: Bacteroides, as one of the most abundant and diverse genera in the human gut, is regarded as a window into the study of gut microbiota-host interactions. Currently, CRISPR/Cas-based gene editing systems targeting Bacteroides have been widely applied, while the large size of Cas nucleases limits their potential application scenarios (such as in situ gut Bacteroides editing based on phage delivery). Therefore, this study aims to develop a compact and highly efficient genetic editing tool in Bacteroides., We developed a miniaturized CRISPR/Cas gene editing system for human gut Bacteroides. First, the editing capabilities of different miniaturized CRISPR/Cas systems, including AsCas12f, CasΦ2, and ISDge10, were evaluated in Bacteroides fragilis. Subsequently, the editing capability of AsCas12f was assessed across various Bacteroides species, and the size of this system was further optimized. The results demonstrated that the CRISPR/AsCas12f genome editing system exhibited the highest editing efficiency in B. fragilis. The CRISPR/AsCas12f system achieved efficient genome editing in B. fragilis, Bacteroides thetaiotaomicron, and Phocaeicola vulgatus. Furthermore, with a repair template of 500 bp homologous arms, the editing efficiency remained as high as 94.7%. In conclusion, CRISPR/AsCas12f can serve as a chassis tool enzyme for the development of Bacteroides-based miniature gene editors and derivative technologies, laying a foundation for the further development of gene editing technology for Bacteroides.
CRISPR-Cas Systems/genetics* ; Gene Editing/methods* ; Bacteroides/genetics* ; Humans ; Gastrointestinal Microbiome/genetics* ; Bacteroides fragilis/genetics*

The clinical features and genetic variation of a patient with microcephaly, growth restriction, and increased sister chromatid exchange-2, who was treated in the Department of Gastroenterology, Children′s Hospital of Nanjing Medical University in April 2024 were analyzed, and the pathogenic cause was identified.The clinical data of the patient were collected, and the genomic DNA was extracted from the peripheral blood of the proband and his parents.Gene detection was conducted through whole-exome sequencing, and candidate variants were verified by Sanger sequencing and bioinformatics analysis.The proband presented with intrauterine growth restriction, retarded growth and development, microcephaly, and premature ageing-like facial features.Gene sequencing showed novel compound heterozygous variations c. 1333T>C (p.C445R) and c. 2345dup (p.P783Afs*3) in the proband.Both variants are conserved, and various bioinformatics tools predict them to be deleterious.The compound heterozygous variant (c.1333T>C/c.2345dup) in the TOP3A gene is the likely etiology of the patient′s condition.These two novel variants expand the spectrum of known TOP3A gene variants and provide a basis for genetic counseling for the family.

The clinical features and genetic variation of a patient with microcephaly, growth restriction, and increased sister chromatid exchange-2, who was treated in the Department of Gastroenterology, Children′s Hospital of Nanjing Medical University in April 2024 were analyzed, and the pathogenic cause was identified.The clinical data of the patient were collected, and the genomic DNA was extracted from the peripheral blood of the proband and his parents.Gene detection was conducted through whole-exome sequencing, and candidate variants were verified by Sanger sequencing and bioinformatics analysis.The proband presented with intrauterine growth restriction, retarded growth and development, microcephaly, and premature ageing-like facial features.Gene sequencing showed novel compound heterozygous variations c. 1333T>C (p.C445R) and c. 2345dup (p.P783Afs*3) in the proband.Both variants are conserved, and various bioinformatics tools predict them to be deleterious.The compound heterozygous variant (c.1333T>C/c.2345dup) in the TOP3A gene is the likely etiology of the patient′s condition.These two novel variants expand the spectrum of known TOP3A gene variants and provide a basis for genetic counseling for the family.

Objective:To explore the relevancy between the uridine diphosphate-glucuronylgly-cosyltransferase 1A1 (UGT1A1) gene mutation and the phenotype of indirect hyperbilirubinemia in children.Methods:Sixteen cases with indirect hyperbilirubinemia who visited the Department of Gastroenterology, Children's Hospital of Nanjing Medical University from July 2013 to November 2019 were retrospectively analyzed and were divided into Gilbert syndrome (GS), Crigler-Najjar syndrome type II (CNS-II), and indirect hyperbilirubinemia groups unexplained by UGT1A1 gene mutations. The differences in gene mutation site information and general clinical data were compared. The association between gene mutation spectrum and bilirubin level was explored by t-test analysis.Results:Ten of the sixteen cases with indirect hyperbilirubinemia had GS, three had CNS-II, and three had indirect hyperbilirubinemia unexplained by UGT1A1 gene mutations. A total of six mutation types were detected, of which c.211G?>?A accounted for 37.5% (6/16), c.1456T?>?G accounted for 62.5% (10/16), and TATA accounted for 37.5% (6/16), respectively. Compared with the GS group, the CNS group had early disease onset incidence, high serum total bilirubin ( t ?=?5.539, P ??0.05) and age of onset ( t ?=?0.3611, P ?>?0.05) between the two groups. There was no significant correlation between the number of UGT1A1 gene mutations and serum bilirubin levels. Children with c.1456T?>?G homozygous mutations had the highest serum bilirubin levels. Conclusion:The common pathogenic variants of the UGT1A1 gene sequence are c.1456T?>?G, c.211G?>?A, and TATA, indicating that these site mutations are related to the occurrence of indirect hyperbilirubinemia and have important guiding significance for the etiological analysis of indirect hyperbilirubinemia in children.

OBJECTIVE: To explore the clinical features and genetic basis of a patient with glycogen storage disease type VI (GSD-VI). METHODS: Clinical data of the patient was collected. Genomic DNA was extracted from peripheral blood samples of the proband and his parents. Genetic variants were detected by using whole exome sequencing. Candidate variants were verified by Sanger sequencing followed by bioinformatics analysis. RESULTS: The proband presented fasting hypoglycemia, hepatomegaly, growth retardation, transaminitis, metabolic acidosis and hyperlactatemia. Liver biopsy indicated GSD. Novel compound heterozygous PYGL gene variants (c.2089A>G/c.158_160delACT) were detected in the proband. Compound heterozygosity was confirmed by Sanger sequencing of the patient's genomic DNA. Provean and MutationTaster predicted the two variants as deleterious and the variant sites are highly conserved. CONCLUSION The compound heterozygous variants (c.2089A>G/c.158_160delACT) of PYGL gene probably underlay the GSD in the patient. The two novel variants have expanded the spectrum of PYGL gene variants and provided the basis for genetic counseling of the family.
Child ; Family ; Genetic Testing ; Glycogen Storage Disease Type VI/genetics* ; Humans ; Mutation ; Whole Exome Sequencing

A 2-year- and 2-month-old girl developed recurrent eczema-like rashes 7 days after birth, followed by the occurrence of poikiloderma and hair loss. Cholestasis occurred at the age of 1 month and 10 days, which was improved but serum transaminase levels were elevated after 4 months. The patient usually presented with slight sweating, heat intolerance, and delayed gross motor development. Skin examination showed generalized mottled hypo- and hyper-pigmented patches, especially in the exposed areas, and sparse hair and eyebrows. Her parents had no similar clinical manifestations. Whole-exome sequencing showed a mutation c.1883G>A (p.Ser628Asn) in the FAM111B gene in the child, which was not found in her parents. According to the typical skin lesions, abnormal liver function and genetic testing results, this patient was diagnosed with hereditary fibrosing poikiloderma with tendon contracture, myopathy, and pulmonary fibrosis, and the mutation c.1883G>A in the FAM111B gene may be the cause of the patient′s clinical manifestations. The patient received hepatoprotective therapy, sun screen intervention, rehabilitation training, etc. After 10-month follow-up, the patient still presented with skin lesions and elevated transaminases, but without other discomforts.

Objective To compare the clinical features, diagnosis, treatment and prognosis between macrophages activation syndrome (MAS) and other hemophagocytic syndrome (HPS). Methods Thirty-six children with HPS were identified at Nanjing Children's Hospital during January 2006 to March 2009. They could be classi-fied into MAS group (13 patients) and other HPS group (23 patients). All relevant clinical features, laboratory data, treatments and outcomes were analyzed with t test,χ2 test and Fisher's exact test.Results Patients with MAS tended to be elder than those with other HPSs [(7.7±1.3) years vs (2.6±0.5)years, t=3.899, P=0.004]. There was no difference in gender distribution. In MAS cases, the central nervous system (69% vs 13%, P=0.001), circulatory system (23% vs 9%, P=0.047) and the urinary system (38% vs 9%, P=0.033) were usually involved. The clinical symptoms of MAS were more sever than other HPS. Serum ferritin [(9703±9819) μg/L vs (4569±1396) μg/L, t=2.854, P=0.015] and erythrocyte sedimentation rate (ESR) [(53±32) mm/1 h vs (20±14) mm/1 h, t=2.708, P=0.020] changed more obviously in MAS cases compared with other HPS. Conclusion, Childhood MAS is different from other HPS in terms of age, etiology, clinical manifestations, laboratory tests and treatments.