Comprehensive analysis of genomic complexity in the 5' end coding region of the DMD gene in patients of exons 1-2 duplications based on long-read sequencing.

BACKGROUND: Dystrophinopathies are the most common X-linked inherited muscle diseases, and the disease-causing gene is DMD. Exonic duplications are a common type of pathogenic variants in the DMD gene, however, 5' end exonic duplications containing exon 1 are less common. When assessing the pathogenicity of exonic duplications in the DMD gene, consideration must be given to their impact on the reading frame. Traditional molecular methods, such as multiplex ligation-dependent probe amplification (MLPA) and next-generation sequencing (NGS), are commonly used in clinics. However, they cannot discriminate the precise physical locations of breakpoints and structural features of genomic rearrangement. Long-read sequencing (LRS) can effectively overcome this limitation. RESULTS: We used LRS technology to perform whole genome sequencing on three families and analyze the structural variations of the DMD gene, which involves the duplications of exon 1 and/or exon 2. Two distinct variant types encompassing exon 1 in the DMD Dp427m isoform and/or Dp427c isoform are identified, which have been infrequently reported previously. In pedigree 1, the male individuals harboring duplication variant of consecutive exons 1-2 in the DMD canonical transcript (Dp427m) and exon 1 in the Dp427c transcript are normal, indicating the variant is likely benign. In pedigree 3, the patient carries complex SVs involving exon 1 of the DMD Dp427c transcript showing an obvious phenotype. The locations of the breakpoints and the characteristics of structural variants (SVs) are identified by LRS, enabling the classification of the variants' pathogenicity. CONCLUSIONS: Our research sheds light on the complexity of DMD variants encompassing Dp427c/Dp427m promoter regions and emphasizes the importance of cautious interpretation when assessing the pathogenicity of DMD 5' end exonic duplications, particularly in carrier screening scenarios without an affected proband.

The gut microbiota composition and metabolites are different in women with hypertensive disorders of pregnancy and normotension: A pilot study.

INTRODUCTION: Hypertensive disorders of pregnancy (HDP) are one of the main causes of perinatal morbidity. Gut microbiota influences host inflammatory pathways, glucose, and lipid metabolism. However, there is a lack of studies available on gut microbiota in HDP. OBJECTIVES: We investigate the mechanistic and pathogenic role of microbiota in the development of HDP, and want to treat HDP with gut microbiota. METHODS: We performed a case-control study to compare fecal samples of HDP and normotensive pregnant women by 16S ribosomal RNA sequencing. Fecal samples, collected from pregnant women, were divided into groups P and C (pregnant women with HDP and normotension, respectively). There were six pregnant women in group P and nine pregnant women in group C. Age of pregnant women is from 18 to 40 years and gestational age is from 27 to 40 weeks. DNA was extracted from fecal samples; a gene library was constructed and analyzed using bioinformatics. Finally, we determined the changes in the microbiome by alpha diversity, beta diversity, classification abundance, and taxonomic composition analyses. RESULTS: Escherichia (10.48% in group P and 0.61% in group C) was the dominant bacterium in HDP patients by classification abundance analysis, which can lead to the development of preeclampsia through inflammatory response. We found that pregnant women with HDP had higher abundance of Rothia (p = 0.04984), Actinomyces (p = 0.02040), and Enterococcus (p = 0.04974) and lower abundance of Coprococcus (p = 0.04955) than pregnant women with normotension for the first time by taxonomic composition analysis. Based on the Kyoto Encyclopedia of Genes and Genomes database analysis, physiological and biochemical functions of HDP patients were significantly weakened, especially in energy metabolism. CONCLUSIONS: We found the effect of changes in gut microbiota on the development of HDP. In comparison with group C, group P contained more harmful bacteria and less beneficial bacteria, which are associated with HDP. Our research further provides a basis for a clinical application for HDP treatment using antibiotics and probiotic supplementation.

De Novo Mutation in KRT1 Leads to Epidermolytic Palmoplantar Keratoderma: from Chinese Traditional Treatment to Prenatal Diagnosis Using Whole-Exome Sequencing-Plus.

Congenital skin disorders are a class of complex genetic diseases that are difficult to diagnose and treat. We developed trio whole-exome sequencing-plus (WES-plus) for detecting de novo mutations and evaluated the use of traditional Chinese medicine (TCM) for treating congenital skin disorders. In this study, we successively performed panel-based next-generation sequencing (NGS) and Trio WES-plus in a child with frequent large blisters. Panel-based NGS revealed no pathogenic mutations. Trio WES-plus for resequencing based on cutaneous keratosis of the palms and feet detected a missense mutation (c.1436T>A, p.Ile479Asn) in the coding region of KRT1 in the child but not in his parents. Following prenatal diagnosis, a healthy second baby without the mutation was born. The disease symptoms of epidermolytic palmoplantar keratoderma (EPPK) application were improved by TCM and Western medicine. Our study revealed the pathogenicity of a de novo mutation in human KRT1, which expands the mutation spectrum of EPPK. Trio WES-plus is useful for diagnosing genetic diseases and providing genetic guidance from prenatal diagnosis to treatment.

Highly diastereo- and enantioselective construction of a spiro[cyclopenta[b]indole-1,3'-oxindole] scaffold via catalytic asymmetric formal [3+2] cycloadditions.

An organocatalytic asymmetric formal [3+2] cycloaddition of isatin-derived 3-indolylmethanol with 3-methyl-2-vinylindole has been established, leading to highly stereoselective construction of a spiro[cyclopenta[b]indole-1,3'-oxindole] scaffold with the concomitant creation of three contiguous stereogenic centers (72-99% yield, all >95 : 5 dr, 90-98% ee), one of which is an all-carbon quaternary stereogenic center.