ARID1B as the top gene of interest in the pediatric chordoma cohort with significantly high dn/ds ratio.

List of rare ARID1B variants identified in the skull-base chordoma cohort.

Allele frequency of mtDNA variants in the skull base chordoma cohort across multiple samples. Comparisons are broken down by sample number and by variant class.

Rare nucleic variants of pediatric chordomas in COSMIC Cancer Census Genes

Rare nucleic variants of adult chordomas in COSMIC Cancer Census Genes, extracted from the original study, and lifted over from GRCh37 build to GRCh38 build.

Pediatric chordoma cohort counts of rare nonsynonymous variants determined from somatic exome sequencing in COSMIC Cancer Census Genes, broken down by variant class (VEP).

Rare mtDNA variants of pediatric chordomas

Nucleic variants of the pediatric chodromas found in the COSMIC Cancer Census Genes

Supplementary Figure 1. Mitochondrial gene variant hotspot analysis in the pediatric chordoma cohort based on VEP variant classifications.

To evaluate age, TNW, or tumor diameter (TD) as continuous prognostic variables for outcomes in early stage FHWT after accounting for biology and treatment. Patient age (< 2 vs. ≥ 2 years) and tumor nephrectomy weight (TNW; < 550g vs. ≥ 550 grams) have been used to risk stratify children with stage I favorable histology Wilms tumor (FHWT) on Children’s Oncology Group (COG) studies and select patients for omission of chemotherapy. Included patients had stage I or II FHWT per central review and were treated with nephrectomy only, EE4A, or DD4A on COG trials. Restricted cubic splines models were used to estimate the stage-specific effects of age, TNW, and TD on event-free survival (EFS) and overall survival (OS), accounting for treatment and biology. In pooled analyses of 775 stage I and 936 stage II patients, age was not significantly associated with EFS or OS for stage I or II patients after accounting for adverse biology that is more prevalent with older age. Greater TNW and larger TD were associated with increased risk of relapse in stage I and increased risk of death in stage II, but not when restricted to patients less than 4 years old. Age, TNW, and TD are each prognostic for EFS or OS in some cohorts of patients with stage I or II FHWT. However, after accounting for adverse biology that becomes more prevalent at older ages, these factors are no longer independently prognostic. The next COG FHWT study will implement and validate these findings.

The objective of this study is to report the long‐term timing and patterns of relapse for children enrolled in Children's Oncology Group AREN0534, a multicenter phase III clinical trial conducted from 2009 to 2015. Participants included children with bilateral Wilms tumor (BWT) or unilateral WT with genetic predisposition to develop BWT followed for up to 10 years. Smoothed hazard (risk) functions for event‐free survival (EFS) were plotted so that the timing of events could be visualized, both overall and within pre‐specified groups. Two hundred and twenty‐two children (190 BWT and 32 unilateral WT with BWT predisposition) were followed for a median of 8.6 years. Fifty events were reported, of which 48 were relapse/progression. The overall 8‐year EFS was 75% (95% confidence interval: 69%–83%). The highest risk for an EFS event was immediately after diagnosis with a declining rate over 2 years. A second peak of events was observed around 4 years after diagnosis, and a small number of events were reported until the end of the follow‐up period. In subset analyses, later increases in risk were more commonly observed in patients with female sex, anaplastic histology, negative lymph nodes or margins, and favorable histology Wilms tumor patients with post‐chemotherapy intermediate risk. Among relapses that occurred after 2 years, most were to the kidney. These patterns suggest that late events may be second primary tumors occurring more commonly in females, although more investigation is required. Clinicians may consider observation of patients with BWT beyond 4 years from diagnosis.

INTRODUCTION:The purpose of this study is to examine the outcomes in children with anaplastic bilateral Wilms tumor (BWT) from study AREN0534 in order to define potential prognostic factors and areas to target in future clinical trials.METHODS:Demographic and clinical data from AREN0534 study patients with anaplasia (focal anaplasia [FA], or diffuse anaplasia [DA]) were compared. Event-free survival (EFS) and overall survival (OS) were reported using Kaplan-Meier estimation with 95% confidence bands, and differences in outcomes between FA and DA compared using log-rank tests. The impact of margin status was analyzed.RESULTS:Twenty-seven children who enrolled on AREN0534 had evidence of anaplasia (17 DA, 10 FA) in at least one kidney and were included in this analysis. Twenty-six (96%) had BWT. Nineteen percent had anaplastic histology in both kidneys (four of 17 DA, and one of 10 FA). Forty-six percent with BWT had bilateral nephron-sparing surgery (NSS); one child who went off protocol therapy, eventually required bilateral completion nephrectomies. Median follow-up for EFS and OS was 8.6 and 8.7 years from enrollment. Four- and 8-year EFS was 53% [95% confidence interval (CI): 34%-83%] for DA; 4-year EFS was 80% [95% CI: 59%-100%], and 8-year EFS 70% [95% CI: 47%-100%] for FA. Three out of 10 children with FA and eight out of 17 children with DA had events. EFS did not differ statistically by margin status (p = .79; HR = 0.88). Among the six children who died (five DA, one FA), all experienced prior relapse or progression within 18 months.CONCLUSION:Events in children with DA/FA in the setting of BWT occurred early. Caution should be taken about interpreting the impact of margin status outcomes in the context of contemporary multimodal therapy. Future targeted investigations in children with BWT and DA/FA are needed.

Little is known about the genomic alterations in chordoma, with the exception of loss of SMARCB1, a core member of the SWI/SNF complex, in poorly differentiated chordomas. A TBXT duplication and rs2305089 polymorphism, located at 6q27, are known genetic susceptibility loci. A comprehensive genomic analysis of the nuclear and mitochondrial genomes in pediatric chordoma has not yet been reported. In this study, we performed WES and mtDNA genome sequencing on 29 chordomas from 23 pediatric patients. Findings were compared with that from whole-genome sequencing datasets of 80 adult patients with skull base chordoma. In the pediatric chordoma cohort, 81% of the somatic mtDNA mutations were observed in NADH complex genes, which is significantly enriched compared with the rest of the mtDNA genes (P = 0.001). In adult chordomas, mtDNA mutations were also enriched in the NADH complex genes (P < 0.0001). Furthermore, a progressive increase in heteroplasmy of nonsynonymous mtDNA mutations was noted in patients with multiple tumors (P = 0.0007). In the nuclear genome, rare likely germline in-frame indels in ARID1B, a member of the SWI/SNF complex located at 6q25.3, were observed in five pediatric patients (22%) and four patients in the adult cohort (5%). The frequency of rare ARID1B indels in the pediatric cohort is significantly higher than that in the adult cohort (P = 0.0236, Fisher's exact test), but they were both significantly higher than that in the ethnicity-matched populations (P < 5.9e-07 and P < 0.0001174, respectively). Implications: germline ARID1B indels and mtDNA aberrations seem important for chordoma genesis, especially in pediatric chordoma.

Setting: General community, academic hospital setting.Patients or Other Participants: Pregnant AL patients.Main Outcome Measures: Maternal and fetal outcomes.Results: We identified 6 pregnant AL patients: acute promyelocytic leukemia (APL)=1, core binding factor acute myeloid leukemia (AML)=2, acute lymphoblastic leukemia (ALL)=3 (T-cell lymphoblastic leukemia [ATL]=2, BCR-ABL-negative B-ALL=1).The median age was 24.5 (range, 21-31) years.Subject races were 1 White, 1 Asian, 3 African American, and 1 Hispanic.The APL patient presented with intracranial hemorrhage at 25 weeks gestation and died within 48 hours of admission.A cesarean section was performed, but the fetus was dead.The ATL patient, diagnosed at 12 weeks, received induction chemotherapy (IC) with hyperfractionated cyclophosphamide, vincristine, doxorubicin, and dexamethasone (hyper-CVAD A), and achieved a complete response (CR).She delivered at 32 weeks but died from relapsed ATL 10 months after diagnosis.The second ATL patient, diagnosed at 32 weeks, started IC with hyper-CVAD A 72 hours after cesarean section, achieving a CR.The B-ALL patient was diagnosed at 22 weeks and had refractory disease after one cycle of hyper-CVAD A. She received blinatumomab salvage therapy and remains in CR.One AML patient, diagnosed at 32 weeks, underwent cesarean section, and started IC 72 hours later with fludarabine, cytarabine, and idarubicin, achieving a CR, but died from septic shock 8 months after diagnosis.The second AML patient, diagnosed at 17 weeks, received fludarabine, cytarabine, and gemtuzumab ozogamicin, achieved a CR, and delivered at 34 weeks.Four of the six women are currently alive and leukemia-free.Five of the six children are alive.Conclusion: Treating AL during pregnancy is challenging; a multidisciplinary team of maternal-fetal medicine and malignant hematology specialists is critical to improve outcomes.Standard leukemia IC regimens can be safely administered during the second or third trimester of pregnancy.

Measurable residual disease (MRD) is the most important post-treatment predictor of relapse in acute myeloid leukemia (AML) [PMID 33030517]. The bulk of clinical MRD studies in AML have been performed via multi-parameter flow cytometry and no molecular MRD platform is established for clinical use in AML. Droplet digital PCR (ddPCR) has been identified as a highly sensitive and precise modality for mutation monitoring in AML and other malignancies, but to date the range of mutations evaluated for AML has been limited [PMIDs 32629801, 28525762, 29472349]. Here we demonstrate the feasibility of retrospectively detecting molecular MRD with a broad panel of ddPCR assays in adult AML patients. We confirm the association of ddPCR MRD status with outcomes in patients receiving both standard chemotherapy and venetoclax/azacitidine, including a subset of patients who proceeded to stem cell transplant (SCT). All patients signed Colorado Multiple Institution Review Board (IRB) approved consent for collection of tissue used in this analysis, and an additional IRB approval allowed retrospective data analysis. Adult patients with a known AML mutational profile at diagnosis from clinical targeted NGS and with at least one post-remission bone marrow sample available for DNA extraction were included. Genomic DNA was extracted from whole bone marrow aspirates using Qiagen QIAsymphony DSP DNA kits. Concentration and quality of DNA was evaluated via Qubit spectrophotometer. A total of 57 AML-associated mutations were evaluated in this patient cohort using mutation-specific primer/probe ddPCR assays purchased commercially (BioRad) or custom designed. All assays were experimentally validated to a limit of detection of 0.02-0.15% variant allelic frequency (VAF). ddPCR was performed on a BioRad QX200 Droplet Digital PCR instrument using gDNA input of 150 ng per sample and appropriate positive and negative controls. Data were analyzed via the BioRad QuantaSoft Analysis Pro v1.0 software. Between one and five non-DTA mutations [PMID 29601269] per patient were serially monitored. For survival analyses, patients were categorized as MRD positive or negative according to their best response to therapy. Relapse-free survival (RFS) and overall survival (OS) were defined from the date of diagnosis to the respective endpoint. Individuals were censored at date of last follow-up. A total of 87 patients with at least one non-DTA mutation identified on diagnostic clinical NGS and available DNA from post-treatment time points had MRD quantified by ddPCR. Twenty patients received anthracycline + high-dose cytarabine-based therapies ('7+3'), 65 patients received venetoclax + azacitidine (ven/aza), and 2 patients received alternate low-intensity therapies (ivosedenib or decitabine + anti-CD123 antibody). Median follow-up for the entire cohort was 25.4 months (2.5-90.1 months). Fifty of 87 patients (19 '7+3', 30 ven/aza, 1 other) became MRD negative by ddPCR during the course of their therapy with median cohort survival of 36.4 months (6.9-90.1 months). The other 37 patients (1 '7+3', 35 ven/aza, 1 other) remained MRD positive at all evaluated time points post-therapy with median cohort survival of 12.9 months (2.5-67.1 months). Survival curves based on ddPCR MRD status are shown in Figure 1. A total of 39 patients (20 '7+3', 18 ven/aza, 1 "other" therapy) proceeded to SCT as part of their AML therapy, of which 9 were MRD negative prior to SCT, 27 became MRD negative post-SCT, and 3 had persistent MRD. There was no relationship between clearance of a mutation and its VAF at diagnosis (p=0.15). Of note, 12 patients (6 receiving '7+3', 6 receiving ven/aza) who achieved MRD negativity subsequently relapsed; of these 4 patients had reappearance of MRD by ddPCR between 1-4 months prior to clinical relapse. One patient was MRD negative pre-SCT and did not have post-SCT samples available prior to relapse. The other 7 patients had bone marrow evaluations every 2-3 months yet did not have a positive MRD time point prior to clinical relapse. ddPCR MRD is prognostic of outcomes in adult AML patients on therapy, including those receiving venetoclax/azacitidine. Evaluation of a broad range of mutations with ddPCR is possible and based on these data is expected to be a valuable prospective tool for clinical decisions about escalation or de-escalation of therapy. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Background: Abdominal wall endometrioma (AWE) is a rare sequela of cesarean sections and other pelvic surgeries. We present a case of AWE after drainage of hematometrocolpos with vaginostomy tube placement. While vaginostomy tube drainage is an option for acute management of hematometrocolpos, AWE could be a complication of this procedure.

IntroductionSince the initial attempts to treat children with renal cancer over 50 years ago, outcome for children with renal cancer has generally become promising. While the first endeavors mainly included surgical treatment, in the early 60s radiotherapy and chemotherapy were introduced, leading to cure of patients, including some with metastatic disease. (1) Since then, overall survival rates for the most common type of renal tumors in childhood (nephroblastoma or Wilms tumor) have improved to more than 90 percent. These excellent treatment outcomes are similar in the 2 largest clinical trial groups (the Children’s Oncology Group Renal Tumor Committee (COG-RTC; former National Wilms Tumor Study Group (NTWSG)), and the International Society of Pediatric Oncology Renal Tumor Study Group (SIOP-RTSG). Despite the difference in upfront treatment choice (primary surgery when feasible (COG-RTC) or preoperative chemotherapy (SIOP-RTSG)) both groups have optimized the stratification of patients in their trials by modifying the intensity of treatment according to individual risk factors, in order to improve outcome for high-risk renal tumor types, but also to reduce early and late toxicity in lower and intermediate risk tumors as much as possible. (2-4)This improvement in risk stratification has resulted in better outcomes and less cancer related toxicity. However, for remaining small subgroups of pediatric renal tumor patients, with very poor outcomes, further understanding of the underlying biology, in correlation with clinic-pathological characteristics, is an unmet need. Further, standard multidisciplinary treatment (surgery, radiotherapy, chemotherapy) can be challenging to access and/or deliver in some low and middle income countries (LMIC). The power inherent in international collaboration to address these challenges was a driving principle that supported the creation of the HARMONICA (HARMONIzation and COllaboration) initiative in 2015, when we established an organized collaborative structure for transatlantic experts from COG-RTC and SIOP-RTSG. The mandate of HARMONICA is to identify specific challenges for pediatric renal tumor subsets in order to meet the aims of our global approach to cure every child with a renal tumor with limited toxicity.The HARMONICA group meets at least once a month by videoconferences, and as much as possible also face to face, at least once or twice a year, during existing pediatric cancer conferences. In addition, several transatlantic HARMONICA expert subgroups are collaborating on specific topics. All work is currently done by a tremendous engagement of many enthusiastic members of both study groups. Despite the fact of obvious advantages, HARMONICA is still lacking funding and needs to optimize their structure as a legal entity. Notwithstanding such limitations, in this special issue of PBC, we present the achievements, the challenges, and the future perspectives, identified by these expert groups.

Acute kidney injury (AKI) is a common cause of morbidity after congenital heart disease surgery. Progress on diagnosis and therapy remains limited, however, in part due to poor mechanistic understanding and a lack of relevant translational models. Metabolomic approaches could help identify novel mechanisms of injury and potential therapeutic targets. In the present study, we used a piglet model of cardiopulmonary bypass with deep hypothermic circulatory arrest (CPB/DHCA) and targeted metabolic profiling of kidney tissue, urine, and serum to evaluate metabolic changes specific to animals with histological acute kidney injury. CPB/DHCA animals with acute kidney injury were compared with those without acute kidney injury and mechanically ventilated controls. Acute kidney injury occurred in 10 of 20 CPB/DHCA animals 4 h after CPB/DHCA and 0 of 7 control animals. Injured kidneys showed a distinct tissue metabolic profile compared with uninjured kidneys (R2 = 0.93, Q2 = 0.53), with evidence of dysregulated tryptophan and purine metabolism. Nine urine metabolites differed significantly in animals with acute kidney injury with a pattern suggestive of increased aerobic glycolysis. Dysregulated metabolites in kidney tissue and urine did not overlap. CPB/DHCA strongly affected the serum metabolic profile, with only one metabolite that differed significantly with acute kidney injury (pyroglutamic acid, a marker of oxidative stress). In conclusion, based on these findings, kidney tryptophan and purine metabolism are candidates for further mechanistic and therapeutic investigation. Urine biomarkers of aerobic glycolysis could help diagnose early acute kidney injury after CPB/DHCA and warrant further evaluation. The serum metabolites measured at this early time point did not strongly differentiate based on acute kidney injury. NEW & NOTEWORTHY This project explored the metabolic underpinnings of postoperative acute kidney injury (AKI) following pediatric cardiac surgery in a translationally relevant large animal model of cardiopulmonary bypass with deep hypothermic circulatory arrest. Here, we present novel evidence for dysregulated tryptophan catabolism and purine catabolism in kidney tissue and increased urinary glycolysis intermediates in animals who developed histological AKI. These pathways represent potential diagnostic and therapeutic targets for postoperative AKI in this high-risk population.

B-lymphoblastic leukemia/lymphoma (B-ALL) is the most common pediatric malignancy and the most commonly diagnosed adult lymphoblastic leukemia. Recent advances have broadened the spectrum of B-ALL, with DUX4 gene fusions implicated in a subclass occurring in adolescents and young adults and harboring a favorable prognosis. DUX4 fusions have been challenging to identify. We aimed to determine whether expression of the DUX4 oncoprotein, as detected by targeted immunohistochemistry, might serve as a surrogate for molecular detection of DUX4 fusions in B-ALL. A cohort of investigational B-ALLs was generated with enrichment for DUX4 fusions by the inclusion of cases with characteristic demographic features and immunophenotypic properties. B-ALLs with mutually exclusive cytogenetics were collected. Immunohistochemical staining by a monoclonal antibody raised against the N-terminus of the DUX4 protein was performed. N-DUX4 immunohistochemistry demonstrated strong, crisp nuclear staining in blasts of seven investigational cases, six of which had nucleic acid material available for molecular evaluation. Five of these cases demonstrated RNA-seq DUX4-fusion positivity. One N-DUX4 immunohistochemistry positive case lacked a definitive DUX4-fusion by RNA-seq, though demonstrated a gene expression profile characteristic of DUX4-rearranged B-ALLs, a CD2+ immunophenotype, and a lack of staining by C-terminus DUX4 antibody immunohistochemistry. At least 83.3% [5/6] positive predictive value. N-DUX4 immunohistochemistry was negative in blasts of three RNA-seq DUX4-fusion-negative cases (3/3; 100% negative predictive value). B-ALLs with mutually exclusive cytogenetic profiles were all N-DUX4 negative (0/10, specificity 100%). N-DUX4 immunohistochemistry is reliable for the distinction of DUX4-rearranged B-ALLs from other B-ALLs. We recommend its use for subclassification of B-ALLs in adolescents and young adults and in B-ALLs that remain "not otherwise specified."