SickKids

Imputation methods for missing data may not always be applicable, namely, when the data were completely missing for the whole sample. To estimate the missing data, we compared three missing item substitution methods: (1) mean substitution; (2) last observation carried forward (LOCF); and (3) regression-predicted values. A total of 384 parents reported their 8- to 18-year-old children's anxiety level using the 9-item Screen for Child Anxiety Related Disorders at baseline (Time 1) and two later time points, drawing from a larger longitudinal study (Ontario COVID-19 and Kids' Mental Health Study). We predicted a survey item measured one month after baseline (Time 2) using: (1) the mean value of the rest of the test items; (2) the value of the same item measured at baseline; and (3) the predicted value from the linear regression with all other test items as predictors. Within-Subjects ANOVA results showed a main effect of substitution methods on total score at Time 2. Post-hoc analysis indicated that mean substitution was significantly different from the actual data. Regression-predicted values overestimated the median compared to the actual values, while the LOCF estimation produced comparable means and identical medians. Similar results were found while using other indicators and extending the analysis to a larger 4-month time interval (Time 3), suggesting LOCF is more accurate and reliable than mean substitution or regression-prediction. This study proposes when advanced substitution methods are not applicable, a systematic comparison of alternative methods may help researchers to arrive at a more informed decision in data processing.

Objective. Cerebral arterial and venous flow (A/V) classification is a key parameter for understanding dynamic changes in neonatal brain perfusion. Currently, transfontanellar ultrasound Doppler imaging is the reference clinical technique able to discriminate between A/V using vascular indices such as resistivity index (RI) or pulsatility index (PI). However, under conditions of slow arterial and venular flow, small signal fluctuations can lead to potential misclassifications of vessels. Recently, ultrafast ultrasound imaging has paved the way for better sensitivity and spatial resolution. Here, we show that A/V classification can be performed robustly using ultrafast Doppler spectrogram. Approach. The overall classification steps are as follows: for any pixel within a vessel, a normalized Doppler spectrogram (NDS) is computed that allows for normalized correlation analysis with ground-truth signals that were established semi-automatically based on anatomical/physiological references. Furthermore, A/V classification is performed by computing Pearson correlation coefficient between NDS in ground-truth domains and the individual pixel’s NDS inside vessels and finding an optimal threshold. Main Results. When applied to human newborns (n = 40), the overall accuracy, sensitivity, and specificity were found to be 88.5% ± 6.7%, 88.5% ± 6.5%, and 87.0% ± 8.8% respectively. We also examined strategies to fully automate this process, leading to a moderate decrease of 1%–3% in the same metrics. Additionally, when compared to the main clinical metrics such as RI, and PI, the receiver operating characteristic curves exhibited higher areas under the curve; on average by +36% (p < 0.0001) in the full imaging sector, +35% (p = 0.0116) in the cortical regions, +53% (p < 0.0001) in the basal ganglia, +28% (p = 0.0051) in the cingulate gyrus, and +35% (p < 0.0001) in the remaining brain structures. Significance: Our findings suggest that the proposed NDS-based approach can distinguish between A/V when studying cerebral perfusion in neonates.

Dyrk1A deficiency is linked to various neurodevelopmental disorders, including developmental delays, intellectual disability (ID) and autism spectrum disorders (ASD). Haploinsufficiency of Dyrk1a in mice reportedly leads to ASD-related phenotypes. However, the key pathological mechanisms remain unclear and human DYRK1A mutations remain uncharacterized in mice. Here, we generated and studied Dyrk1a-knockin mice carrying a human ASD patient mutation (Ile48LysfsX2; Dyrk1a-I48K mice). These mice display severe microcephaly, social and cognitive deficits, dendritic shrinkage, excitatory synaptic deficits, and altered phospho-proteomic patterns enriched for multiple signaling pathways and synaptic proteins. Early chronic lithium treatment of newborn mutant mice rescues the brain volume, behavior, dendritic, synaptic, and signaling/synapse phospho-proteomic phenotypes at juvenile and adult stages. These results suggest that signaling/synaptic alterations contribute to the phenotypic alterations seen in Dyrk1a-I48K mice, and that early correction of these alterations by lithium treatment has long-lasting effects in preventing juvenile and adult-stage phenotypes.

The molecular mechanism by which inborn errors of the human RNA lariat–debranching enzyme 1 (DBR1) underlie brainstem viral encephalitis is unknown. We show here that the accumulation of RNA lariats in human DBR1-deficient cells interferes with stress granule (SG) assembly, promoting the proteasome degradation of at least G3BP1 and G3BP2, two key components of SGs. In turn, impaired assembly of SGs, which normally recruit PKR, impairs PKR activation and activity against viruses, including HSV-1. Remarkably, the genetic ablation of PKR abolishes the corresponding antiviral effect of DBR1 in vitro. We also show that Dbr1Y17H/Y17H mice are susceptible to similar viral infections in vivo. Moreover, cells and brain samples from Dbr1Y17H/Y17H mice exhibit decreased G3BP1/2 expression and PKR phosphorylation. Thus, the debranching of RNA lariats by DBR1 permits G3BP1/2- and SG assembly-mediated PKR activation and cell-intrinsic antiviral immunity in mice and humans. DBR1-deficient patients are prone to viral disease because of intracellular lariat accumulation, which impairs G3BP1/2- and SG assembly-dependent PKR activation.

Sepsis is the leading postnatal cause of neonatal mortality worldwide. Globally Klebsiella pneumoniae is the leading cause of sepsis in hospitalized neonates. This study reports the development and evaluation of an ELISA for anti-Klebsiella IgG using dried blood spot (DBS) samples and evaluates the association of anti-Klebsiella IgG (anti-Kleb IgG) antibodies in maternal and neonatal samples with the risk of neonatal sepsis. Neonates and their mothers were enrolled at 0–96 hours of life in the neonatal unit of a tertiary referral hospital in Gaborone, Botswana and followed until death or discharge to assess for episodes of blood culture-confirmed neonatal sepsis. Neonates with sepsis had significantly lower levels of Kleb-IgG compared to neonates who did not develop sepsis (Mann-Whitney U, p = 0.012). Similarly, samples from mothers of neonates who developed sepsis tended to have less Kleb-IgG compared to mothers of controls. The inverse correlation between Kleb-IgG levels and all-cause bacteremia suggests that maternal Kleb-IgG may be protective through cross-reactivity with common bacterial epitopes. These data support the continued use of immunoglobulin assays using DBS samples to explore the role of passive immunity on neonatal sepsis risk and reaffirm the critical need for research supporting the development of maternal vaccines for neonatal sepsis.

Background The human gut microbiota is inoculated at birth and undergoes a process of assembly and diversification during the first few years of life. Studies in mice and humans have revealed associations between the early-life gut microbiome and future susceptibility to immune and metabolic diseases. To resolve microbe and host contributing factors to early-life development and to disease states requires experimental platforms that support reproducible, longitudinal, and high-content analyses. Results Here, we deployed a continuous single-stage chemostat culture model of the human distal gut to study gut microbiota from 18- to 24-month-old children integrating both culture-dependent and -independent methods. Chemostat cultures recapitulated multiple aspects of the fecal microbial ecosystem enabling investigation of relationships between bacterial strains and metabolic function, as well as a resource from which we isolated and curated a diverse library of early life bacterial strains. Conclusions We report the reproducible, longitudinal dynamics of early-life bacterial communities cultured in an advanced model of the human gut providing an experimental approach and a characterized bacterial resource to support future investigations of the human gut microbiota in early childhood.

This analysis evaluated literature on patients with activated phosphoinositide 3-kinase delta syndrome (APDS) to better understand the genetic etiologies and occurrence of mortality in this population. A systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses approach, including all articles published in English prior to March 13, 2023, in PubMed and Embase. Patients included in the study had reported either (1) APDS diagnosis or (2) ≥ 1 clinical sign consistent with APDS and a first-degree relative with genetically confirmed APDS. Reported age at last observation was also a required outcome. Publications not meeting these criteria were excluded. Data were summarized using descriptive statistics. The search identified 108 publications describing 351 unique patients with 39 distinct disease-causing variants. Among these, 41 (12%) deaths were reported, with a mean age at last follow-up of 19.6 (range, 1–64) years. A cause of death was reported for 80% (33/41) of deaths; lymphoma (24%, 10/41) and infections (22%, 9/41) were the most common causes. Types of infections causing death were severe uncontrollable infections (n = 3), sepsis (n = 2), viral infection (varicella zoster pneumonitis [n = 1], cytomegalovirus and adenovirus [n = 1], and Epstein-Barr virus [n = 1]), and infection (n = 1). Mean age at death for lymphoma was 24.9 (range, 1–41) years, and all nine patients who died from infections died before the age of 15 years. The mean age at first APDS symptom was 2.0 (range, < 1–22) years, and mean age at APDS diagnosis was 13.4 (range, 0–56) years; the mean time between symptoms and diagnosis was 10.6 (range, 0–44) years. Limitations of the study were primarily related to the data source. Patients with APDS suffer early mortality, largely from lymphoma and infection, with large time gaps between symptoms and diagnosis. These findings highlight the need for improved diagnostics, earlier genetic testing for APDS, increased awareness of familial testing, and targeted therapies.

Background Very large sample sizes are often needed to capture heterogeneity in autism, necessitating data sharing across multiple studies with diverse assessment instruments. In these cases, data harmonization can be a critical tool for deriving a single dataset for analysis. This can be done through computational approaches that enable the conversion of scores across various instruments. To this end, our study examined the use of analytical approaches for mapping scores on two measures of adaptive functioning, namely predicting the scores on the vineland adaptive behavior scales II (VABS) from the scores on the adaptive behavior assessment system II (ABAS). Methods Data from the province of Ontario neurodevelopmental disorders network were used. The dataset included scores VABS and the ABAS for 720 participants (autism n = 547, 433 male, age: 11.31 ± 3.63 years; neurotypical n = 173, 95 male, age: 12.53 ± 4.05 years). Six regression approaches (ordinary least squares (OLS) linear regression, ridge regression, ElasticNet, LASSO, AdaBoost, random forest) were used to predict VABS total scores from the ABAS scores, demographic variables (age, sex), and phenotypic measures (diagnosis; core and co-occurring features; IQ; internalizing and externalizing symptoms). Results The VABS scores were significantly higher than the ABAS scores in the autism group, but not the neurotypical group (median difference: 8, 95% CI = (7,9)). The difference was negatively associated with age (beta = -1.2 ± 0.12, t = -10.6, p < 0.0001). All estimators demonstrated similar performance, with no statistically significant differences in mean absolute error (MAE) values across estimators (MAE range: 4.96–6.91). The highest contributing features to the prediction model were ABAS composite score, diagnosis, and age. Limitations This study has several strengths, including the large sample. We did not examine the conversion of domain scores across the two measures of adaptive functioning and suggest this as a future area of investigation. Conclusion Overall, our results supported the feasibility of harmonization. Our results suggest that a linear regression model trained on the ABAS composite score, the ABAS raw domain scores, and age, sex, and diagnosis would provide an acceptable trade-off between accuracy, parsimony, and data collection and processing complexity.

In humans, misprocessed mRNAs containing intact 5′ Splice Site (5′SS) motifs are nuclear retained and targeted for decay by ZFC3H1, a component of the Poly(A) Exosome Targeting complex, and U1-70K, a component of the U1 snRNP. In S. pombe , the ZFC3H1 homolog, Red1, binds to the YTH domain–containing protein Mmi1 and targets certain RNA transcripts to nuclear foci for nuclear retention and decay. Here we show that YTHDC1 and YTHDC2, two YTH domain-containing proteins that bind to N -6-methyladenosine (m6A) modified RNAs, interact with ZFC3H1 and U1-70K, and are required for the nuclear retention of mRNAs with intact 5′SS motifs. Disruption of m6A deposition inhibits both the nuclear retention of these transcripts and their accumulation in YTHDC1-enriched foci that are adjacent to nuclear speckles. Endogenous RNAs with intact 5′SS motifs, such as intronic poly-adenylated transcripts, tend to be m6A-modified at low levels. Thus, the m6A modification acts on a conserved quality control mechanism that targets misprocessed mRNAs for nuclear retention and decay.

Importance Single gene variants can cause cerebral palsy (CP) phenotypes, yet the impact of genetic diagnosis on CP clinical management has not been systematically evaluated. Objective To evaluate how frequently genetic testing results would prompt changes in care for individuals with CP and the clinical utility of precision medicine therapies. Data Sources Published pathogenic or likely pathogenic variants in OMIM genes identified with exome sequencing in clinical (n = 1345) or research (n = 496) cohorts of CP were analyzed. A systematic literature review for evidence of effective therapies for specific genetic etiologies was performed. Study Selection Nonstandard interventions that led to a detectable improvement in a defined outcome in individuals with variants in the gene of interest were included. Data Extraction and Synthesis Literature was evaluated using PRISMA guidelines. A diverse, expert working group was established, scoring rubrics adapted, and scoring consensus built with a modified Delphi approach. Main Outcomes and Measures Overall clinical utility was calculated from metrics assessing outcome severity if left untreated, safety and practicality of the intervention, and anticipated intervention efficacy on a scale from 0 to 3. Results Of 1841 patients with CP who underwent exome sequencing, 502 (27%) had pathogenic or likely pathogenic variants related to their phenotype. A total of 243 different genes were identified. In 1841 patients with identified genetic etiologies of CP, 140 (8%) had a genetic etiology classified as actionable, defined as prompting a change in clinical management. Also identified were 58 of 243 genes with pathogenic or likely pathogenic variants with actionable treatment options: 16 targeting the primary disease mechanism, 16 with specific prevention strategies, and 26 with specific symptom management. The level of evidence was also graded according to ClinGen criteria; 45 of 101 interventions (44.6%) had evidence class D or below. The potential interventions have clinical utility with 98 of 101 outcomes (97%) being moderate-high severity if left untreated and 63 of 101 interventions (62%) predicted to be of moderate-high efficacy. Most interventions (72 of 101 [71%]) were considered moderate-high safety and practicality. Conclusions and Relevance The findings indicate that actionable genetic findings occurred in 8% of individuals referred for genetic testing with CP. Evaluation of potential efficacy, outcome severity, and intervention safety and practicality indicates moderate-high clinical utility of these genetic findings. Genetic sequencing can identify precision medicine interventions that provide clinical benefit to individuals with CP. The relatively limited evidence base underscores the need for additional research.

Objective Lower urinary tract obstruction (LUTO) is a chronic condition with a spectrum of outcomes. It is usually suspected prenatally based on ultrasound features (USFs). Given the unknown postnatal trajectory and the potential for significant morbidity and mortality, many families choose termination of pregnancy (TOP), often based on USFs alone. Herein, we sought to develop a tool that can be used to predict postnatal outcome based on combinations of USFs, which can aid prenatal counseling and parental decision‐making. Methods This was a retrospective study of cases with suspected fetal LUTO that were seen at a high‐risk fetal center and a tertiary pediatric center in Canada. Data were collected on USFs, prenatal/postnatal death and postnatal need for transplantation and/or dialysis. USFs from pregnancies with a gestational age of 13–26 weeks on initial ultrasound at the high‐risk fetal center that underwent TOP were collected and matched to fetuses with comparable prenatal USFs that were not terminated, which had a known postnatal outcome, to build a random forest model. The random forest model was fitted for each outcome (death, dialysis or transplantation) and tested for accuracy using leave‐one‐out cross‐validation. Each predictor was assessed independently with combined importance when accounting for other predictors. The model was used to predict the most likely postnatal outcomes for cases of TOP had the pregnancy been continued. Results USF data from 85 cases of TOP and 125 cases of expectantly managed pregnancy with prenatally suspected LUTO were retrieved. For expectantly managed cases, there was a median follow‐up duration of 5.7 (interquartile range, 0.2–14.5) years among the liveborn infants. There were 14 prenatal and 22 postnatal deaths in the expectantly managed cohort. The random forest model demonstrated the highest predictive accuracy for transplantation (77% accuracy, 50% sensitivity, 80% specificity), followed by death (72% accuracy, 83% sensitivity, 67% specificity) and dialysis (71% accuracy, 70% sensitivity, 71% specificity). For the TOP cohort, had the pregnancies been continued, the model predicted transplantation and dialysis in 21/85 (25%) and 37/85 (44%) cases, respectively; pre‐ or postnatal death was predicted in 69/85 (81%) cases. Conclusions Our data suggest that it is possible to predict death and postnatal transplantation and/or dialysis from USFs in fetuses with suspected LUTO with acceptable accuracy. Predictive accuracy will improve with continued follow‐up of more patients, enabling more personalized prenatal counseling and more informed decision‐making for families. © 2024 The Author(s). Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.

Background and Aims Studies examing the impact of socioeconomic factors on outcomes in childhood acute lymphoblastic leukemia (ALL) have yielded inconsistent findings. We aimed to determine whether socioeconomic status (SES) or healthcare access are associated with the presence of potentially time‐sensitive high‐risk features at diagnosis, times to diagnosis or treatment, or survival among children with ALL in Canada. Methods We conducted a retrospective cohort study of all children aged less than 15 years diagnosed with first primary ALL between 2001 and 2019 using the Cancer in Young People in Canada national Data Tool, which is population‐based. SES was measured using neighborhood income quintiles, and healthcare access proxy measured as distance to treating center. We used logistic regression to examine the associations between income quintile and distance and two potentially time‐sensitive indicators of high‐risk ALL at diagnosis, white blood cell count (WBC) ≥50 × 10 ⁹ /L, and central nervous system (CNS) disease. We used Cox proportional hazards to examine associations with time‐to‐event outcomes (times to diagnosis and treatment, event‐free survival [EFS], and overall survival [OS]). Results We included 4189 patients. In multivariable analyses, no associations were found between income quintile and potentially time‐sensitive high‐risk features at diagnosis, time to diagnosis or treatment, or OS. The only significant SES measure in multivariable survival analysis was superior EFS among those in income quintile 4 as compared to those in the lowest income quintile with a hazard ratio (HR) of 0.70 (confidence interval [CI]: 0.54–0.91). Living at increased distance from treating center was not associated with high WBC at diagnosis, time to diagnosis, EFS, or OS. Associations were seen between distance to treating center and CNS disease at diagnosis and time to treatment, but without a clear pattern across distance quartiles. Conclusions Children diagnosed with ALL and treated within Canada's universal healthcare system experience similar treatment and survival outcomes regardless of SES and distance to treatment center. Further work is required using individual‐level SES and demographic data to determine if any associations exist, and qualitative assessments to understand barriers to care.

Stem cells perceive and respond to biochemical and physical signals to maintain homeostasis. Yet, it remains unclear how stem cells sense mechanical signals from their niche in vivo. In this work, we investigated the roles of PIEZO mechanosensitive channels in the intestinal stem cell (ISC) niche. We used mouse genetics and single-cell RNA sequencing analysis to assess the requirement for PIEZO channels in ISC maintenance. In vivo measurement of basement membrane stiffness showed that ISCs reside in a more rigid microenvironment at the bottom of the crypt. Three-dimensional and two-dimensional organoid systems combined with bioengineered substrates and a stretching device revealed that PIEZO channels sense extracellular mechanical stimuli to modulate ISC function. This study delineates the mechanistic cascade of PIEZO activation that coordinates ISC fate decision and maintenance.

Background Necrotising enterocolitis (NEC) in preterm infants is associated with high morbidity and mortality. In most neonates, it is a progressive disease from medical NEC (mNEC) to surgical NEC (sNEC); however, in some, it presents as sNEC from onset. Objective To evaluate the rate, the timing of progression, different surgical approaches, and outcomes of mNEC and sNEC in preterm neonates. Design A retrospective cohort study of preterm infants with diagnosis of NEC between 2010 and 2020 was conducted. Data on clinical presentation, NEC progression, treatment received, different surgical approaches, resource utilization, and outcomes were abstracted. Infants were classified into 3 groups: mNEC, mNEC that progressed to sNEC, and sNEC at presentation. Results Among 208 included infants with NEC, 109 (52%) were mNEC, 66 (32%) progressed from mNEC to sNEC, and 33 (16%) presented with sNEC. Gestational age, birth weight, and postnatal age at NEC were inversely associated with the development of sNEC. mNEC progressed to sNEC occurred after a median of 2.5 (IQR 1–4.25) days. Ninety (91%) of sNEC patients underwent interventions: peritoneal drain only in 19 (21%), laparotomy in 59 (66%), or both in 12 (13%). In comparison with mNEC, those with sNEC infants had longer duration on antibiotics, inotropes, respiratory support, length of stay, and time to reaching full enteral feeds; and were more likely to have recurrent NEC episodes, BPD, and mortality. Conclusion There is a high burden of illness for sNEC cases. Insight into the expected clinical course of sNEC patients can facilitate anticipatory management and provide a window of opportunity for timely interventions that may ameliorate the course of sNEC.

Background Rare variants in epigenes (a.k.a. chromatin modifiers), a class of genes that control epigenetic regulation, are commonly identified in both pediatric neurodevelopmental syndromes and as somatic variants in cancer. However, little is known about the extent of the shared disruption of signaling pathways by the same epigene across different diseases. To address this, we study an epigene, Additional Sex Combs-like 1 (ASXL1), where truncating heterozygous variants cause Bohring-Opitz syndrome (BOS, OMIM #605039), a germline neurodevelopmental disorder, while somatic variants are driver events in acute myeloid leukemia (AML). No BOS patients have been reported to have AML. Methods This study explores common pathways dysregulated by ASXL1 variants in patients with BOS and AML. We analyzed whole blood transcriptomic and DNA methylation data from patients with BOS and AML with ASXL1-variant (AML-ASXL1) and examined differential exon usage and cell proportions. Results Our analyses identified common molecular signatures between BOS and AML-ASXL1 and highlighted key biomarkers, including VANGL2, GRIK5 and GREM2, that are dysregulated across samples with ASXL1 variants, regardless of disease type. Notably, our data revealed significant de-repression of posterior homeobox A (HOXA) genes and upregulation of Wnt-signaling and hematopoietic regulator HOXB4. While we discovered many shared epigenetic and transcriptomic features, we also identified differential splice isoforms in RUNX3 where the long isoform, p46, is preferentially expressed in BOS, while the shorter p44 isoform is expressed in AML-ASXL1. Conclusion Our findings highlight the strong effects of ASXL1 variants that supersede cell-type and even disease states. This is the first direct comparison of transcriptomic and methylation profiles driven by pathogenic variants in a chromatin modifier gene in distinct diseases. Similar to RASopathies, in which pathogenic variants in many genes lead to overlapping phenotypes that can be treated by inhibiting a common pathway, our data identifies common pathways for ASXL1 variants that can be targeted for both disease states. Comparative approaches of high-penetrance genetic variants across cell types and disease states can identify targetable pathways to treat multiple diseases. Finally, our work highlights the connections of epigenes, such as ASXL1, to an underlying stem-cell state in both early development and in malignancy.