RESUMEN
OBJECTIVES: Pathology is an essential component of disease diagnosis and management in pediatric gastroenterology. Pathology reports have not been standardized in some areas of pediatric gastrointestinal pathology and pathology reporting varies. Development of electronic medical record (EMR) pathology synoptic report templates (PSRT) enables pathology data collection in a specific format and can help standardize pathology reporting. We developed, implemented, and evaluated EMR PSRTs for eosinophilic esophagitis (EoE) and inflammatory bowel disease (IBD). METHODS: PSRTs were developed by a multidisciplinary team of pediatric experts of allergy, gastroenterology, and pathology for both EoE and IBD based on available literature and validated scales. Likert surveys (range 1 low acceptance to 5 high acceptance) based on the Technology Acceptance Model assessed user acceptance of the developed PSRTs. The use of PSRTs was monitored via control charts. RESULTS: Overall, evaluation questionnaires achieved >80% response rates. Clinicians and pathologists reported moderate-to-high levels of Perceived Usefulness (median [interquartile range) for EoE PSRT: clinicians 4.0 (4.0, 5.0) and pathologists 3.5 (3.5, 4.0); and IBD PSRT: clinicians 4.0 (3.0, 4.0) and pathologists 4.0 (4.0, 5.0)) and Perceived Ease of Use (EoE PSRT: clinicians 4.5 (4.0, 5.0) and pathologists 4.0 (4.0, 4.0); and IBD PSRT: clinicians 4.0 (4.0, 5.0) and pathologists 4.0 (4.0, 5.0)) of the developed PSRTs. Control charts demonstrated 100% utilization by 2-5 months from launch. CONCLUSIONS: We demonstrate successful implementation of synoptic reporting for both pediatric EoE and IBD pathology. EMR synoptic reporting provides standardization of pathology reporting and improved methods of pathology data presentation, which could potentially optimize provider efficiency, clinician interpretation of pathology results and disease trajectory, patient care, and clinician satisfaction.
RESUMEN
Importance: Young children are ingesting illicit drugs at increased rates, but it is unknown what the associated child protection system (CPS) responses are when a child tests positive. Objective: To document the child protection system involvement and the characteristics of children who test positive for illicit substances. Design, Setting, and Participants: This retrospective cross-sectional study linked medical discharge and child protection system administrative data. The setting was Rady Children's Hospital San Diego, a free-standing pediatric hospital in California. Participants included all emergency department and inpatient medical encounters involving children aged 12 years or younger with a positive urine drug test between 2016 and 2021. Statistical analysis was performed from February 2023 to January 2024. Exposure: Drug type, including amphetamines, barbiturates, benzodiazepines, cannabis, cocaine, fentanyl, opiates, and phencyclidine. Main Measures and Outcomes: CPS responses associated with the medical encounter including reports, substantiations, case openings, and out-of-home placements. Results: A total of 511 emergency department and inpatient medical encounters involving children had a positive drug test (262 [51.3%] were female; 309 [60.5%] were age 6 years or younger; fewer than 10 [<3.0%] were American Indian or Alaska Native; 252 [49.3%] were Hispanic [any race], 20 [3.9%] were non-Hispanic Asian, 56 [11.0%] were non-Hispanic Black, 143 [28.0%] were non-Hispanic White, 36 [7.0%] had other or unknown race and ethnicity; 233 [43.6%] had a CPS report prior to the medical encounter). Following the positive screen, 244 (47.7%) were reported to child protection, and 61 (11.9%) were placed out-of-home within 30 days. Mean (SD) quarterly counts of encounters with positive drug tests doubled after the COVID-19 pandemic onset (32.9 [9.8]) compared with prior to the pandemic onset (16.5 [4.7]); for encounters positive for cannabis, mean (SD) quarterly counts were 3 times as high after the pandemic onset than prior (16.6 [4.7] vs 5.7 [2.9]). Encounters for children under age 1 were significantly more likely to have associated child protection reports (relative risk [RR], 2.91 [95% CI, 2.21-3.83]) and child protection case openings (RR, 1.71 [95% CI, 1.07-2.72]) than encounters involving older children. Conclusions and Relevance: In this cross-sectional study of emergency department and inpatient medical encounters, less than half of children with positive urine drug screens were reported to CPS; out-of-home placements were uncommon. With increased encounters for positive drug tests, it is unclear what services these children and families are receiving.
Asunto(s)
Cannabis , Alucinógenos , Niño , Humanos , Femenino , Adolescente , Preescolar , Masculino , Estudios Transversales , Pandemias , Estudios Retrospectivos , Orina , Urinálisis , Agonistas de Receptores de CannabinoidesRESUMEN
Pathogenic variants in the DES gene clinically manifest as progressive skeletal muscle weakness, cardiomyopathy with associated severe arrhythmias, and respiratory insufficiency, and are collectively known as desminopathies. While most DES pathogenic variants act via a dominant mechanism, recessively acting variants have also been reported. Currently, there are no effective therapeutic interventions for desminopathies of any type. Here, we report an affected individual with rapidly progressive dilated cardiomyopathy, requiring heart transplantation at age 13 years, in the setting of childhood-onset skeletal muscle weakness. We identified biallelic DES variants (c.640-13 T>A and c.1288+1 G>A) and show aberrant DES gene splicing in the affected individual's muscle. Through the generation of an inducible lentiviral system, we transdifferentiated fibroblast cultures derived from the affected individual into myoblasts and validated this system using RNA sequencing. We tested rationally designed, custom antisense oligonucleotides to screen for splice correction in these transdifferentiated cells and a functional minigene splicing assay. However, rather than correctly redirecting splicing, we found them to induce undesired exon skipping. Our results indicate that, while an individual precision-based molecular therapeutic approach to splice-altering pathogenic variants is promising, careful preclinical testing is imperative for each novel variant to test the feasibility of this type of approach for translation.
Asunto(s)
Cardiomiopatías , Cardiomiopatía Dilatada , Adolescente , Humanos , Cardiomiopatías/genética , Cardiomiopatía Dilatada/genética , Mutación , Empalme del ARN/genéticaRESUMEN
Brain tumors in children are a devastating disease in a high proportion of patients. Owing to inconsistent results in clinical trials in unstratified patients, the role of immunotherapy remains unclear. We performed an in-depth survey of the single-cell transcriptomes and clonal relationship of intra-tumoral T cells from children with brain tumors. Our results demonstrate that a large fraction of T cells in the tumor tissue are clonally expanded with the potential to recognize tumor antigens. Such clonally expanded T cells display enrichment of transcripts linked to effector function, tissue residency, immune checkpoints and signatures of neoantigen-specific T cells and immunotherapy response. We identify neoantigens in pediatric brain tumors and show that neoantigen-specific T cell gene signatures are linked to better survival outcomes. Notably, among the patients in our cohort, we observe substantial heterogeneity in the degree of clonal expansion and magnitude of T cell response. Our findings suggest that characterization of intra-tumoral T cell responses may enable selection of patients for immunotherapy, an approach that requires prospective validation in clinical trials.
Asunto(s)
Neoplasias Encefálicas , Linfocitos T , Humanos , Neoplasias Encefálicas/inmunología , Neoplasias Encefálicas/patología , Neoplasias Encefálicas/genética , Niño , Linfocitos T/inmunología , Antígenos de Neoplasias/inmunología , Inmunoterapia/métodos , Preescolar , Masculino , Femenino , Adolescente , Linfocitos Infiltrantes de Tumor/inmunología , Análisis de la Célula Individual/métodos , Transcriptoma , Células ClonalesRESUMEN
Circular extrachromosomal DNA (ecDNA) in patient tumors is an important driver of oncogenic gene expression, evolution of drug resistance and poor patient outcomes. Applying computational methods for the detection and reconstruction of ecDNA across a retrospective cohort of 481 medulloblastoma tumors from 465 patients, we identify circular ecDNA in 82 patients (18%). Patients with ecDNA-positive medulloblastoma were more than twice as likely to relapse and three times as likely to die within 5 years of diagnosis. A subset of tumors harbored multiple ecDNA lineages, each containing distinct amplified oncogenes. Multimodal sequencing, imaging and CRISPR inhibition experiments in medulloblastoma models reveal intratumoral heterogeneity of ecDNA copy number per cell and frequent putative 'enhancer rewiring' events on ecDNA. This study reveals the frequency and diversity of ecDNA in medulloblastoma, stratified into molecular subgroups, and suggests copy number heterogeneity and enhancer rewiring as oncogenic features of ecDNA.
Asunto(s)
Neoplasias Cerebelosas , Meduloblastoma , Neoplasias , Humanos , ADN Circular , Meduloblastoma/genética , Estudios Retrospectivos , Neoplasias/genética , Oncogenes , Neoplasias Cerebelosas/genéticaAsunto(s)
Neoplasias del Sistema Nervioso Central , Ependimoma , Neoplasias Neuroepiteliales , Humanos , Adolescente , Neoplasias Neuroepiteliales/genética , Factores de Transcripción/genética , Ependimoma/genética , Ependimoma/cirugía , Fusión Génica , Proteínas Represoras/genética , Factores de Transcripción de Tipo Kruppel/genética , Proteína EWS de Unión a ARN/genéticaRESUMEN
Ependymoma is a tumor of the brain or spinal cord. The two most common and aggressive molecular groups of ependymoma are the supratentorial ZFTA-fusion associated and the posterior fossa ependymoma group A. In both groups, tumors occur mainly in young children and frequently recur after treatment. Although molecular mechanisms underlying these diseases have recently been uncovered, they remain difficult to target and innovative therapeutic approaches are urgently needed. Here, we use genome-wide chromosome conformation capture (Hi-C), complemented with CTCF and H3K27ac ChIP-seq, as well as gene expression and DNA methylation analysis in primary and relapsed ependymoma tumors, to identify chromosomal conformations and regulatory mechanisms associated with aberrant gene expression. In particular, we observe the formation of new topologically associating domains ('neo-TADs') caused by structural variants, group-specific 3D chromatin loops, and the replacement of CTCF insulators by DNA hyper-methylation. Through inhibition experiments, we validate that genes implicated by these 3D genome conformations are essential for the survival of patient-derived ependymoma models in a group-specific manner. Thus, this study extends our ability to reveal tumor-dependency genes by 3D genome conformations even in tumors that lack targetable genetic alterations.
Asunto(s)
Ependimoma , Recurrencia Local de Neoplasia , Niño , Humanos , Preescolar , Recurrencia Local de Neoplasia/genética , Cromosomas , Mapeo Cromosómico , Ependimoma/genética , Ependimoma/patología , Genoma , Cromatina/genéticaRESUMEN
Diffuse midline glioma (DMG) is a leading cause of brain tumor death in children. In addition to hallmark H3.3K27M mutations, significant subsets also harbor alterations of other genes, such as TP53 and PDGFRA. Despite the prevalence of H3.3K27M, the results of clinical trials in DMG have been mixed, possibly due to the lack of models recapitulating its genetic heterogeneity. To address this gap, we developed human iPSC-derived tumor models harboring TP53R248Q with or without heterozygous H3.3K27M and/or PDGFRAD842V overexpression. The combination of H3.3K27M and PDGFRAD842V resulted in more proliferative tumors when gene-edited neural progenitor (NP) cells were implanted into mouse brains compared to NP with either mutation alone. Transcriptomic comparison of tumors and their NP cells of origin identified conserved JAK/STAT pathway activation across genotypes as characteristic of malignant transformation. Conversely, integrated genome-wide epigenomic and transcriptomic analyses, as well as rational pharmacologic inhibition, revealed targetable vulnerabilities unique to the TP53R248Q; H3.3K27M; PDGFRAD842V tumors and related to their aggressive growth phenotype. These include AREG-mediated cell cycle control, altered metabolism, and vulnerability to combination ONC201/trametinib treatment. Taken together, these data suggest that cooperation between H3.3K27M and PDGFRA influences tumor biology, underscoring the need for better molecular stratification in DMG clinical trials.
RESUMEN
We present 4 children (diagnosed between 1 and 8 y, 3 females and 1 male) with molecularly distinct tectal gliomas (2 KRAS mutant, 1 EGFR mutant, 1 SRGAP3-RAF-1 fusion) that contributes to the growing literature of this uncommonly biopsied tumor. The patient with EGFR R222C mutation had a more severe course, earlier diagnosis, subsequent leptomeningeal metastatic disease, required more aggressive therapies, and died 9 years after diagnosis. Patients with KRAS mutations and SRGAP3-RAF-1 fusion had a more indolent course. Our series expands the molecular phenotype of tectal glioma with the potential for leptomeningeal dissemination. Future studies on establishing genotypic/phenotypic correlation from those who undergo biopsy are needed.
Asunto(s)
Neoplasias Encefálicas , Neoplasias del Tronco Encefálico , Glioma , Femenino , Masculino , Humanos , Glioma/genética , Glioma/patología , Neoplasias del Tronco Encefálico/genética , Neoplasias del Tronco Encefálico/diagnóstico , Neoplasias del Tronco Encefálico/patología , Proteínas Proto-Oncogénicas p21(ras)/genética , Receptores ErbB/genética , Mutación , Neoplasias Encefálicas/genéticaRESUMEN
PURPOSE: To highlight the clinical, neuroradiographic, neuropathologic, and molecular features of histologically identified neurocytoma in a pediatric cohort and highlight the evolving use methylation profiling in providing diagnostic clarity in difficult to diagnosis pediatric brain tumors. METHODS: Five consecutive children (ages 9-13, 2 girls 3 boys) were histologically diagnosed with neurocytoma at Rady Children's Hospital San Diego from 2012 to 2018. Clinical and molecular features were analyzed with regards to treatment course and outcome. RESULTS: Presenting symptoms included seizures (n = 2), syncope (n = 1), headache (n = 2), visual disturbances (n = 2) and emesis (n = 2). Tumor location included intraventricular (n = 2), intraventricular with parenchymal spread (n = 1), and extraventricular (n = 2). Magnetic resonance imaging demonstrated reduced diffusivity (2/5), signal abnormality on susceptibility-weighted sequences (3/5), and varying degrees of contrast enhancement (4/5). All patients underwent surgical resection alone. Recurrence occurred in four children that were treated with surgery (4/4), adjuvant radiation (2/4), and chemoradiation (1/4). Neuropathologic features included positivity for GFAP (4/5), synaptophysin (4/5), NSE (2/2), NeuN (4/4), and variable Ki-67 (< 1% to 15%). Next generation sequencing (3/5) and microarray (3/5) collectively were abnormal in four of five tumors. Methylation profiling was successfully performed on four of five samples which led to modification of diagnosis in two patients and the others were either unclassifiable or confirmatory with the histologic diagnosis. Mean time to follow up was 77 months (range 44-112 months). Mean progression free survival and overall survival were 24 months (range 6 to 52 months) and 100% respectively. CONCLUSION: Neurocytomas are a rare clinical entity that warrants further investigation into molecular and pathologic prognosticating features. Methylation profiling may aid in differentiation of neurocytoma from other difficult to diagnose tumors who share similar histologic features.
Asunto(s)
Neoplasias Encefálicas , Neurocitoma , Neoplasias Encefálicas/diagnóstico por imagen , Neoplasias Encefálicas/genética , Niño , Femenino , Humanos , Antígeno Ki-67 , Imagen por Resonancia Magnética , Masculino , Metilación , Neurocitoma/patología , SinaptofisinaAsunto(s)
Neoplasias del Tronco Encefálico , Síndrome de DiGeorge , Glioma , Glándula Pineal , Pinealoma , Neoplasias del Tronco Encefálico/complicaciones , Neoplasias del Tronco Encefálico/diagnóstico por imagen , Niño , Deleción Cromosómica , Cromosomas Humanos Par 22 , Síndrome de DiGeorge/complicaciones , Síndrome de DiGeorge/diagnóstico , Síndrome de DiGeorge/genética , Glioma/complicaciones , Glioma/diagnóstico por imagen , Glioma/genética , HumanosAsunto(s)
Astrocitoma , Neoplasias Encefálicas , Ganglioglioma , Neurofibromatosis 1 , Adolescente , Astrocitoma/complicaciones , Astrocitoma/diagnóstico por imagen , Neoplasias Encefálicas/complicaciones , Neoplasias Encefálicas/diagnóstico por imagen , Ganglioglioma/complicaciones , Ganglioglioma/diagnóstico por imagen , Humanos , Neurofibromatosis 1/complicacionesRESUMEN
Iron-sulfur cluster proteins are involved in critical functions for gene expression regulation and mitochondrial bioenergetics including the oxidative phosphorylation system. The c.215G>A p.(Arg72Gln) variant in NFS1 has been previously reported to cause infantile mitochondrial complex II and III deficiency. We describe three additional unrelated patients with the same missense variant. Two infants with the same homozygous variant presented with hypotonia, weakness and lactic acidosis, and one patient with compound heterozygous p.(Arg72Gln) and p.(Arg412His) variants presented as a young adult with gastrointestinal symptoms and fatigue. Skeletal muscle biopsy from patients 1 and 3 showed abnormal mitochondrial morphology, and functional analyses demonstrated decreased activity in respiratory chain complex II and variably in complexes I and III. We found decreased mitochondrial and cytosolic aconitase activities but only mildly affected lipoylation of pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase enzymes. Our studies expand the phenotypic spectrum and provide further evidence for the pathogenicity and functional sequelae of NFS1-related disorders with disturbances in both mitochondrial and cytosolic iron-sulfur cluster containing enzymes.