLUSIONS

Patients with medulloblastoma are at elevated risk for SMNs in comparison with the general population. Variations in O/E for SMNs by organ systems were found for treatment modality, age at diagnosis, and time of diagnosis. The most common site, the CNS, was involved more often in younger patients and those given chemotherapy with RT.

Global health disparities in childhood cancers

PURPOSE OF REVIEW

The high cure rates of children with cancer in high-income countries (HICs) are due to the impact of biomedical innovations on children with highly fatal diseases. We discuss why these innovations have not benefitted most children with cancer globally and propose broad strategies to reduce these disparities.

RECENT FINDINGS

Over 85% of children with cancer in HIC are cured while less than 20% in many low-income countries survive the disease. Hence, childhood cancer survival is poor globally since over 80% of children with cancer live in low-income and middle-income countries (LMICs). Inadequate skilled workforce and health infrastructure across all disciplines of pediatrics in LMIC are the main reasons for these disparities. Although biological differences may contribute to these disparities as well, many are unconfirmed because they are confounded by differences in referral patterns and clinical capacity. HIC partnerships with LMIC that focus on locally based pediatrics training and clinical infrastructure building are beginning to close the gap.

SUMMARY

Pediatric oncology is symbolic of the significant disparities in childhood survival arising from poverty, inadequate pediatric infrastructure, and skilled workforce in LMIC. Partnerships with HIC that build multidisciplinary pediatrics capacity and clinical infrastructure are beginning to make transformative improvements.

PATH-29. HIGH FREQUENCY OF CLINICALLY-RELEVANT TUMOR VARIANTS DETECTED BY MOLECULAR TESTING OF HIGH-RISK PEDIATRIC CNS TUMORS – PRELIMINARY FINDINGS FROM THE TEXAS KidsCanSeq STUDY

BACKGROUND

DNA and RNA-based tumor sequencing tests have the potential to guide the clinical management of children with CNS tumors. However, data describing the utility of these tests are limited.

METHODS

Children with high-risk or recurrent CNS tumors are included in the diverse cohort of patients enrolling in the KidsCanSeq study from six Texas sites. DNA and RNA from FFPE tumor is subjected to targeted sequencing using a 124-gene mutation panel and an 81-gene fusion panel. Tumor capture transcriptome sequencing, exome sequencing, and copy number array (as well as germline panel and exome testing) are also performed. Tumor variants are classified using AMP/ASCO/CAP consensus guidelines.

RESULTS

A total of 74 children with high-risk/recurrent CNS tumors enrolled as of 1/28/20. Targeted tumor DNA and RNA panel testing was completed for 57 patients with varied diagnoses. At least one tumor variant with strong or potential clinical significance was identified in 43 of 57 (75%) tumors, with therapeutic significance in 20 of 57 (35%) tumors. The 38 therapeutically-relevant variants most frequently affected MAPK signaling (BRAF x9, EGFR x3, FGFR2, FGFR3, KRAS, NF1, NTRK2) and the AKT/mTOR pathway (PIK3CA x3, PTEN x2, mTOR, TSC1, PIK3R1). Most had not been detected by prior targeted diagnostic testing (27/38, 71%).

CONCLUSION

Integrated DNA and RNA-based panel testing identified variants with potential to impact clinical decision-making in a majority of children with high-risk/recurrent CNS tumors. The comparative yield of panel testing vs. exome/transcriptome/array will be evaluated in the KidsCanSeq study cohort.

Development of second primary tumors and outcomes in medulloblastoma by treatment modality: A Surveillance, Epidemiology, and End Results analysis

BACKGROUND

As treatment modalities for medulloblastoma have developed and overall survival (OS) has improved, there are relatively limited data on the impact of long-term effects such as risk of second primary tumors (SPT). To address the knowledge gap, we analyzed factors associated with the risk of SPT and OS by treatment modality for medulloblastoma.

METHODS

We queried the Surveillance, Epidemiology, and End Results (SEER)-18 database for patients diagnosed with medulloblastoma in 1973-2014. Patients were then grouped by age, gender, race, geographic region, histology, adjuvant treatment (no radiation [RT] and no chemotherapy [CT], RT and CT, RT alone, or CT alone), era of diagnosis (1973-1994 or 1995-2014), and survival time. Cumulative incidence, factors associated with SPT and OS were analyzed.

RESULTS

Of 2271 patients, 146 developed SPT, of which 42 were benign. The incidence of SPT was 3.1% and 4.9% at 10 and 15 years, respectively. The incidence of SPT was 3.1% with RT + CT versus 3.7% with RT alone at 10 years. The most common site for an SPT was the central nervous system. Female gender (P = 0.01) and longer OS of ≥21 years (P < 0.01) were associated with higher risk of SPT. RT + CT led to better OS than RT only (66.1% and 61.4% vs 55.6% and 49.7% at 10 and 15 years) (P < 0.01).

CONCLUSIONS

Medulloblastoma patients have a relatively low risk of SPT at 10 years with treatment. Use of RT + CT led to better OS with no statistical difference in SPT compared with the RT alone.

Results of Treatment for Patients With Multicentric or Bilaterally Predisposed Unilateral Wilms Tumor (AREN0534): A report from the Children's Oncology Group

BACKGROUND

A primary objective of Children's Oncology Group study AREN0534 (Treatment for Patients With Multicentric or Bilaterally Predisposed, Unilateral Wilms Tumor) was to facilitate partial nephrectomy in 25% of children with bilaterally predisposed unilateral tumors (Wilms tumor/aniridia/genitourinary anomalies/range of developmental delays [WAGR] syndrome; and multifocal and overgrowth syndromes). The purpose of this prospective study was to achieve excellent event-free survival (EFS) and overall survival (OS) while preserving renal tissue through preoperative chemotherapy, completing definitive surgery by 12 weeks from diagnosis, and modifying postoperative chemotherapy based on histologic response.

METHODS

The treating institution identified whether a predisposition syndrome existed. Patients underwent a central review of imaging studies through the biology and classification study AREN03B2 and then were eligible to enroll on AREN0534. Patients were treated with induction chemotherapy determined by localized or metastatic disease on imaging (and histology if a biopsy had been undertaken). Surgery was based on radiographic response at 6 or 12 weeks. Further chemotherapy was determined by histology. Patients who had stage III or IV disease with favorable histology received radiotherapy as well as those who had stage I through IV anaplasia.

RESULTS

In total, 34 patients were evaluable, including 13 males and 21 females with a mean age at diagnosis of 2.79 years (range, 0.49-8.78 years). The median follow-up was 4.49 years (range, 1.67-8.01 years). The underlying diagnosis included Beckwith-Wiedemann syndrome in 9 patients, hemihypertrophy in 9 patients, multicentric tumors in 10 patients, WAGR syndrome in 2 patients, a solitary kidney in 2 patients, Denys-Drash syndrome in 1 patient, and Simpson-Golabi-Behmel syndrome in 1 patient. The 4-year EFS and OS rates were 94% (95% CI, 85.2%-100%) and 100%, respectively. Two patients relapsed (1 tumor bed, 1 abdomen), and none had disease progression during induction. According to Response Evaluation Criteria in Solid Tumor 1.1 criteria, radiographic responses included a complete response in 2 patients, a partial response in 21 patients, stable disease in 11 patients, and progressive disease in 0 patients. Posttherapy histologic classification was low-risk in 13 patients (including the 2 complete responders), intermediate-risk in 15 patients, and high-risk in 6 patients (1 focal anaplasia and 5 blastemal subtype). Prenephrectomy chemotherapy facilitated renal preservation in 22 of 34 patients (65%).

CONCLUSIONS

A standardized approach of preoperative chemotherapy, surgical resection within 12 weeks, and histology-based postoperative chemotherapy results in excellent EFS, OS, and preservation of renal parenchyma.

Patterns of failure and toxicity profile following proton beam therapy for pediatric bladder and prostate rhabdomyosarcoma

PURPOSE/OBJECTIVE(S)

Bladder and prostate are unfavorable sites for rhabdomyosarcoma (B/P-RMS), and represent a challenging location for radiotherapy.

MATERIALS/METHODS

Nineteen patients with B/P-RMS were enrolled on a prospective registry protocol (2008-2017) and treated with chemotherapy, proton beam therapy (PBT), and surgical resection (n = 8; 42%). Emphasis was given to treatment technique, disease-related outcomes, and toxicity associated with PBT.

RESULTS

The majority of patients had bladder RMS (74%) of embryonal histology (95%), Group III (68%), and intermediate-risk disease by Children's Oncology Group (COG) risk stratification (89%). Seven patients (37%) had primary tumors >5 cm in size. All patients were treated according to COG protocols. With a median follow-up of 66.2 months, 5-year overall survival (OS) and progression-free survival (PFS) were 76%. Four patients (21%) experienced disease relapse, all presenting with local failure. The 5-year local control (LC) rate was 76%. Tumor size predicted LC, with 5-year LC for patients with >5 cm tumors being 43% versus 100% for those with ≤5 cm tumors (P = .006). Univariate analysis demonstrated an effect of tumor size on OS (tumor >5 cm, hazard ratio [HR] 17.7, P = .049) and PFS (HR 17.7, P = .049). Acute grade 2 toxicity was observed in two patients (11%, transient proctitis). Late grade 2+ toxicity was observed in three patients (16%; n = 1 grade 2 skeletal deformity; n = 3 transient grade 2 urinary incontinence; one patient experienced both).

CONCLUSIONS

PBT for B/P-RMS affords promising disease-related outcomes with an acceptable toxicity profile. Higher local failure rates were observed for larger tumors, supporting dose-escalation components of ongoing RMS clinical trials.

Abstract 1575: DNA methylation-derived neutrophil-to-lymphocyte ratio and survival among pediatric medulloblastoma patients

Background/Objectives: Medulloblastoma is the most common malignant brain tumor diagnosed in children. Current risk-stratification methods of pediatric medulloblastoma do not fully explain the observed variability in clinical outcomes. Methylation-derived neutrophil-to-lymphocyte ratio (mdNLR) captures immune-specific information and has been identified as a potential prognostic biomarker of outcomes in various cancers, including adult brain tumors. Therefore, we evaluated the association between blood-derived mdNLR and overall survival in a cohort of patients with pediatric medulloblastoma.

Design/Methods: We identified pediatric patients diagnosed and treated for medulloblastoma at Texas Children’s Cancer Center between 1995 and 2015. Peripheral blood DNA methylation was measured using the Infinium Human Methylation 450K Beadchip. Methylation data underwent quality control, including beta-mixture quantile normalization and batch correction. Immune cell proportions (CD4+ T-Cells, CD8+ T-Cells, B-cells, natural killer cells, monocytes, and granulocytes) were estimated using cellular deconvolution methods and used to estimate mdNLR, which was then log-transformed to improve normality. Cox regression models were estimated to evaluate the association between mdNLR and overall survival.

Results: Of the 78 eligible patients include in this analysis, 83% (n=65) were alive at last follow-up (median follow-up=7.8 years). Deceased patients (n=13; median follow-up=2.6 years) had a higher mean mdNLR than patients who were alive at last contact (12.3 vs. 4.0, P = 0.046). Elevated log-transformed mdNLR was associated with an increased risk of death in both unadjusted models (HR=1.68, 95%CI: 1.11-2.55) and models accounting for age, sex, race, and clinical risk group (HR=1.97, 95%CI: 1.12-3.45).

Conclusion: We identified a significant association between peripheral blood mdNLR and survival in pediatric medulloblastoma. As a promising prognostic biomarker of outcomes, mdNLR captures immune-specific information and is a potential avenue of research in settings where cytologic determination of NLR may not be possible. Future work should investigate the relationship between elevated mdNLR and specific pediatric medulloblastoma molecular subtypes.

Citation Format: Vidal M. Arroyo, Philip J. Lupo, Michael E. Scheurer, Surya P. Rednam, Jeffrey C. Murray, M F. Okcu, Murali M. Chintagumpala, Austin L. Brown. DNA methylation-derived neutrophil-to-lymphocyte ratio and survival among pediatric medulloblastoma patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1575.

Increased risk of pseudoprogression among pediatric low-grade glioma patients treated with proton versus photon radiotherapy

BACKGROUND

Pseudoprogression (PsP) is a recognized phenomenon after radiotherapy (RT) for high-grade glioma but is poorly characterized for low-grade glioma (LGG). We sought to characterize PsP for pediatric LGG patients treated with RT, with particular focus on the role of RT modality using photon-based intensity-modulated RT (IMRT) or proton beam therapy (PBT).

METHODS

Serial MRI scans from 83 pediatric LGG patients managed at 2 institutions between 1998 and 2017 were evaluated. PsP was scored when a progressive lesion subsequently decreased or stabilized for at least a year without therapy.

RESULTS

Thirty-two patients (39%) were treated with IMRT, and 51 (61%) were treated with PBT. Median RT dose for the cohort was 50.4 Gy(RBE) (range, 45-59.4 Gy[RBE]). PsP was identified in 31 patients (37%), including 8/32 IMRT patients (25%) and 23/51 PBT patients (45%). PBT patients were significantly more likely to have post-RT enlargement (hazard ratio [HR] 2.15, 95% CI: 1.06-4.38, P = 0.048). RT dose >50.4 Gy(RBE) similarly predicted higher rates of PsP (HR 2.61, 95% CI: 1.20-5.68, P = 0.016). Multivariable analysis confirmed the independent effects of RT modality (P = 0.03) and RT dose (P = 0.01) on PsP incidence. Local progression occurred in 10 patients: 7 IMRT patients (22%) and 3 PBT patients (6%), with a trend toward improved local control for PBT patients (HR 0.34, 95% CI: 0.10-1.18, P = 0.099).

CONCLUSIONS

These data highlight substantial rates of PsP among pediatric LGG patients, particularly those treated with PBT. PsP should be considered when assessing response to RT in LGG patients within the first year after RT.

Patterns of failure following proton beam therapy for head and neck rhabdomyosarcoma

PURPOSE

Pediatric patients with rhabdomyosarcoma (RMS) of the head and neck (H&N) are treated with multimodal therapy, often with radiotherapy (RT) as definitive local therapy. We report on the patterns of failure following proton beam therapy (PBT) for H&N RMS.

METHODS

Forty-six H&N RMS patients were enrolled on a prospective registry protocol between 2006 and 2015. All were treated with a combination of chemotherapy (ChT) and PBT. Most patients (25 patients, 54%) had parameningeal tumors, of which 11 (24%) had intracranial extension (ICE). Thirteen patients (28%) had primary tumors greater than 5 cm. Median total cyclophosphamide (CPM) equivalent dose was 13.2 g/m² (range 0-16.8 g/m²). Median RT dose was 50.4 Gy(RBE) (range 36 Gy[RBE]-50.8 Gy[RBE]).

RESULTS

With median follow-up of 3.9 years, five-year overall survival was 76%, and five-year progression-free survival was 57%. Seventeen patients (37%) experienced relapse, including 7 with local failure (LF). Five-year local control (LC) was 84%. Tumor size greater than 5 cm predicted increased risk of LF (hazard ratio [HR] 6.49, p = 0.03), as did the presence of ICE at diagnosis (HR 5.21, p = 0.03). Six relapses occurred in patients with ICE; all included a component of central nervous system relapse, with leptomeningeal disease and/or LF with an intracranial component. Delayed RT delivery after week 4 of ChT predicted increased risk of relapse for ICE patients (HR 10.49, p = 0.006).

CONCLUSIONS

PBT confers excellent LC, and a favorable late toxicity profile as compared with prior photon RT data. Our observations support ongoing trial efforts to dose-escalate RT for patients with larger tumors. However, these data raise concerns regarding excess failures among patients with ICE.

Pilot study of DNA methylation-derived neutrophil-to-lymphocyte ratio and survival in pediatric medulloblastoma

INTRODUCTION

Methylation-derived neutrophil-to-lymphocyte ratio (mdNLR) has been identified as a potential prognostic biomarker of outcomes in various cancers. We evaluated the prognostic value of blood-derived mdNLR within a retrospective cohort of pediatric medulloblastoma patients.

MATERIALS AND METHODS

DNA methylation was measured in archival peripheral blood samples collected on 56 pediatric medulloblastoma patients. Hazard ratios (HR) and 95% confidence intervals (CI) for the association between mdNLR and survival were evaluated using Cox proportional hazard models.

RESULTS

Compared to patients who were alive at last follow-up (n = 43), the mean mdNLR value was slightly higher in deceased patients (n = 13) (12.3 vs. 5.2,P =  0.163). Elevated log-transformed mdNLR was suggestively associated with an increased likelihood of death in unadjusted models (HR=1.43, 95%CI: 0.92-2.22) and significantly associated with mortality in adjusted models (HR=1.61, 95%CI: 1.01-2.58).

DISCUSSION

Future work is warranted to investigate the relationship between mdNLR outcomes in specific pediatric medulloblastoma molecular subgroups.

Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort

BACKGROUND

Medulloblastoma is associated with rare hereditary cancer predisposition syndromes; however, consensus medulloblastoma predisposition genes have not been defined and screening guidelines for genetic counselling and testing for paediatric patients are not available. We aimed to assess and define these genes to provide evidence for future screening guidelines.

METHODS

In this international, multicentre study, we analysed patients with medulloblastoma from retrospective cohorts (International Cancer Genome Consortium [ICGC] PedBrain, Medulloblastoma Advanced Genomics International Consortium [MAGIC], and the CEFALO series) and from prospective cohorts from four clinical studies (SJMB03, SJMB12, SJYC07, and I-HIT-MED). Whole-genome sequences and exome sequences from blood and tumour samples were analysed for rare damaging germline mutations in cancer predisposition genes. DNA methylation profiling was done to determine consensus molecular subgroups: WNT (MBWNT), SHH (MBSHH), group 3 (MBGroup3), and group 4 (MBGroup4). Medulloblastoma predisposition genes were predicted on the basis of rare variant burden tests against controls without a cancer diagnosis from the Exome Aggregation Consortium (ExAC). Previously defined somatic mutational signatures were used to further classify medulloblastoma genomes into two groups, a clock-like group (signatures 1 and 5) and a homologous recombination repair deficiency-like group (signatures 3 and 8), and chromothripsis was investigated using previously established criteria. Progression-free survival and overall survival were modelled for patients with a genetic predisposition to medulloblastoma.

FINDINGS

We included a total of 1022 patients with medulloblastoma from the retrospective cohorts (n=673) and the four prospective studies (n=349), from whom blood samples (n=1022) and tumour samples (n=800) were analysed for germline mutations in 110 cancer predisposition genes. In our rare variant burden analysis, we compared these against 53 105 sequenced controls from ExAC and identified APC, BRCA2, PALB2, PTCH1, SUFU, and TP53 as consensus medulloblastoma predisposition genes according to our rare variant burden analysis and estimated that germline mutations accounted for 6% of medulloblastoma diagnoses in the retrospective cohort. The prevalence of genetic predispositions differed between molecular subgroups in the retrospective cohort and was highest for patients in the MBSHH subgroup (20% in the retrospective cohort). These estimates were replicated in the prospective clinical cohort (germline mutations accounted for 5% of medulloblastoma diagnoses, with the highest prevalence [14%] in the MBSHH subgroup). Patients with germline APC mutations developed MBWNT and accounted for most (five [71%] of seven) cases of MBWNT that had no somatic CTNNB1 exon 3 mutations. Patients with germline mutations in SUFU and PTCH1 mostly developed infant MBSHH. Germline TP53 mutations presented only in childhood patients in the MBSHH subgroup and explained more than half (eight [57%] of 14) of all chromothripsis events in this subgroup. Germline mutations in PALB2 and BRCA2 were observed across the MBSHH, MBGroup3, and MBGroup4 molecular subgroups and were associated with mutational signatures typical of homologous recombination repair deficiency. In patients with a genetic predisposition to medulloblastoma, 5-year progression-free survival was 52% (95% CI 40-69) and 5-year overall survival was 65% (95% CI 52-81); these survival estimates differed significantly across patients with germline mutations in different medulloblastoma predisposition genes.

INTERPRETATION

Genetic counselling and testing should be used as a standard-of-care procedure in patients with MBWNT and MBSHH because these patients have the highest prevalence of damaging germline mutations in known cancer predisposition genes. We propose criteria for routine genetic screening for patients with medulloblastoma based on clinical and molecular tumour characteristics.

FUNDING

German Cancer Aid; German Federal Ministry of Education and Research; German Childhood Cancer Foundation (Deutsche Kinderkrebsstiftung); European Research Council; National Institutes of Health; Canadian Institutes for Health Research; German Cancer Research Center; St Jude Comprehensive Cancer Center; American Lebanese Syrian Associated Charities; Swiss National Science Foundation; European Molecular Biology Organization; Cancer Research UK; Hertie Foundation; Alexander and Margaret Stewart Trust; V Foundation for Cancer Research; Sontag Foundation; Musicians Against Childhood Cancer; BC Cancer Foundation; Swedish Council for Health, Working Life and Welfare; Swedish Research Council; Swedish Cancer Society; the Swedish Radiation Protection Authority; Danish Strategic Research Council; Swiss Federal Office of Public Health; Swiss Research Foundation on Mobile Communication; Masaryk University; Ministry of Health of the Czech Republic; Research Council of Norway; Genome Canada; Genome BC; Terry Fox Research Institute; Ontario Institute for Cancer Research; Pediatric Oncology Group of Ontario; The Family of Kathleen Lorette and the Clark H Smith Brain Tumour Centre; Montreal Children's Hospital Foundation; The Hospital for Sick Children: Sonia and Arthur Labatt Brain Tumour Research Centre, Chief of Research Fund, Cancer Genetics Program, Garron Family Cancer Centre, MDT's Garron Family Endowment; BC Childhood Cancer Parents Association; Cure Search Foundation; Pediatric Brain Tumor Foundation; Brainchild; and the Government of Ontario.

Intensive multi-modality therapy for extra-ocular retinoblastoma (RB): A Children's Oncology Group (COG) trial (ARET0321)

10506

Background: Metastatic RB is associated with a poor prognosis. Previous small series suggested that intensified systemic chemotherapy with or without radiation therapy (RT) may improve outcomes in this population. COG opened this prospective, multi-institutional, international trial to study the effectiveness of this approach. Methods: Patients with regional extra-ocular RB (stage 2 or 3) were treated with 4 cycles of intensive conventional chemotherapy (vincristine 0.05 mg/kg/day, cisplatin 3.5 mg/kg/day, cyclophosphamide 65 mg/kg x 2 days, etoposide 4 mg/kg x 2 days) followed by involved-field RT (4500 cGy). Two strata of patients with metastatic RB [stage 4a: distant metastases not involving the central nervous system involvement (CNS); and stage 4b (CNS metastases)/trilateral RB)] were treated with 4 cycles of the same chemotherapy. Patients with ≥ partial response then received 1 cycle of high-dose carboplatin (Calvert formula with AUC = 7/day, maximum 16.7 mg/kg/day) on days -8 to -6, thiotepa (10 mg/kg/day), & etoposide (8.3 mg/kg/day) on days -5 to -3 with autologous hematopoietic stem cell rescue on day 0. Patients with metastatic RB who did not achieve an adequate response to chemotherapy also received RT. Results: Sixty subjects (20 in each stratum) were enrolled; 57 were eligible and included in the analyses (based on data current to June 30, 2016). Toxicity was significant as expected and there were 2 therapy related deaths. Event-free survival (EFS) at 36 months was 87.7% (90% CI 65.4 to 96.0%) for subjects with stage 2 or 3 disease, 79.3% (90% CI 54.2 to 91.6%) for subjects with stage 4a disease and 8.0% (90% CI 1.0 to 25.1%) for subjects with stage 4b/trilateral disease. The observed results significantly improved the EFS in each stratum compared with historical results used for planning the study. Conclusions: This is the first prospective, multi-institutional, international study to show that intensive multi-modality therapy is highly effective for patients with regional extra-ocular RB and metastatic RB not involving the CNS. More effective therapy is required for patients with CNS RB. Clinical trial information: NCT00554788.

Genome-wide discovery of novel susceptibility loci for treatment-associated hypothyroidism among survivors of pediatric medulloblastoma

10571

Background: Pediatric medulloblastoma patients exposed to craniospinal radiation (CSI) are at high risk of developing endocrinopathies, including hypothyroidism. We sought to evaluate the role of genetic variation on hypothyroidism susceptibility among survivors of pediatric medullobastoma. Methods: Records from 61 medulloblastoma survivors treated at Texas Children’s Hospital between 1997 and 2013 were reviewed. All patients completed baseline and yearly follow-up thyroid assessments. Genome-wide genotyping was performed on Illumina HumanOmni1 and HumanOmni2.5 BeadChip single nucleotide polymorphism (SNP) arrays. Following standard quality control measures and exclusion of rare variants (minor allele frequency [MAF] < 5%), 572,562 autosomal SNPs were included in our analyses. The association between each SNP and hypothyroidism was tested using Fisher’s exact test and logistic regression, assuming additive allelic effects. Results: A total of 25 patients (41%) developed hypothyroidism with median follow-up of 8.3 years from diagnosis (range: 1.8-17.2 years). Primary hypothyroidism was identified in 9 (36%) cases, while the remaining 16 (64%) developed central hypothyroidism. Hypothyroidism was detected in 13 of 40 (33%) individuals exposed to < 30 Gy CSI and 12 of 21 (57%) individuals exposed to ≥30 Gy CSI (p = 0.06). Genome-wide association analysis identified several risk loci, including 3 variants associated with hypothyroidism (p-value < 1x10-5) at chromosome 2q11.2 ( NPAS2 gene). The top overall SNP (MAF = 27.5%, p-value = 6.5x10-7) remained strongly associated with hypothyroidism after accounting for possible confounders, including CSI dose, CSI type (proton/photon), age, sex, and genetic ancestry. Conclusions: Our findings suggest susceptibility to treatment-related hypothyroidism is strongly influenced by common genetic variation in NPAS2. The NPAS2 gene, a central component of the circadian rhythm network, is a transcriptional activator and regulator of DNA damage response and DNA repair genes.

Progression-free survival of children with localized ependymoma treated with intensity-modulated radiation therapy or proton-beam radiation therapy

BACKGROUND

The treatment for childhood intracranial ependymoma includes maximal surgical resection followed by involved-field radiotherapy, commonly in the form of intensity-modulated radiation therapy (IMRT). Proton-beam radiation therapy (PRT) is used at some centers in an effort to decrease long-term toxicity. Although protons have the theoretical advantage of a minimal exit dose to the surrounding uninvolved brain tissue, it is unknown whether they have the same efficacy as photons in preventing local recurrence.

METHODS

A retrospective review of medical records from September 2000 to April 2013 was performed. Seventy-nine children with newly diagnosed localized intracranial ependymomas treated with either IMRT (n = 38) or PRT (n = 41) were identified, and progression-free survival (PFS) was analyzed with Kaplan-Meier and Cox multivariate analyses.

RESULTS

The median age at diagnosis was 3.7 years for all patients (range, 0.4-18.7 years). There were 54 patients with infratentorial tumors (68% of the total population). Patients treated with PRT were younger (median age, 2.5 vs 5.7 years; P = .001) and had a shorter median follow-up (2.6 vs 4.9 years; P < .0001). Gross total resection (GTR) was achieved in 67 patients (85%) and was more frequent in the PRT group versus the IMRT group (93% vs 76%; P = .043). The 3-year PFS rates were 60% and 82% with IMRT and PRT, respectively (P = .031).

CONCLUSIONS

Children with localized ependymomas treated with PRT have a 3-year PFS rate comparable to that of children treated with IMRT. This analysis suggests that local control is not compromised by the use of PRT. The data also support GTR as the only prognostic factor for PFS. Cancer 2017;123:2570-78. © 2017 American Cancer Society.

Integrated tumor and germline whole-exome sequencing identifies mutations in MAPK and PI3K pathway genes in an adolescent with rosette-forming glioneuronal tumor of the fourth ventricle

The integration of genome-scale studies such as whole-exome sequencing (WES) into the clinical care of children with cancer has the potential to provide insight into the genetic basis of an individual's cancer with implications for clinical management. This report describes the results of clinical tumor and germline WES for a patient with a rare tumor diagnosis, rosette-forming glioneuronal tumor of the fourth ventricle (RGNT). Three pathogenic gene alterations with implications for clinical care were identified: somatic activating hotspot mutations in FGFR1 (p.N546K) and PIK3CA (p.H1047R) and a germline pathogenic variant in PTPN11 (p.N308S) diagnostic for Noonan syndrome. The molecular landscape of RGNT is not well-described, but these data are consistent with prior observations regarding the importance of the interconnected MAPK and PI3K/AKT/mTOR signaling pathways in this rare tumor. The co-occurrence of FGFR1, PIK3CA, and PTPN11 alterations provides further evidence for consideration of RGNT as a distinct molecular entity from pediatric low-grade gliomas and suggests potential therapeutic strategies for this patient in the event of tumor recurrence as novel agents targeting these pathways enter pediatric clinical trials. Although RGNT has not been definitively linked with cancer predisposition syndromes, two prior cases have been reported in patients with RASopathies (Noonan syndrome and neurofibromatosis type 1 [NF1]), providing an additional link between these tumors and the mitogen-activated protein kinase (MAPK) signaling pathway. In summary, this case provides an example of the potential for genome-scale sequencing technologies to provide insight into the biology of rare tumors and yield both tumor and germline results of potential relevance to patient care.

Exploratory analysis of ERCC2 DNA methylation in survival among pediatric medulloblastoma patients

AIM

Medulloblastoma is the most frequent malignant pediatric brain tumor. While survival rates have improved due to multimodal treatment including cisplatin-based chemotherapy, there are few prognostic factors for adverse treatment outcomes. Notably, genes involved in the nucleotide excision repair pathway, including ERCC2, have been implicated in cisplatin sensitivity in other cancers. Therefore, this study evaluated the role of ERCC2 DNA methylation profiles on pediatric medulloblastoma survival.

METHODS

The study population included 71 medulloblastoma patients (age <18years at diagnosis) and recruited from Texas Children's Cancer Center between 2004 and 2009. DNA methylation profiles were generated from peripheral blood samples using the Illumina Infinium Human Methylation 450 Beadchip. Sixteen ERCC2-associated CpG sites were evaluated in this analysis. Multivariable regression models were used to determine the adjusted association between DNA methylation and survival. Cox regression and Kaplan-Meier curves were used to compare 5-year overall survival between hyper- and hypo-methylation at each CpG site.

RESULTS

In total, 12.7% (n=9) of the patient population died within five years of diagnosis. In our population, methylation of the cg02257300 probe (Hazard Ratio=9.33; 95% Confidence Interval: 1.17-74.64) was associated with death (log-rank p=0.01). This association remained suggestive after correcting for multiple comparisons (FDR p<0.2). No other ERCC2-associated CpG site was associated with survival in this population of pediatric medulloblastoma patients.

CONCLUSION

These findings provide the first evidence that DNA methylation within the promoter region of the ERCC2 gene may be associated with survival in pediatric medulloblastoma. If confirmed in future studies, this information may lead to improved risk stratification or promote the development of novel, targeted therapeutics.

Diagnostic Yield of Clinical Tumor and Germline Whole-Exome Sequencing for Children With Solid Tumors

Importance

Whole-exome sequencing (WES) has the potential to reveal tumor and germline mutations of clinical relevance, but the diagnostic yield for pediatric patients with solid tumors is unknown.

Objective

To characterize the diagnostic yield of combined tumor and germline WES for children with solid tumors.

Design

Unselected children with newly diagnosed and previously untreated central nervous system (CNS) and non-CNS solid tumors were prospectively enrolled in the BASIC3 study at a large academic children's hospital during a 23-month period from August 2012 through June 2014. Blood and tumor samples underwent WES in a certified clinical laboratory with genetic results categorized on the basis of perceived clinical relevance and entered in the electronic health record.

Main Outcomes and Measures

Clinical categorization of somatic mutations; frequencies of deleterious germline mutations related to patient phenotype and incidental medically-actionable mutations.

Results

Of the first 150 participants (80 boys and 70 girls, mean age, 7.4 years), tumor samples adequate for WES were available from 121 patients (81%). Somatic mutations of established clinical utility (category I) were reported in 4 (3%) of 121 patients, with mutations of potential utility (category II) detected in an additional 29 (24%) of 121 patients. CTNNB1 was the gene most frequently mutated, with recurrent mutations in KIT, TSC2, and MAPK pathway genes (BRAF, KRAS, and NRAS) also identified. Mutations in consensus cancer genes (category III) were found in an additional 24 (20%) of 121 tumors. Fewer than half of somatic mutations identified were in genes known to be recurrently mutated in the tumor type tested. Diagnostic germline findings related to patient phenotype were discovered in 15 (10%) of 150 cases: 13 pathogenic or likely pathogenic dominant mutations in adult and pediatric cancer susceptibility genes (including 2 each in TP53, VHL, and BRCA1), 1 recessive liver disorder with hepatocellular carcinoma (TJP2), and 1 renal diagnosis (CLCN5). Incidental findings were reported in 8 (5%) of 150 patients. Most patients harbored germline uncertain variants in cancer genes (98%), pharmacogenetic variants (89%), and recessive carrier mutations (85%).

Conclusions and Relevance

Tumor and germline WES revealed mutations in a broad spectrum of genes previously implicated in both adult and pediatric cancers. Combined reporting of tumor and germline WES identified diagnostic and/or potentially actionable findings in nearly 40% of newly diagnosed pediatric patients with solid tumors.

Abstract 04: Impact of whole exome sequencing results on clinical decision making for pediatric solid tumor patients in the hypothetical scenario of tumor relapse: A survey of pediatric oncologists

Background: The development of molecularly-targeted agents has made it possible to personalize therapy for patients by targeting the specific mutations in their tumor. Pediatric clinical trials utilizing such strategies are being planned but little is known about the opinions of pediatric oncologists regarding the utility of genomic data for guiding treatment decisions. The goals of this study were to (1) characterize those opinions in the context of children with relapsed/refractory solid tumors and (2) assess the potential impact of clinical whole exome sequencing (WES) data on medical decision-making in that context.

Methods: As part of the ongoing BASIC3 clinical sequencing study at Texas Children's Cancer Center, clinical germline and tumor (if sample available) WES were performed for unselected newly-diagnosed pediatric CNS and non-CNS solid tumor patients. The primary oncologist for each (n=17) received online surveys for each study patient before and after review of WES reports. The pre- and post-WES surveys asked oncologists to rank options for off-study systemic chemotherapy (of any type) for their patient in the hypothetical scenario of tumor relapse. Oncologists were then asked if they would consider using a molecularly-targeted agent in the context of a clinical trial, and if so, which agents (from a representative list), their rank order and the rationale for those choices. Post-WES surveys also included questions regarding perceived utility of the tumor WES results for patient care. Pre-WES surveys were analyzed for baseline oncologist responses regarding these hypothetical treatment decisions. When available, pre- and post-WES surveys were analyzed as pairs as an initial assessment of the influence of the WES results on the oncologist's choice of therapy.

Results: 177/189 (94%) of pre-WES surveys and 111/161 (69%) post-WES surveys were available for analysis. Analysis of pre-exome surveys revealed that oncologists would recommend systemic chemotherapy for 127/177 (72%) patients in the hypothetical event of tumor relapse but would consider a molecularly-targeted agent off-study as their first option in only 8/177 (4%) cases. In contrast, oncologists indicated that they would consider targeted therapies in the context of a clinical trial for 99/177 (56%) patients, most commonly sorafenib (n=21), cixutumumab (n=17), and crizotinib (n=13). There were 26 cases in which somatic mutations were identified in genes categorized as having established or potential clinical relevance, and for which both pre- and post-WES surveys were available. A corresponding targeted agent was ranked for consideration in the hypothetical scenario of relapse on the post-WES survey for 8/26 (31%) of these patients (somatic mutations in MET, JAK2, HRAS, NRAS X 2, ALK, BRAF, KIT), having only been chosen on the pre-WES survey in 2 of those cases. On 8 of 111 (7%) post-WES surveys, the oncologist removed a targeted agent that had been prioritized on the pre-WES survey after no relevant mutation was detected, including the Sonic Hedgehog inhibitor GDC-0449 in 5 cases.

Conclusion: Although genomic tests such as WES have the potential to identify molecular targets for therapy in children with relapsed tumors, a survey of pediatric oncologists revealed that most consider such therapies as options only in the context of a clinical trial. These findings support the potential utility of WES in precision oncology approaches as well as the need for clinical trials evaluating the use of integrated genomic testing to guide treatment of children with relapsed solid tumors.

Citation Format: Abhishek Bavle, Tao Wang, Frank Y. Lin, Angshumoy Roy, Robin A. Kerstein, Sarah Scollon, Katie Bergstrom, Stephanie Gutierrez, Uma Ramamurthy, Yaping Yang, Christine M. Eng, Richard A. Gibbs, Murali M. Chintagumpala, Susan G. Hilsenbeck, Sharon E. Plon, Stacey L. Berg, D. Williams Parsons. Impact of whole exome sequencing results on clinical decision making for pediatric solid tumor patients in the hypothetical scenario of tumor relapse: A survey of pediatric oncologists. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr 04.

Abstract IA16: Clinical genomics for children with solid tumors: Current realities and future opportunities

Genome-scale sequencing methods such as whole exome sequencing (WES) have provided significant insight into the pathogenesis of cancer. However, experience with the use of these tests in the clinical care of cancer patients remains limited. Sequencing of tumor and matched normal samples can reveal multiple types of results with implications for clinical practice. The identification of somatic (tumor-specific) mutations has the potential to offer diagnostic and prognostic information and inform selection of therapies. Detection of germline mutations in cancer susceptibility genes may prompt further genetic testing and guide cancer surveillance strategies for both the patient and family members. Germline mutations may also explain non-cancer phenotypes, predict drug responses, or provide reproductive counseling information for parents. The goal of the BASIC3 (Baylor College of Medicine Advancing Sequencing into Childhood Cancer Care) study is to determine the clinical impact of incorporating clinical tumor and constitutional WES into the care of children with newly diagnosed solid tumors. This study follows pediatric patients with newly diagnosed CNS and non-CNS solid tumors at Texas Children's Cancer Center for two years after performing CLIA-certified WES of blood and frozen tumor samples. Results are deposited into the electronic health record and disclosed to families by their oncologist and a genetic counselor. The potential impact of tumor exome findings on clinical decision-making is assessed through review of the medical record over the two year follow-up period as well as through surveys of the oncologists regarding prioritization of treatment options in the hypothetical event of tumor recurrence before and after receiving tumor exome results. Preferences of patient families and oncologists for reporting this complex information are obtained by interviews and audio recording of the WES result disclosure visits. Since the study opened in August 2012, more than 210 subjects have been enrolled (~80% of potentially eligible patients), representing the expected distribution of both CNS and non-CNS tumors. WES results have been reported for 170 subjects, revealing potentially-clinically relevant germline and somatic mutations in cancer genes known to be related to pediatric solid tumors as well as others known to be mutated primarily in adult cancer patients. Data will be presented regarding the diagnostic yield of combined tumor and germline WES for children with newly-diagnosed solid tumors. These results demonstrate the feasibility of routine tumor WES in the pediatric oncology clinic and a significant level of parental interest in receiving WES results and have significant implications for the treatment of children with relapsed and refractory solid tumors and the design of clinical trials using precision oncology approaches for these patients. Further analyses of the clinical utility of the WES data and the preferences of oncologists and parents for reporting of these results are under study. The BASIC3 study is a Clinical Sequencing Exploratory Research (CSER) program project supported by NHGRI/NCI 1U01HG006485.

Citation Format: D. William Parsons, Angshumoy Roy, Yaping Yang, Tao Wang, Sarah Scollon, Katie Bergstrom, Robin A. Kerstein, Stephanie Gutierrez, Abhishek Bavle, Frank Y. Lin, Dolores H. López-Terrada, Federico A. Monzon, Jed G. Nuchtern, Uma Ramamurthy, Amy L. McGuire, Susan G. Hilsenbeck, Jeffrey G. Reid, Donna M. Muzny, David A. Wheeler, Stacey L. Berg, Murali M. Chintagumpala, Christine M. Eng, Richard A. Gibbs, Sharon E. Plon. Clinical genomics for children with solid tumors: Current realities and future opportunities. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr IA16.

Recurrent internal tandem duplications of BCOR in clear cell sarcoma of the kidney

The X-linked BCL-6 co-repressor (BCOR) gene encodes a key constituent of a variant polycomb repressive complex (PRC) that is mutated or translocated in human cancers. Here we report on the identification of somatic internal tandem duplications (ITDs) clustering in the C terminus of BCOR in 23 of 27 (85%) pediatric clear cell sarcomas of the kidney (CCSK) from two independent cohorts. We profile CCSK tumours using a combination of whole-exome, transcriptome and targeted sequencing. Identical ITD mutations are found in primary and relapsed tumour pairs but not in adjacent normal kidney or blood. Mutant BCOR transcripts and proteins are markedly upregulated in ITD-positive tumours. Transcriptome analysis of ITD-positive CCSKs reveals enrichment for PRC2-regulated genes and similarity to undifferentiated sarcomas harbouring BCOR–CCNB3 fusions. The discovery of recurrent BCOR ITDs defines a major oncogenic event in this childhood sarcoma with significant implications for diagnostic and therapeutic approaches to this tumour.

The genetic basis of clear cell sarcomas of the kidney is not well understood. In this study, Roy et al. perform whole-exome and RNA sequencing of these tumours and identify recurrent internal tandem duplications in BCOR, a key constituent of a variant polycomb repressive complex.

Abstract 5169: Diagnostic yield of clinical tumor and germline exome sequencing for newly diagnosed children with solid tumors

Background: Advances in sequencing technologies allow for provision of genome-scale data to physicians caring for pediatric cancer patients but current experience with the clinical application of genomic sequencing is limited and the diagnostic yield of these methods is unclear.

Methods: The goal of the BASIC3 (Baylor Advancing Sequencing into Childhood Cancer Care) study is to determine the clinical impact of incorporating tumor and constitutional whole exome sequencing (WES) into the care of children with newly diagnosed solid tumors at Texas Children's Cancer Center (target enrollment n=280). WES of patient blood and frozen tumor samples is being conducted in the CLIA-certified Whole Genome Laboratory at Baylor College of Medicine using the VCRome 2.1 capture reagent and Illumina paired-end sequencing with reports incorporated in the medical record.

Results: 120 patients have enrolled to date, including 39 (33%) and 81 (67%) with CNS and non-CNS tumors, respectively. Despite limited diagnostic biopsies in many patients, tumor samples adequate for WES have been obtained from 97 subjects (81%). WES results have been reported for 89 patients. Tumor WES (n=73) revealed 20 of 73 tumors (27%) to contain mutations classified as having proven or potential clinical utility, including recurrent alterations of CTNNB1, BRAF, KIT, and NRAS/KRAS. Notably, less than 50% of somatic mutations would have been detected on an adult-focused cancer panel, BCM Cancer Gene Mutation Panel v.2. Germline WES (n=89) identified diagnostic findings in 11 cases (12%) including 8 patients with pathogenic mutations in dominant cancer susceptibility genes (singletons except for 2 patients with TP53 mutations). Four of these 8 patients had genetic testing recommended clinically. There were 2 patients with mutations providing the genetic cause of non-cancer medical problems and 1 patient with a mutation which explained both liver disease and hepatocellular carcinoma. Downstream testing of at-risk relatives has occurred rapidly in several families and cancer screening recommendations implemented. Seven (8%) medically actionable incidental findings unrelated to phenotype were reported, predominantly in cardiovascular genes and mitochondrial DNA.

Conclusions: These data demonstrate the feasibility of routine WES in the pediatric oncology setting. Early results demonstrate that clinically relevant findings are identified by tumor and germline WES in 38% of pediatric solid tumor patients. The yield of clinically relevant somatic and germline alterations would likely increase further by incorporation of complementary genomic methods (e.g. RNA-seq or copy number analysis). Assessment of the clinical utility of the tumor and germline exomes and preferences for reporting of these results to physicians and parents are under study. Supported by NHGRI/NCI 1U01HG006485.

Citation Format: Donald W. Parsons, Angshumoy Roy, Federico A. Monzon, Yaping Yang, Dolores H. López-Terrada, Murali M. Chintagumpala, Stacey L. Berg, Susan G. Hilsenbeck, Tao Wang, Robin A. Kerstein, Sarah Scollon, Katie Bergstrom, Richard L. Street, Laurence B. McCullough, Amy L. McGuire, Uma Ramamurthy, Jeff G. Reid, Donna M. Muzny, David A. Wheeler, Christine M. Eng, Richard A. Gibbs, Sharon E. Plon. Diagnostic yield of clinical tumor and germline exome sequencing for newly diagnosed children with solid tumors. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5169. doi:10.1158/1538-7445.AM2014-5169

Obtaining informed consent for clinical tumor and germline exome sequencing of newly diagnosed childhood cancer patients

BACKGROUND

Effectively educating families about the risks and benefits of genomic tests such as whole exome sequencing (WES) offers numerous challenges, including the complexity of test results and potential loss of privacy. Research on best practices for obtaining informed consent (IC) in a variety of clinical settings is needed. The BASIC3 study of clinical tumor and germline WES in an ethnically diverse cohort of newly diagnosed pediatric cancer patients offers the opportunity to study the IC process in the setting of critical illness. We report on our experience for the first 100 families enrolled, including study participation rates, reasons for declining enrollment, assessment of clinical and demographic factors that might impact study enrollment, and preferences of parents for participation in optional genomics study procedures.

METHODS

A specifically trained IC team offered study enrollment to parents of eligible children for procedures including clinical tumor and germline WES with results deposited in the medical record and disclosure of both diagnostic and incidental results to the family. Optional study procedures were also offered, such as receiving recessive carrier status and deposition of data into research databases. Stated reasons for declining participation were recorded. Clinical and demographic data were collected and comparisons made between enrolled and non-enrolled patients.

RESULTS

Over 15 months, 100 of 121 (83%) eligible families elected to enroll in the study. No significant differences in enrollment were detected based on factors such as race, ethnicity, use of Spanish interpreters and Spanish consent forms, and tumor features (central nervous system versus non-central nervous system, availability of tumor for WES). The most common reason provided for declining enrollment (10% of families) was being overwhelmed by the new cancer diagnosis. Risks specific to clinical genomics, such as privacy concerns, were less commonly reported (5.5%). More than 85% of parents consented to each of the optional study procedures.

CONCLUSIONS

An IC process was developed that utilizes a specialized IC team, active communication with the oncology team, and an emphasis on scheduling flexibility. Most parents were willing to participate in a clinical germline and tumor WES study as well as optional procedures such as genomic data sharing independent of race, ethnicity or language spoken.

Implementation and evaluation of clinical exome sequencing in childhood cancer care: The BASIC3 study

10023

Background: Advances in sequencing technologies allow for provision of genome-scale data to oncologists and geneticists caring for pediatric cancer patients. The goal of the BASIC3 (Baylor Advancing Sequencing into Childhood Cancer Care) study is to determine the clinical impact of incorporating CLIA-certified tumor and constitutional exome sequencing into the care of children with newly diagnosed solid tumors. Methods: Blood and frozen tumor samples obtained at initial surgery are submitted for clinical exome sequencing (target enrollment 280 patients). Results are deposited into the electronic medical record and disclosed to families by their oncologist and a genetic counselor. Identification of germline cancer susceptibility mutations is compared with standard testing practices. Oncologists are surveyed on prioritization of treatment options in the hypothetical event of tumor recurrence before and after receiving tumor exome results. Patients will be followed for two years to assess the clinical utility of exome data. Preferences for reporting this complex information are obtained by interviews and audiorecording of disclosure visits. Results: Initial results reveal that41 of 49 (84%) ethnically diverse families have consented to enroll on study. Adequate tumor samples were available from 35 of 41 patients (85%), including 11 of 15 (73%) patients with CNS tumors and 24 of 26 (92%) with non-CNS tumors. Pathogenic germline cancer susceptibility mutations (TP53, MSH2) were reported in 2 of the first 11 patients, with a medically-actionable mutation in a gene (SCN5A) unrelated to cancer in 1 patient and 0-4 (median of 2) recessive carrier mutations per patient. Between 9 and 33 protein altering mutations (median of 11) have been identified in tumors, including known cancer genes such as TP53 and others with no known link to pediatric cancer. Conclusions: A robust clinical pipeline for exome sequencing of blood and tumor samples has been successfully developed with significant parental interest. Data assessing the clinical utility of both the tumor and constitutional exomes and the preferences of oncologists and parents for reporting of these results are under study. Supported by NHGRI 1U01HG006485.

IQ change within three years of radiation therapy in pediatric brain tumor patients treated with proton beam radiation therapy versus photon radiation therapy

10009

Background: Radiation therapy (RT), an essential treatment for pediatric brain tumors, increases the risk of cognitive impairment. Advanced RT techniques reduce the volume of normal tissues receiving radiation dose. Proton beam radiation therapy (PBRT) minimizes irradiation to surrounding healthy brain tissue, with the potential to preserve cognitive function better than photon radiotherapy (XRT). We examined change in IQ over time between patients treated for pediatric brain tumors with PBRT versus XRT. Methods: IQ scores obtained in the first 3 years post-RT were abstracted for pediatric brain tumor patients treated with PBRT or XRT. Results: Baseline and follow-up IQ scores were available for 53 survivors (31 PBRT, 22 CRT). A linear regression model predicted follow-up IQ scores controlling for baseline IQ, age-at-RT, time-since-RT, and craniospinal irradiation (CSI), F(7,45)=23.4, p<.001. Follow-up IQ scores were significantly lower in the XRT group compared to the PBRT group (p<.05). The XRT group lost 10.3 IQ points on average with each additional year post-RT (p<.01), while the PBRT group remained stable, losing only 0.1 points per year on average (p<.05). CSI was associated with IQ decline in both groups (p<.05), while age-at-RT was not in either group (p=.154). Total RT dose was not associated with IQ with the above variables in the model. Conclusions: Findings suggest significant cognitive risk is associated with XRT, with IQ scores declining by more than half a standard deviation with each additional year post-RT. In contrast, IQ remained stable in the PBRT group. Preliminary findings suggest that PBRT may spare cognitive functioning in the first 3 years post-RT. Future research should replicate these findings with a larger sample and should study longer-term cognitive outcomes in patients treated with PBRT versus XRT. [Table: see text]

Correlation of insurance status, ethnicity, and race with pathologic risk in retinoblastoma: A Children's Oncology Group (COG) study

e17573

Background: Insurance status affects cancer diagnosis and outcome in adults, but the impact has not been well studied in pediatric cancer. In children with retinoblastoma, time to diagnosis correlates with tumor invasiveness and patient survival, and therefore the disease can be a model to study the effect of demographic variables on delays in diagnosis. Methods: Our patient population consisted of all 203 patients from the United States enrolled on Children’s Oncology Group ARET0332, a study of patients with unilateral retinoblastoma requiring enucleation. All surgical specimens underwent central review by three pathologists to determine the presence of well-defined histopathologic features that correlate with a higher risk of disease progression. Data on insurance status, ethnicity, and race were collected for each patient. For variables not collected, including English proficiency, income, and educational attainment, analyses were conducted indirectly by matching patient zip code with census data for each variable. Results: On univariate analysis, a higher rate of high-risk pathologic findings was found in patients of Hispanic ethnicity (p=0.021) and non-white race (p=0.037), and in those with Medicaid or no insurance (p=0.035). On multivariate analysis, although no one variable correlated with high-risk features independently from the others, Hispanic ethnicity had the greatest impact on risk. Zip code-based analysis did not show significant differences in rates of high-risk findings based on English proficiency, income, or education. Conclusions: Hispanic ethnicity, non-white race, and Medicaid or no insurance all correlated with high-risk pathologic features in a large group of retinoblastoma patients who had central pathology review, and we believe these findings are due to delays in diagnosis for these groups. Future work should use direct methods to study the impact of other variables, including English proficiency, since indirect, zip code-based analysis may be inadequately powered to do so. Further effort should also focus on where in the diagnostic process delays exist, so that interventions can be designed to overcome barriers to care for these groups.

Pulmonary function after treatment for embryonal brain tumors on SJMB03 that included craniospinal irradiation

10021

Background: Treatment of children with embryonal brain tumors (EBT) includes craniospinal irradiation. There are limited data regarding the effect of radiation therapy (RT) on pulmonary function. Methods: Protocol SJMB03 enrolled patients 3 to 21 years of age with EBT. Pulmonary function tests (PFTs) [forced expiratory volume in one second (FEV1) and forced vital capacity (FVC) by spirometry, total lung capacity (TLC) by plethysmography and diffusing capacity of the lung for carbon monoxide (DLCO)] were obtained following completion of RT, prior to each of four courses of high-dose chemotherapy (cumulative cyclophosphamide dose, 16 g/m2), and 24 months after completion of treatment (ACT). Differences between PFTs obtained following the completion of RT and 24 months ACT were compared using exact Wilcoxon signed rank tests. Results: 303 eligible patients were enrolled between June 24, 2003 and March 1, 2010, 258 of whom had at least one PFT. Median age at diagnosis - 8.9 years (range, 3.1 to 20.4 years). Median spinal RT dose - 23.4 Gy (range, 23.4 to 50.4 Gy). Median cyclophosphamide dose was 16.24 g (range, 0 to 34.38 g). 24 months ACT, DLCO was < 75% predicted in 23% (27/115 evaluated), FEV1 was < 80% predicted in 21% (32/150 evaluated), FVC was < 80% predicted in 27% (46/168 evaluated) and TLC was < 80% predicted in 18% (24/135 evaluated) of patients. DLCO was significantly decreased 24 months ACT compared to the end of RT (median difference (MD) in % predicted, - 3.00%; p = 0.035). Race and cumulative cyclophosphamide dose were not significant predictors of DLCO. DLCO was significantly higher among males (p = 0.037) than females in a model that included time point, sex, RT dose group, RT dose*time interaction and age at diagnosis. The differences in FEV1 ((MD, - 1.00%), FVC (MD, 0.00%) and TLC (MD, -2.00%) were not statistically significant. Conclusions: Among patients with EBT treated with spinal RT, DLCO was significantly decreased 24 months after completion of treatment compared to immediately post-RT. TLC was decreased 24 months ACT, suggesting that a significant minority of patients have restrictive lung disease. Continued monitoring of this cohort to five years ACT is planned. Clinical trial information: NCT00085202.

A large prospective trial of children with unilateral retinoblastoma with and without histopathologic high-risk features and the role of adjuvant chemotherapy: A Children’s Oncology Group (COG) study

9515

Background: The definition of histopathologic high-risk features (HRF) in enucleated eyes of children with unilateral retinoblastoma and their contribution to metastases is controversial. The COG completed a large, prospective international study to determine the prevalence of strictly defined histopathologic HRF that are predictors of recurrence and the role of chemotherapy to prevent recurrences. Methods: All patients who underwent enucleation for unilateral retinoblastoma were eligible for the study. Pathology slides were submitted for central review within 21 days of enucleation. Patients with evidence of one or more high-risk features (posterior uveal invasion grades IIC and D, concurrent optic nerve and choroid involvement and post-lamina optic nerve involvement) as determined by central review, received 6 cycles of chemotherapy consisting of carboplatin, vincristine and etoposide. All others were observed. All patients were followed for extraocular recurrences. Results: Patients were enrolled from February of 2005 until May 2010. As of July 2011, the median follow-up from enrollment was 1.9 years (max=5.3 years). Of 312 patients with central histopathology review, 49 patients had their risk classification changed (13% with no HRF had HRF, 24% with HRF had no HRF). Two patients developed extraocular disease and one patient died of unknown cause. The death and one of the extraocular relapses occurred among the 93 (2/93=2.2%, upper 95% CI 3.4%) patients assigned by the central review to receive chemotherapy, while one patient experienced extraocular relapse among the 209 (1/209=0.5%, upper 95% CI 0.6%) assigned to observation only. There is no evidence of a difference in the EFS and OS in these two groups. Conclusions: Preliminary results strongly suggest that a central review of pathology can spare a significant number of patients from exposure to chemotherapy. Chemotherapy may have contributed to fewer relapses in patients with high-risk features as defined in this study. The preliminary results from this study indicate an excellent outcome with this approach.