Genome-wide study identifies novel genes associated with bone toxicities in children with acute lymphoblastic leukaemia.

Bone toxicities are common among paediatric patients treated for acute lymphoblastic leukaemia (ALL) with potentially major negative impact on patients' quality of life. To identify the underlying genetic contributors, we conducted a genome-wide association study (GWAS) and a transcriptome-wide association study (TWAS) in 260 patients of European-descent from the DFCI 05-001 ALL trial, with validation in 101 patients of European-descent from the DFCI 11-001 ALL trial. We identified a significant association between rs844882 on chromosome 20 and bone toxicities in the DFCI 05-001 trial (p = 1.7 × 10-8). In DFCI 11-001 trial, we observed a consistent trend of this variant with fracture. The variant was an eQTL for two nearby genes, CD93 and THBD. In TWAS, genetically predicted ACAD9 expression was associated with an increased risk of bone toxicities, which was confirmed by meta-analysis of the two cohorts (meta-p = 2.4 × 10-6). In addition, a polygenic risk score of heel quantitative ultrasound speed of sound was associated with fracture risk in both cohorts (meta-p = 2.3 × 10-3). Our findings highlight the genetic influence on treatment-related bone toxicities in this patient population. The genes we identified in our study provide new biological insights into the development of bone adverse events related to ALL treatment.

Supplemental Nutrition Assistance Program participation gaps within a pediatric leukemia clinical trial cohort.

Poverty-exposed children with cancer are more likely to experience adverse outcomes. Supplemental Nutrition Assistance Program (SNAP) benefits improve food insecurity and child health outcomes, and could be used to mitigate disparities. We conducted a secondary analysis of parent-reported data collected in a frontline pediatric leukemia trial (NCT03020030) to assess SNAP eligibility (proxied by other means-tested program participation) and participation. At diagnosis, 105/287 families (37%) were SNAP-eligible, of whom 53 (50%) were SNAP participants. At 6 months, 104/257 families (41%) were SNAP-eligible, and 59 (57%) were SNAP participants. Interventions to increase benefits participation during childhood cancer treatment represent an immediate opportunity to reduce disparities.

Drivers of Differential Time to Diagnosis in Pediatric ALL Tied to Race and Ethnicity.

Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy, with diagnosis preceded by symptoms that may include fever, weight loss, fatigue, bleeding, and bruising. Timely diagnosis and treatment of ALL may lead to improved outcomes and reduced morbidity from associated complications, including tumor lysis syndrome, hyperviscosity, and stroke. We performed a retrospective cohort analysis of 274 pediatric pre-B cell ALL and acute lymphoblastic lymphoma patients within Montefiore Health System to determine whether there were factors associated with time from symptom onset to diagnosis. The median time to diagnosis for all patients was 11.5 days (interquartile range: 7.8, 14.3). Those with Medicaid insurance (n=189) were diagnosed sooner than those with private/self-pay insurance (n=85) (median of 10 vs. 16 days; P =0.05). English and other language speakers experienced fewer median days from symptom onset to diagnosis date compared with Spanish speakers (11 vs. 7 vs. 14; P =0.05). Insurance status may impact the time to diagnosis to a greater degree in non-Hispanic patients, while the English language and female sex may represent a greater advantage to Hispanic patients. Insurance status and language preference may impact the time to diagnosis of pediatric ALL. There is a further need to confirm our findings and to study possible causes driving these disparities.

Feasibility of oncology clinical trial-embedded evaluation of social determinants of health.

Social determinants of health (SDoH) are associated with stark disparities in cancer outcomes, but systematic SDoH data collection is virtually absent from oncology clinical trials. Trial-based SDoH data are essential to ensure representation of marginalized populations, contextualize outcome disparities, and identify health-equity intervention opportunities. We report the feasibility of a pediatric oncology multicenter therapeutic trial-embedded SDoH investigation. Among 448 trial participants, 392 (87.5%) opted-in to the embedded SDoH study; 375 (95.7%) completed baseline surveys, with high longitudinal response rates (88.9-93.1%) over 24 months. Trial-embedded SDoH data collection is feasible and acceptable and must be consistently included within future oncology trials.

Identification of prognostic factors in childhood T-cell acute lymphoblastic leukemia: Results from DFCI ALL Consortium Protocols 05-001 and 11-001.

BACKGROUND/OBJECTIVES: While outcomes for pediatric T-cell acute lymphoblastic leukemia (T-ALL) are favorable, there are few widely accepted prognostic factors, limiting the ability to risk stratify therapy. DESIGN/METHODS: Dana-Farber Cancer Institute (DFCI) Protocols 05-001 and 11-001 enrolled pediatric patients with newly diagnosed B- or T-ALL from 2005 to 2011 and from 2012 to 2015, respectively. Protocol therapy was nearly identical for patients with T-ALL (N = 123), who were all initially assigned to the high-risk arm. End-induction minimal residual disease (MRD) was assessed by reverse transcription polymerase chain reaction (RT-PCR) or next-generation sequencing (NGS), but was not used to modify postinduction therapy. Early T-cell precursor (ETP) status was determined by flow cytometry. Cases with sufficient diagnostic DNA were retrospectively evaluated by targeted NGS of known genetic drivers of T-ALL, including Notch, PI3K, and Ras pathway genes. RESULTS: The 5-year event-free survival (EFS) and overall survival (OS) for patients with T-ALL was 81% (95% CI, 73-87%) and 90% (95% CI, 83-94%), respectively. ETP phenotype was associated with failure to achieve complete remission, but not with inferior OS. Low end-induction MRD (<10-4 ) was associated with superior disease-free survival (DFS). Pathogenic mutations of the PI3K pathway were mutually exclusive of ETP phenotype and were associated with inferior 5-year DFS and OS. CONCLUSIONS: Together, our findings demonstrate that ETP phenotype, end-induction MRD, and PI3K pathway mutation status are prognostically relevant in pediatric T-ALL and should be considered for risk classification in future trials. DFCI Protocols 05-001 and 11-001 are registered at www.clinicaltrials.gov as NCT00165087 and NCT01574274, respectively.

Severe Vincristine-related Neurotoxicity in 5 Patients With Pediatric Acute Lymphoblastic Leukemia Requiring Discontinuation of Vincristine: A Description of Long-term Outcome.

Vincristine, a key agent in the treatment of many pediatric malignancies, causes sensory, motor and autonomic neuropathy. We report the clinical courses of 5 patients who required cessation of vincristine after developing severe neurotoxicity during treatment for acute lymphoblastic leukemia. All 5 patients lost the ability to ambulate and 3 had additional severe neurotoxic side effects including vision loss and vocal cord dysfunction. Although prior literature reports poor outcomes for children in whom vincristine was discontinued during acute lymphoblastic leukemia therapy, all 5 patients described here achieved and have maintained complete continuous remission.

Decreasing Prescribing Errors in Antimicrobial Stewardship Program-Restricted Medications.

OBJECTIVES: Antimicrobial stewardship programs (ASPs) restrict prescribing practices to regulate antimicrobial use, increasing the risk of prescribing errors. This quality improvement project aimed to decrease the proportion of prescribing errors in ASP-restricted medications by standardizing workflow. METHODS: The study took place on all inpatient units at a tertiary care children's hospital between January 2020 and February 2022. Patients <22 years old with an order for an ASP-restricted medication course were included. An interprofessional team used the Model for Improvement to design interventions targeted at reducing ASP-restricted medication prescribing errors. Plan-Do-Study-Act cycles included standardizing communication and medication review, implementing protocols, and developing electronic health record safety nets. The primary outcome was the proportion of ASP-restricted medication orders with a prescribing error. The secondary outcome was time between prescribing errors. Outcomes were plotted on control charts and analyzed for special cause variation. Outcomes were monitored for a 3-month sustainability period. RESULTS: Nine-hundred ASP-restricted medication orders were included in the baseline period (January 2020-December 2020) and 1035 orders were included in the intervention period (January 2021-February 2022). The proportion of prescribing errors decreased from 10.9% to 4.6%, and special cause variation was observed in Feb 2021. Mean time between prescribing errors increased from 2.9 days to 8.5 days. These outcomes were sustained. CONCLUSIONS: Quality improvement methods can be used to achieve a sustained reduction in the proportion of ASP-restricted medication orders with a prescribing error throughout an entire children's hospital.

Impact of race/ethnicity and language preferences on pediatric ALL survival outcomes.

BACKGROUND: Ethnic and racial disparities have recently been observed both in treatment-related toxicities and rates of long-lasting cure in acute lymphoblastic leukemia (ALL) and acute lymphoblastic lymphoma (ALLy), the most common pediatric malignancy. Despite significant improvements in overall survival in the recent past, a large number of children die from aggressive disease. METHODS: We performed a retrospective cohort analysis of 274 pediatric ALL/ALLy patients within Montefiore Health System from 2004 to 2021 to determine differences in all-cause mortality within the Pediatric Hematologic Malignancies Cohort using Cox Proportional Hazard regression modeling, adjusted for age at diagnosis, race/ethnicity, administration of intensive chemotherapy, preferred language, maximum glucose, and hypertension. RESULTS: Among our 274 patients, 132 were Hispanic, 54 Non-Hispanic Black, and 25 Non-Hispanic White, with 25 identified as "Non-Hispanic Other," including Asian, Arabic, and Other. Hispanic patients were 78% less likely to die (HR 0.22; 95% CI 0.07, 0.73) when compared with Non-Hispanic Black individuals. Spanish speakers were 2.91 times more likely to die compared with those who spoke English (HR 2.91; 95% CI 1.08, 7.82). Among those English speakers, the diagnosis of hypertension and Hispanic ethnicity significantly impacted the risk of death, while these factors did not impact survival in Spanish speakers. High-risk cytogenetics did not impact survival. CONCLUSIONS: Hispanic children with ALL/ALLy have improved survival outcomes compared with Non-Hispanic Blacks. Additionally, Spanish language preference was strongly associated with poorer survival, a novel finding that should be validated in future studies.

Disparities in parental distress in a multicenter clinical trial for pediatric acute lymphoblastic leukemia.

BACKGROUND: Parent psychological distress during childhood cancer treatment has short- and long-term implications for parent, child, and family well-being. Identifying targetable predictors of parental distress is essential to inform interventions. We investigated the association between household material hardship (HMH), a modifiable poverty-exposure defined as housing, food, or utility insecurity, and severe psychological distress among parents of children aged 1-17 years with acute lymphoblastic leukemia (ALL) enrolled on the multicenter Dana-Farber ALL Consortium Trial 16-001. METHODS: This was a secondary analysis of parent-reported data. Parents completed an HMH survey within 32 days of clinical trial enrollment (T0) and again at 6 months into therapy (T1). The primary exposure was HMH at T0 and primary outcome was severe parental distress at T0 and T1, defined as a score greater than or equal to 13 on the Kessler-6 Psychological Distress Scale. Multivariable models were adjusted for ALL risk group and single parent status. RESULTS: Among 375 evaluable parents, one-third (32%; n = 120/375) reported HMH at T0. In multivariable analyses, T0 HMH was associated with over twice the odds of severe psychological distress at T0 and T1 HMH was associated with over 5 times the odds of severe distress at T1. CONCLUSIONS: Despite uniform clinical trial treatment of their children at well-resourced pediatric centers, HMH-exposed parents-compared with unexposed parents-experienced statistically significantly increased odds of severe psychological distress at the time of their child's leukemia diagnosis, which worsened 6 months into therapy. These data identify a high-risk parental population who may benefit from early psychosocial and HMH-targeted interventions to mitigate disparities in well-being.

Whole-transcriptome analysis in acute lymphoblastic leukemia: a report from the DFCI ALL Consortium Protocol 16-001.

The molecular hallmark of childhood acute lymphoblastic leukemia (ALL) is characterized by recurrent, prognostic genetic alterations, many of which are cryptic by conventional cytogenetics. RNA sequencing (RNA-seq) is a powerful next-generation sequencing technology that can simultaneously identify cryptic gene rearrangements, sequence mutations and gene expression profiles in a single assay. We examined the feasibility and utility of incorporating RNA-seq into a prospective multicenter phase 3 clinical trial for children with newly diagnosed ALL. The Dana-Farber Cancer Institute ALL Consortium Protocol 16-001 enrolled 173 patients with ALL who consented to optional studies and had samples available for RNA-seq. RNA-seq identified at least 1 alteration in 157 patients (91%). Fusion detection was 100% concordant with results obtained from conventional cytogenetic analyses. An additional 56 gene fusions were identified by RNA-seq, many of which confer prognostic or therapeutic significance. Gene expression profiling enabled further molecular classification into the following B-cell ALL (B-ALL) subgroups: high hyperdiploid (n = 36), ETV6-RUNX1/-like (n = 31), TCF3-PBX1 (n = 7), KMT2A-rearranged (KMT2A-R; n = 5), intrachromosomal amplification of chromosome 21 (iAMP21) (n = 1), hypodiploid (n = 1), Philadelphia chromosome (Ph)-positive/Ph-like (n = 16), DUX4-R (n = 11), PAX5 alterations (PAX5 alt; n = 11), PAX5 P80R (n = 1), ZNF384-R (n = 4), NUTM1-R (n = 1), MEF2D-R (n = 1), and others (n = 10). RNA-seq identified 141 nonsynonymous mutations in 93 patients (54%); the most frequent were RAS-MAPK pathway mutations. Among 79 patients with both low-density array and RNA-seq data for the Philadelphia chromosome-like gene signature prediction, results were concordant in 74 patients (94%). In conclusion, RNA-seq identified several clinically relevant genetic alterations not detected by conventional methods, which supports the integration of this technology into front-line pediatric ALL trials. This trial was registered at www.clinicaltrials.gov as #NCT03020030.

Matched Targeted Therapy for Pediatric Patients with Relapsed, Refractory, or High-Risk Leukemias: A Report from the LEAP Consortium.

Despite a remarkable increase in the genomic profiling of cancer, integration of genomic discoveries into clinical care has lagged behind. We report the feasibility of rapid identification of targetable mutations in 153 pediatric patients with relapsed/refractory or high-risk leukemias enrolled on a prospective clinical trial conducted by the LEAP Consortium. Eighteen percent of patients had a high confidence Tier 1 or 2 recommendation. We describe clinical responses in the 14% of patients with relapsed/refractory leukemia who received the matched targeted therapy. Further, in order to inform future targeted therapy for patients, we validated variants of uncertain significance, performed ex vivo drug-sensitivity testing in patient leukemia samples, and identified new combinations of targeted therapies in cell lines and patient-derived xenograft models. These data and our collaborative approach should inform the design of future precision medicine trials. SIGNIFICANCE: Patients with relapsed/refractory leukemias face limited treatment options. Systematic integration of precision medicine efforts can inform therapy. We report the feasibility of identifying targetable mutations in children with leukemia and describe correlative biology studies validating therapeutic hypotheses and novel mutations.See related commentary by Bornhauser and Bourquin, p. 1322.This article is highlighted in the In This Issue feature, p. 1307.

Unilateral absence of the pulmonary veins: an unusual diagnosis with characteristic imaging findings.

BACKGROUND: Congenital unilateral absence of the pulmonary vein (UCAPV) is a rare entity with characteristic clinical and imaging findings. Despite its congenital nature, the radiographic findings and symptoms of UCAPV may not be recognized at birth and patients may present in childhood or early adulthood with findings that may mimic other diagnoses. METHODS: The evolution of imaging findings in UCAPV is presented through two cases, one of which demonstrates the progression of findings over several years. The embryologic basis of this entity is reviewed and the clinical presentation and characteristic imaging findings including radiographs, nuclear scintigraphy, computed tomography, magnetic resonance imaging and cardiac catheterization are demonstrated. RESULTS: Characteristically, normal at birth, radiographs demonstrate the gradual development of a small lung and ipsilateral pulmonary artery over time. In addition to unilateral absence of the pulmonary veins on CT or MRI, a mediastinal "soft tissue mass" reflecting the development of mediastinal collaterals is a common finding and should be recognized as secondary to the absent ipsilateral pulmonary veins rather than as a primary process causing occlusion of the pulmonary veins. Scintigraphy will show absent perfusion to the affected lung. CONCLUSION: Awareness of the distinctive imaging findings in this unusual condition is critical to avoid misdiagnosis and to prevent the consequences of UCAPV which include pulmonary hypertension and extensive venous collaterals with or without hemoptysis, both of which may prevent definitive repair.