A study of two Chinese patients with tetrasomy and pentasomy 15q11q13 including Prader-Willi/Angelman syndrome critical region present with developmental delays and mental impairment

BACKGROUND: The proximal chromosome 15q is prone to unequal crossover, leading to rearrangements. Although 15q11q13 duplications are common in patients with developmental delays and mental impairment, 15q aneusomies resulting in greater or equal to 4 copies of 15q11q13 are rare and no pentasomy 15q11q13 has been reported in the literature. Thus far, all reported high copy number 15q11q13 cases are from the West populations and no such study in Chinese patients have been documented. Dosage-response pattern of high copy number 15q11q13 on clinical presentations is still a subject for further study. CASE PRESENTATION: In this study, we characterized two Han Chinese patients with high copy number 15q11q13. Using chromosome banding, high resolution SNP-based cytogenomic array, Fluorescence in situ hybridization, and PCR-based microsatellite analysis, we identified two patients with tetrasomy 15q11q13 and pentasomy 15q11q13. Both 15q11q13 aneusomies resulted from a maternally inherited supernumerary marker chromosome 15, and each was composed of two different sized 15q11q13 segments covering the Prader-Willi/Angelman critical region: one being about 10 Mb with breakpoints at BP1 and BP5 regions on 15q11 and 15q13, respectively, and another about 8 Mb in size with breakpoints at BP1 and BP4 regions on 15q. Both patients presented with similar clinical features that included neurodevelopmental delays, mental impairment, speech and autistic behavior, and mild dysmorphism. The patient with pentasomy 15q11q13 was more severely affected than the patient with tetrasomy 15q11q13. Low birth weight was noted in patient with pentasomy 15q1q13. CONCLUSIONS: To the best of our knowledge, this is the first case of pentasomy 15q11q13 and the first study of high copy number 15q11q13 in Han Chinese patients. Our findings demonstrate that patients with tetrasomy and pentasomy of chromosome 15q11q13 share similar spectrum of phenotypes reported in other high copy number 15q11q13 patients in the West, and positive correlation between 15q11q13 copy number and degree of severity of clinical phenotypes. Low birth weight observed in the pentasomy 15q11q13 patient was not reported in other patients with high copy number 15q11q13. Additional studies would be necessary to further characterize high copy number 15q11q13 aneusomies

Development and Validation of a Nomogram for Predicting Pathological Intussusceptions in Children Prior to Surgical Intervention

PurposeEstablish and validate a nomogram to help predict the preoperative risk of a pathological intussusception.MethodsA primary cohort of patients who underwent surgery for an intussusception were enrolled from one center, while a validation cohort consisted of patients from another center. Multivariate logistic regression analysis was used to identify the variables to build the nomogram. A calibration curve accompanied by the Hosmer-Lemeshow test was used to assess the calibration of the nomogram. To quantify the discrimination of the nomogram, Harrell’s C-index was calculated. The performance of the validated nomogram was tested in the external validation cohort. The logistic regression formulae created during the analysis of the primary cohort was applied to all patients in the external validation cohort, and the total points for each patient were calculated.ResultsThe primary cohort consisted of 368 patients and the validation cohort included 74. The LASSO logistic algorithm identified three (recurrence episodes, mass size, and infection history) out of 11 potential clinical variables as significantly predictive of a pathologic intussusception. The C-index for the predictive nomogram was 0.922 (95% CI, 0.885–0.959) for the primary cohort and 0.886 (95% CI, 0.809–0.962) for the validation cohort. The decision curve showed that if the threshold probability of a patient in the validation cohort was > 7%, then the nomogram was more beneficial than either indiscriminately treating all or none of the patients.ConclusionWe developed a nomogram based on clinical risk factors that could be used to individually predict pathological intussusceptions in children prior to surgical intervention

Whole Exome Sequencing Identifies a Novel Pathogenic RET Variant in Hirschsprung Disease

Hirschsprung disease is a birth defect characterized by complete absence of neuronal ganglion cells from a portion of the intestinal tract. To uncover genetic variants contributing to HSCR, we performed whole exome sequencing on seven members of an HSCR family. With the minor allele frequency (MAF) calculated by gnomAD, we finally filtered a total of 1,059 rare variants in this family (MAF < 0.1%). With the mode of inheritance and pathogenicity scores by bioinformatics tools, we identified an in-frameshift variant p.Phe147del in RET as the disease-causing variant. Further analysis revealed that the in-frameshift variant may function by disrupting the glycosylation of RET protein. To our knowledge, this is the first study to report the in-frameshift variant p.Phe147del in RET responsible for heritable HSCR

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

Exome sequencing identifies predisposing and fusion gene in ganglioneuroma, ganglioneuroblastoma and neuroblastoma

This study intended to gain new insight into the genetic basis underlying ganglioneuroma (GN), ganglioneuroblastoma (GNB), and neuroblastoma (NB). Three fresh-frozen surgically resected tumor tissues (GN1, GNB1, and NB1) and matched blood samples (GN2, GNB2, and NB2) were respectively obtained from three pediatric patients with GN, GNB, and NB. After exome sequencing, we predicted the somatic single nucleotide variants (SNV) and insertion and deletion (InDel), and screened the predisposing genes. Finally, we detected and filtered the fusion gene using Fusionmap. Exome sequencing identified 815,985, and 884 somatic SNV, and 56, 43, and 34 InDel for GN, NB, and GNB respectively. Total 29, 19 and 37 predisposing genes were identified from GN, GNB and NB samples, such as PIK3CA (GN), MUC4 (GN), PML (NB), TFR2 (GNB), and MAX (GNB). Additionally, four common fusion genes, such as HOXD11-AGAP3 and SAMD1-CDC42EP5, were identified from three tumor samples. Moreover, SAMD1-CDC42EP5 was also a common fusion position in three blood samples. These previously unrecognized predisposing genes, such as PIK3CA, MUC4, PML, TFR2 and MAX, and fusion genes, like HOXD11-AGAP3, and SAMD1-CDC42EP5 may have the potential to impact the progression and development of neuroblastic tumors

RNA N6-methyladenosine reader IGF2BP3 interacts with MYCN and facilitates neuroblastoma cell proliferation

Abstract Neuroblastoma (NB) is a kind of typical life-threatening extracranial tumor in children. N6-methyladenosine (m6A) modification is closely related to multiple cancer pathological processes. Insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3) is a top-ranked prognostic risk gene in NB; however, its function is uncertain. The expression of m6A-associated enzymes in patients with NB was analyzed using the Gene Expression Omnibus (GEO) and Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. The IGF2BP3 level in NB cell lines and primary samples was tested using quantitative real-time polymerase chain reaction (qRT-PCR), western blot method, and immunohistochemical analysis. The IGF2BP3 function in cell proliferation was clarified based on many functional in vitro and in vivo experiments. The interaction between IGF2BP3 and N-myc was researched via RNA immunoprecipitation (RIP), m6A RNA immunoprecipitation (MeRIP), and chromatin immunoprecipitation (ChIP) assays. The 16 m6A-regulated enzymes in NB were researched, and the result indicated that IGF2BP3 overexpression was related to cancer progression, COG risk, and survival based on the GEO and TARGET databases. Besides, the IGF2BP3 and MYCN levels were positively correlated. IGF2BP3 expression levels increased in MYCN-amplified NB clinical samples and cells. Knockdown of IGF2BP3 inhibited N-myc expression and NB cell proliferation in vitro and in vivo. IGF2BP3 regulates MYCN RNA stability by modifying m6A. In addition, we demonstrated that N-myc is a transcription factor that directly promotes IGF2BP3 expression in NB cells. IGF2BP3 regulates the proliferation of NB cells via m6A modification of MYCN. N-myc also acts as a transcription factor that regulates IGF2BP3 expression. A positive feedback loop between IGF2BP3 and N-myc facilitates NB cell proliferation

Misdiagnosis of scrotal and retroperitoneal lymphangioma in children

Abstract Background Scrotal and retroperitoneal lymphangioma (SRL) in children is relatively rare and its clinical symptoms are usually difficult to distinguish from other conditions such as hydrocele and incarcerated inguinal oblique hernia. This study aimed to explore the clinical diagnosis and treatment of abdominal scrotal lymphangioma in children, and thus, to increase our understandings of this disease in clinical practice. Method This study enrolled nine boys, aged 1–10, who were admitted to Shanghai Children’s Hospital from January 2019 to December 2020 and who were finally confirmed with lymphangioma in the inguinal area. The clinical manifestations, diagnosis, and treatment of these children were analyzed retrospectively. The length of diagnostic process ranged from 3 weeks to 20 months. We also reviewed other cases of initially misdiagnosed cases of SRL in English publications from 2000 to 2022. Results The nine cases were misdiagnosed as hydrocele, hematoma, or inguinal hernia. Three patients received intracystic injection of bleomycin, three underwent laparoscopic mass resection, and three underwent resection of the inguinal lymphangioma under direct vision. Postoperative pathological analysis of the surgical specimens confirmed the diagnosis of benign cystic lesions and lymphangioma. Meanwhile, among the 14 cases of SRL in literature review, eight were misdiagnosed. Six were initially diagnosed as hydrocele, one as inguinal oblique hernia, and one as testicular tumor, all of which underwent ultrasonography scans. All cases were confirmed as lymphangioma after pathological examination. Conclusion The non-specific clinical manifestations may contribute to the misdiagnosis of scrotal masses in children. A detailed and accurate medical history, careful physical examination, and imaging findings are important factors contributing to the preoperative differential diagnosis of scrotal lumps in children, but the final diagnosis is based on pathological examination

CRISPR-Cas9 knockout screening identifies KIAA1429 as an essential gene in Ewing sarcoma

Abstract Background Ewing sarcoma (ES) is an aggressive childhood bone and soft tissue cancer. KIAA1429 is one type of N6-methyladenosine (m6A) writer that plays a tumor-progressive role in various cancers, but the role of KIAA1429 in ES remains to be elucidated. The aim of the study was to investigate the role of KIAA1429 in ES. Methods We performed a multi-omic screen including CRISPR-Cas9 functional genomic and transcriptomic approaches, and identified that KIAA1429 played a significant role in ES progression. Gene knockdown, quantitative real-time PCR (Q-RT-PCR), immunoblotting, CellTiter-Glo assays, clonogenic assays, a subcutaneous xenograft model and immunohistochemistry were used to assess the functional role of KIAA1429 in ES. We mainly conducted RNA sequencing (RNA-seq) in ES cells to analyze the downstream regulatory mechanism of KIAA1429. An integrative analysis of chromatin immunoprecipitation sequencing (ChIP-seq) and RNA-seq indicated the upstream regulatory mechanism of KIAA1429. Results In vitro and in vivo CRISPR-Cas9 knockout screening identified KIAA1429 as an ES-dependent gene. Genetic suppression of KIAA1429 inhibited ES cell proliferation and tumorigenicity both in vitro and in vivo. Further studies revealed that KIAA1429 promotes ES tumorigenesis by regulating the ribosome-associated cell cycle and cancer-related inflammation. Interestingly, we found that STAT3 was a target of KIAA1429 and that a STAT3 inhibitor reduced KIAA1429 transcript levels, indicating positive feedback between KIAA1429 and STAT3. Finally, we found that NKX2-2 bound to the KIAA1429 promoter and transactivated KIAA1429. Conclusion Our study systematically analyzed ES-dependent epigenetic/transcriptional regulatory genes and identified KIAA1429 as a biomarker of tumor progression in ES, providing a potential therapeutic target for treating ES

Elevated expression of histone deacetylase HDAC8 suppresses arginine-proline metabolism in necrotizing enterocolitis

Summary: Epigenetic alterations are especially important in necrotizing enterocolitis (NEC). Here, we reported that histone deacetylase 8 (HDAC8) plays a previously unknown role in modulating arginine metabolism via acetylation of histone 3 lysine 9 (acetyl-H3K9) regulation during the pathogenesis of NEC. We found that HDAC8 was upregulated in humans and mice intestinal samples with NEC, while selective inhibition of HDAC8 expression ameliorated NEC. HDAC8 regulates enzymes involved in the metabolic conversion of proline to arginine (PRODH, PRODH2, OAT, and OTC) and arginine to ornithine (ARG1). The results showed that H3K9ac signal in the PRODH/PRODH2 promoter region was mediated by HDAC8. Additionally, the decreased concentration of butyric acid was strongly correlated with elevated HDAC8 levels and circulating arginine, which may result from an unbalanced Firmicutes/Bacteroidetes ratio. These results reveal previously underappreciated roles of microbial metabolites and HDAC8 to coordinate the arginine metabolism during NEC development

Table 2_v1_The composition of the gut microbiota is altered in biliary atresia with cholangitis.docx

AimTo detect the composition of the gut microbiota in biliary atresia after Kasai surgery.MethodsInfants within six months after the Kasai operation who were diagnosed by cholangiography at Shanghai Children’s Hospital were enrolled in the study. Fecal samples were collected from diapers, placed into sterile tubes in the inpatient department or outpatient department and frozen at −80°C within half an hour. The gut microbiota was detected by 16S rRNA sequences. Then, the patients that were followed up to one year after the Kasai operation who suffered from cholangitis at least one time were grouped into the BAcho group, and the others were grouped into the BAnoncho group.ResultsNine of 18 BA patients were grouped into the BAcho group, and the others were grouped into the BAnoncho group. In the BAcho group, AST, ALT and GGT were significantly increased compared to the BAnoncho group. The number of total OTUs (operational taxonomic units) in feces was more elevated in the BAnoncho group than in the BAcho group. In the BAnoncho group, the Chao index at the OTU level was significantly increased compared to that in the BAcho group (66.37 ± 21.5 vs. 45.64 ± 11.25, p = 0.02 ConclusionThe composition of the gut microbiota was different between BA with cholangitis and BA without cholangitis.</p