Unbiased phenotype and genotype matching maximizes gene discovery and diagnostic yield.

PURPOSE: Widespread application of next-generation sequencing, combined with data exchange platforms, has provided molecular diagnoses for countless families. To maximize diagnostic yield, we implemented an unbiased semi-automated genematching algorithm based on genotype and phenotype matching. METHODS: Rare homozygous variants identified in 2 or more affected individuals, but not in healthy individuals, were extracted from our local database of ∼12,000 exomes. Phenotype similarity scores (PSS), based on human phenotype ontology terms, were assigned to each pair of individuals matched at the genotype level using HPOsim. RESULTS: 33,792 genotype-matched pairs were discovered, representing variants in 7567 unique genes. There was an enrichment of PSS ≥0.1 among pathogenic/likely pathogenic variant-level pairs (94.3% in pathogenic/likely pathogenic variant-level matches vs 34.75% in all matches). We highlighted founder or region-specific variants as an internal positive control and proceeded to identify candidate disease genes. Variant-level matches were particularly helpful in cases involving inframe indels and splice region variants beyond the canonical splice sites, which may otherwise have been disregarded, allowing for detection of candidate disease genes, such as KAT2A, RPAIN, and LAMP3. CONCLUSION: Semi-automated genotype matching combined with PSS is a powerful tool to resolve variants of uncertain significance and to identify candidate disease genes.

Evaluation of gastrointestinal symptoms in pediatric patients post hematopoietic stem cell transplantation: Ileo-colonoscopy versus sigmoidoscopy. A single-center experience and review of literature.

BACKGROUND: Hematopoietic stem cell transplantation (HSCT) is a curative therapy used to treat high-risk hematological malignant disorders and other life-threatening nonmalignant diseases. Gastrointestinal (GI) symptoms post-HSCT might be due to GI graft-versus-host disease (GVHD) or GI infections or both. GI endoscopy with biopsies is safe and beneficial in guiding the management of GI symptoms in children after HSCT, justifying the therapeutic management and contributing to improved outcomes. METHODS: A retrospective cohort study including 16 children with malignant and nonmalignant diseases that underwent allogeneic HSCT who had 24 ileo-colonoscopies performed for GI symptoms. To facilitate an evidence-based approach to the endoscopic evaluation of GI symptoms in pediatric patients post HSCT, we examined whether a full ileo-colonoscopy, which includes right colon and terminal ileum (TI), as opposed to a limited sigmoidoscopy, was more accurate in the evaluation of GI symptoms in pediatric patients post HSCT. RESULTS: Specific findings on the right colon/TI were found in nine out of 24 ileo-colonoscopies (38%, CI = 19%-59%). The macroscopic findings on ileo-colonoscopy were compared with the histopathologic findings. When macroscopic findings were present, there were matching histopathologic findings in 100% of cases. However, even in the absence of any macroscopic findings on ileo-colonoscopy, there were histopathological findings in 29% of the cases (p-value = .016). CONCLUSIONS: This cohort favors ileo-colonoscopy over sigmoidoscopy, with systematic biopsy sampling, in evaluating GI symptoms in pediatric patients post HSCT.

Monitoring Enables Progress: A Nationwide Quality Improvement Program in Children With Crohn Disease.

OBJECTIVES: In this quality improvement program, named quality in pediatric inflammatory bowel disease, we constructed a nation-wide platform that prospectively recorded clinically important quality indicators in pediatric inflammatory bowel diseases (PIBD), aiming at improving clinical management across the country. METHODS: Representatives of all 21 PIBD facilities in Israel formed a Delphi group to select quality indicators (process and outcomes), recorded prospectively over 2 years in children with Crohn's disease 2-18 years of age seen in the outpatient clinics. Monthly anonymized reports were distributed to all centers, allowing comparison and improvement. Trends were analyzed using the Mann-Kendall test, reporting τ (tau) values. RESULTS: The indicators of 3254 visits from 1709 patients were recorded from September 2017 to September 2019 (mean age 14.7 ±â€Š3.1 years, median disease duration 1.8 years (interquartile range 0.69-4.02)). An increase in three of five process indicators was demonstrated: obtaining drug levels of anti-tumor necrosis factor (TNF) (τ = 0.4; P = 0.005), utilization of fecal calprotectin (τ = 0.38; P = 0.008) and bone density testing (τ = 0.45; P = 0.002). Among outcome indicators, three of nine improved as measured during the preceding year: calprotectin <300 µg/mg (τ = 0.35; P = 0.015), and "resolution of inflammation" defined as a composite of endoscopy, imaging and fecal calprotectin (τ = 0.39; P = 0.007). Endoscopic healing reached borderline significance (τ = 0.28; P = 0.055). An increase in the use of biologics throughout the study was observed (τ = 0.47; P = 0.001) with a concurrent decrease in the use of immunomodulators (τ = -0.47; P = 0.001). CONCLUSIONS: Quality improvement nationwide programs can be implemented with limited resources while facilitating standardization of care, and may be associated with improvements in measured indicators.

Characterization and natural history of congenital intrahepatic portosystemic shunts.

Congenital intrahepatic portosystemic shunts are rare vascular malformations in which abnormal communications are created between the portal veins and the hepatic veins or the inferior vena cava system. Diagnosis is made by prenatal or postpartum ultrasound. Published data regarding presentation, symptoms, and prognosis is scarce. This study aimed to better understand the natural history and the course of the intrahepatic portosystemic shunts. Data were collected from children in two medical centers who were diagnosed with congenital intrahepatic portosystemic shunts on either prenatal or postnatal sonographic screening. The subjects' medical information was collected including demographics, medical background, and sonographic and clinical outcome. Blood test results including ammonia levels and liver function tests were documented, as well as the sonographic dimensions of the shunt vessels and the spleen size. The data were analyzed using various statistical methods. Twenty-three children with portosystemic shunts were found and reviewed. Eight children were excluded from the study since records and follow-up were insufficient. Fifteen patients were included in the study (six females). All had intrahepatic shunt diagnosed either by prenatal screening or postnatal abdominal ultrasound and had more than one ultrasound and repeated blood tests. Shunt closure was observed in all children within a mean of 114.31 ± 115.05 days (median 84). There was no correlation between liver enzymes, ammonia, and ultrasound vascular and splenic diameters to time to closure. None of the children had any hepatic or other sequelae.Conclusions: Our study suggests that congenital intrahepatic portosystemic shunt is a benign, self-limiting condition in which no correlation between the size of the shunt and the blood ammonia level to the outcome of the shunt was found. This is the first study that correlated radiological measures to the outcome. These results suggest that the treating physician should reassure families and conduct minimal follow-up and interventions in children with such conditions. Further, larger and prospective studies should be done to corroborate these conclusions. What is Known: • Characteristics and natural history of intrahepatic portosystemic shunts are less defined. • The natural course of the intrahepatic malformations varies, but spontaneous, self-resolution of small shunts, usually occures within 1 to 2 years. What is New: • In this study, congenital intrahepatic portosystemic shunt was shown to be benign, self-limiting condition in which all shunts closed within 3 months. • No correlation between the size of the shunt and the blood ammonia level to the outcome of the shunt was found.

Moderate Gastrointestinal Complications Due to "Superglue" Ingestion in a Pediatric Patient.

ABSTRACT: Childhood cases of cyanoacrylates generally do not cause moderate or severe gastrointestinal complications. We report the case of a 3-year-old boy referred to our pediatric emergency room and admitted to the pediatric department with signs of upper gastrointestinal obstruction that required invasive intervention. Although it is rare, cyanoacrylate ingestion may injure esophageal and gastric mucosa in the pediatric population.

Prevention of acetaminophen-induced liver injury by alginate.

INTRODUCTION: Acetaminophen (APAP) intoxication is a major cause of acute liver failure. Alginate, an anionic polysaccharide, was previously shown as a macroporous scaffold, to reduce liver inflammation and sustain hepatic synthetic function, when implanted on liver remnant after extended partial hepatectomy. In the recent study we wanted to examine in a model of APAP intoxication the potential of a specially formulated alginate solution to prevent APAP toxicity. METHODS: Three alginate solutions from low (30-50 kDa, VLVG), medium (100 kDa, LVG54) and high (150 kDa, LVG150) molecular weights were examined. Mice were orally administered with the alginate solution before, with and after APAP administration and were compared to control mice which received vehicle only. All mice were euthanized 24 h after APAP administration. Liver enzyme, blood APAP, IL-6 and liver histology including Ki-67 proliferation, IgG necrosis and nitrotyrosine staining were studied. RESULTS: VLVG- treated mice presented low ALT levels while 20-40 fold increase was demonstrated in control mice. The effect of LVG solutions was marginal. Accordingly, liver histology was normal with no hepatocytes proliferation in the VLVG group while massive centrilobular necrosis, increased nitrotyrosine staining and high proliferation appeared in livers of control mice. APAP blood levels were comparable in the two groups. Treatment with VLVG was associated with prevention of increase of IL-6 serum levels. CONCLUSION: VLVG, a novel alginate solution, alleviated the liver toxicity and inhibited oncotic necrosis and related immune-mediated damage. VLVG may serve as a novel hepato-protector and prevent drug induced liver injury.

Homozygous variants in MAPRE2 and CDON in individual with skin folds, growth delay, retinal coloboma, and pyloric stenosis.

Cases with multiple molecular diagnoses are challenging to diagnose clinically, yet may be resolved by unbiased exome sequencing analysis. We report an infant with developmental delay, severe growth delay, dysmorphic features, and multiple congenital anomalies including retinal coloboma, congenital pyloric stenosis, and circumferential skin creases. Exome sequencing identified a homozygous missense variant in MAPRE2 and a homozygous stopgain (nonsense) variant in CDON. Variants in MAPRE2, encoding a regulator of microtubule dynamics, lead to congenital symmetric circumferential skin creases type 2, with associated dysmorphism, small growth parameters, and congenital cardiac and genital anomalies. Monoallelic variants in CDON, encoding a coreceptor for sonic hedgehog, have been associated with autosomal dominant pituitary stalk interruption syndrome and holoprosencephaly. Cdon-/- mice have multiple eye defects including coloboma, consistent with the observed human phenotype. Thus, the complex phenotypic presentation of the infant may potentially be attributed to a dual molecular diagnosis. Furthermore, we present CDON as a candidate gene for coloboma formation in addition to the known holoprosencephaly phenotype, and propose to expand the allelic spectrum of CDON to variants associated with autosomal recessive inheritance in addition to dominant inheritance.

Prevention of malnutrition in cystic fibrosis.

PURPOSE OF REVIEW: Malnutrition is one of the major burdens of disease in cystic fibrosis. The prevention of malnutrition remains a priority throughout the life of a patient with cystic fibrosis. Literature and guidelines on the management of nutrition in cystic fibrosis have been published; however, here we review updated findings in cystic fibrosis nutrition as well as the role of novel treatments. RECENT FINDINGS: We review the latest studies on the importance and consequences of nutrition in cystic fibrosis. Novel findings on specific nutrients such as vitamin D and sodium can improve our care and thereby health and growth outcomes. The role of exercise has been further studied. In the field of new treatments, we review the role of cystic fibrosis transmembrane-conductance regulator potentiators and modulators in cystic fibrosis nutrition. A new feeding tube fat-digesting device has been developed and shows promise in cystic fibrosis enteral nutrition. SUMMARY: Advances in the nutritional care of cystic fibrosis are forming and believed to further develop in the near future, adding to the recent progress in cystic fibrosis patients' health, survival, and quality of life.

Celiac Disease and Celiac Antibodies in DM1 Patients: When Are Screening and Biopsy Recommended?

INTRODUCTION: The prevalence of celiac disease (CD) is increased in diabetes mellitus type 1 (DM1) patients. In most cases, CD is diagnosed in asymptomatic patients and hence periodic screening tests are recommended, but the timing, frequency of tests and indication for duodenal biopsy is unclear. The purpose of this study was to investigate the dynamics of CD serology in DM1 and identify risk factors for CD. METHODS: Celiac serology and duodenal biopsy results from 1990 until 2015 were collected from patients with DM1. The outcome of positive celiac serology, the incidence and risk factors for CD in DM1 patients were investigated. RESULTS: A total of 314 DM1 patients who had celiac serology were identified, with follow-up period up to 23 years. Of 31 patients (9.9%) with positive celiac serology, 11(35.4%) had spontaneous normalization after various time periods. Eighteen patients were diagnosed with CD (58.1% of positive celiac serology, 5.73% of the study cohort). Age under 4.5 years was a risk factor for CD, but not family background of autoimmune diseases or gender. All patients with CD diagnosis were diagnosed during the first 6 years following DM1 diagnosis. CONCLUSION: Screening asymptomatic DM1 patients for CD beyond 6 years after diagnosis is not recommended. Spontaneous normalization of CD serology occurs, and hence, serologic follow-up may be performed. In children with DM1 diagnosis under the age of 4.5 years or with positive CD serology at DM1 diagnosis, there is an increased risk for CD and therefore positive serology should lead to biopsy.

Effects of new and emerging therapies on gastrointestinal outcomes in cystic fibrosis.

PURPOSE OF REVIEW: Several new therapeutic modalities have recently become available to be used in patients with cystic fibrosis such as potentiators, modulators, and probiotics. Although the effects on pulmonary function have been well documented, gastrointestinal outcomes have been addressed only rarely. RECENT FINDINGS: Both the potentiator (ivacaftor) and the potentiator/modulator combination (ivacaftor/lumacaftor) that are currently on the market have a positive effect on BMI. Young patients (2-5 years of age) with a gating mutation may show improvement of exocrine pancreatic function on ivacaftor. In this specific patient population this agent also seems to improve intestinal pH and reflux. The effect of these medications on other gastrointestinal outcomes, such as intestinal inflammation and cystic fibrosis liver disease, has not been described so far. Furthermore, the results of several trials suggest that probiotics might reduce intestinal inflammation. Finally, organoids might be used to predict in vitro the clinical effect of potentiators and modulators. SUMMARY: The effect of new interventions on the gastrointestinal outcomes studied so far is favourable. Future studies should address the effect on other gastrointestinal parameters.

Intestinal and gastric permeability in children with eosinophilic esophagitis and reflux esophagitis.

OBJECTIVES: Eosinophilic esophagitis (EoE) is an allergic and immune-mediated entity that leads to a characteristic inflammation of esophageal mucosa. Patients complain of dysphagia and reflux-like symptoms. As many as 80% of patients with EoE may also have a history of atopy, and patients with asthma and eczema have previously been shown to have increased intestinal permeability. This study was designed to assess small intestinal and gastric permeability in patients with EoE and to see whether it differed from healthy individuals and patients with reflux esophagitis (RE). METHODS: Gastric and small intestinal permeability was measured using sugar probe tests containing lactulose, mannitol, and sucrose. Lactulose-to-mannitol (L/M) ratios in the patient's urine were a measure for intestinal permeability, and total sucrose was a measure for gastric permeability. RESULTS: We analyzed samples from 23 patients with EoE, 20 RE, 14 normal upper endoscopy with gastrointestinal symptoms, and 26 healthy controls. All of the 4 groups had L/M ratios less than the upper limit of normal (<0.025). There was no statistically significant difference in gastric permeability between the 4 groups (L/M P = 0.26, sucrose P = 0.46). CONCLUSIONS: Our data suggest that an alteration in gastric and intestinal permeability does not play a role in EoE or RE pathogenesis.

Role of Environmental Factors in the Development of Pediatric Eosinophilic Esophagitis.

BACKGROUND: Despite accumulating data on the pathogenesis of eosinophilic esophagitis, not much is known about risk factors for the development of the disease. The role of factors such as smoking, breastfeeding, early antibiotic exposure and other factors that have been associated with other allergic diseases has not been well studied in children with eosinophilic esophagitis. AIM: To explore the role of environmental and medication exposures in the development of pediatric eosinophilic esophagitis. METHODS: We conducted a cross-sectional case-control study, utilizing a parent and child questionnaire and medical chart review. Urine cotinine levels, measured by high-performance liquid chromatography, were obtained as objective evidence for smoking exposure. RESULTS: One hundred and two children with eosinophilic esophagitis and 167 controls were recruited. The controls were mainly diagnosed with functional gastrointestinal disorders (33%) and gastroesophageal reflux disease (29%). Food allergy, specifically for peanuts and tree nuts, and allergy to pollen, tree, and grass were significantly higher among eosinophilic esophagitis children. Smoking exposure, both primary and secondary, was not associated with pediatric eosinophilic esophagitis when compared to controls (odds ratio 0.96, 95% confidence interval 0.58-1.59). Furthermore, early smoking exposure in the first year of life was higher among controls. Common accepted risk factors for allergy and atopy, such as breastfeeding practices, antibiotics exposure, animals' exposure, and others, were not found to be associated with eosinophilic esophagitis in our study. CONCLUSION: Common risk factors in other allergic and atopic conditions were not found to be associated with eosinophilic esophagitis.

Retrograde tubing as a rescue treatment for megaoesophagus: a case report.

Familial dysautonomia (FD) is a genetic disease of the autonomous and sensory nervous systems. Severe gastro-oesophageal reflux is common and one of the major complications. Some patients with FD develop megaoesophagus. Oesophageal malfunction, accompanied by oesophageal food and secretion retention, results in recurrent aspiration and other severe respiratory complications. Through a traditional case report, we wish to show how reverse tubing of the oesophagus can lead to significant symptomatic improvement in these patients. Moreover, this technique can serve as an alternative treatment for other oesophageal motility disorders.

Sleep disorders in children with celiac disease: a prospective study.

STUDY OBJECTIVES: Celiac disease (CD), an immune-mediated enteropathy, has a clinical spectrum that is remarkably wide and includes neuropsychiatric manifestations. While studies of adults have shown sleep disturbances, there is limited data in children. Our objectives were to assess the association between sleep disturbances and CD in children, and the effect of a gluten-free diet. METHODS: Parents of children 3-12 years old referred for endoscopy completed the Sleep Disturbance Scale for Children and modified Epworth Sleepiness Scale. Children with CD were compared with healthy controls and children with abdominal pain but no definitive findings on investigation. Parents of children with CD and abdominal pain were contacted after 6 months for follow-up. RESULTS: We enrolled 101 patients, mean age 6.5 (2.8), 51% female, 38 with CD, 18 abdominal pain, and 45 healthy. Sleep Disturbance Scale for Children scores were 37.4 (8.7), 41.3 (11.3), and 45.4 (13.7) in healthy controls, CD, and abdominal pain, respectively (P = .024). There was a significant difference in the disorders of arousal domain (P = .044). There were no significant differences on the modified Epworth Sleepiness Scale. A trend toward improvement in Sleep Disturbance Scale for Children scores was seen in children with CD presenting with abdominal pain after 6 months on a gluten-free diet (P = .07). CONCLUSIONS: In this first prospective study of sleep disturbances in children with CD, we show high rates of disturbed sleep compared with healthy children. Sleep disturbances did not improve on a gluten-free diet and may be driven by abdominal pain. CITATION: Reiter J, Abuelhija H, Slae M, et al. Sleep disorders in children with celiac disease: a prospective study. J Clin Sleep Med. 2023;19(3):591-594.

Increased Risk of Celiac Disease in Patients with Uveitis.

PURPOSE: To examine whether patients with non-infectious uveitis (NIU) are at increased risk for celiac disease (CeD). METHODS: Celiac antibody testing was completed in 112 patients. The control group included patients who had undergone upper endoscopy for suspicion of CeD. RESULTS: 2/112 (1.79%) of patients with NIU had positive anti-tTG serology and CeD was confirmed in both patients. When compared to the expected risk of CeD in the general Israeli population of 0.31%, this corresponded to an odds ratio of 5.77 (95% CI 1.4118 to 23.4737, P = 0.049). Three additional patients had positive serology for CeD but the diagnosis was not confirmed. CONCLUSIONS: An increased risk of CeD was detected in patients with NIU. We therefore recommend screening for CeD in NIU patients. Larger prospective studies are required to further validate these results.

Risk and promise: an 11-year, single-center retrospective study of severe acute GVHD in pediatric patients undergoing allogeneic HSCT for nonmalignant diseases.

Background: Hematopoietic stem cell transplantation (HSCT) is the only curative option for many nonmalignant hematopoietic-derived diseases in pediatric patients. Survival after HSCT has improved in recent years and resulted in a 90% survival rate and cure in some nonmalignant diseases. Graft-vs.-host disease (GVHD) remains a frequent and major complication of HSCT, and a leading cause of morbidity and mortality. Prognosis of patients with high-grade GVHD is dismal, with survival rates varying from 25% in the adult population to 55% in pediatric patients. Methods: The main aim of this study is to evaluate the incidence, risk factors, and outcome of severe acute GVHD (AGVHD) in pediatric patients with nonmalignant diseases, following allogeneic HSCT. Clinical and transplant data were retrospectively collected for all pediatric patients who underwent allogeneic HSCT for nonmalignant diseases at the Hadassah Medical Center between 2008 and 2019. Patients who developed severe AGVHD were compared with those who did not. Results: A total of 247 children with nonmalignant diseases underwent 266 allogeneic HSCTs at Hadassah University Hospital over an 11-year period. Seventy-two patients (29.1%) developed AGVHD, 35 of them (14.1%) severe AGVHD (grade 3-4). Significant risk factors for developing severe AGVHD were unrelated donor (p < 0.001), mismatch donor (p < 0.001), and the use of peripheral blood stem cells (PBSCs) (p < 0.001). Survival rates of pediatric patients with severe AGVHD was 71.4%, compared with 91.9% among those with mild (grade 1-2) AGVHD and 83.4% among patients without AGVHD (p = 0.067). Conclusions: These results demonstrate a high survival rate in pediatric patients with nonmalignant diseases despite severe GVHD. Significant mortality risk factors found in these patients were the source of donor PBSC (p = 0.016) and poor response to steroid treatment (p = 0.007).

Cystic fibrosis and the gut.

Cystic fibrosis (CF) is a recessive disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene. The gene product, CFTR protein, has important manifestations in the intestine, pancreas and hepatobiliary system. Increased survival has caused CF to be primarily an adult disease today. Physicians must be knowledgeable as to the varied phenotype in the gastrointestinal tract. This review will outline the main gastrointestinal manifestations including a section on gastrointestinal malignancy in CF. Novel treatments treating the basic effect in CF are now being introduced and their effects on the gastrointestinal tract are discussed.

Neonatal thrombotic microangiopathy secondary to factor I variant with Hirschsprung disease.

Neonatal thrombotic microangiopathy (TMA) is a rare and severe disease characterized by a triad of non-immune hemolytic anemia, thrombocytopenia, and organ dysfunction in neonates. We describe herein an early-term infant who underwent hemicolectomy at 4 days of age due to intestinal perforation. Following surgery, the patient had recurrent bouts of vomiting and abdominal distention, together with acute kidney injury, non-immune hemolytic anemia, and severe thrombocytopenia. Low complement levels raised the possibility of complement-mediated neonatal TMA. Finally, genetic tests identified a heterozygous mutation in the complement factor I gene. Anti-C5 monoclonal antibody therapy led to complete cessation of the hematological and renal manifestations, but symptoms of intestinal obstruction recurred. Intestinal biopsy demonstrated aganglionosis, compatible with Hirschsprung disease. This presentation is the first known case of neonatal complement-mediated TMA associated with Hirschsprung disease. Moreover, it highlights the importance of considering a diagnosis of TMA in cases of atypical neonatal infectious presentation.