Single-cell RNA sequencing reveals dynamic changes in A-to-I RNA editome during early human embryogenesis

BACKGROUND: A-to-I RNA-editing mediated by ADAR (adenosine deaminase acting on RNA) enzymes that converts adenosine to inosine in RNA sequence can generate mutations and alter gene regulation in metazoans. Previous studies have shown that A-to-I RNA-editing plays vital roles in mouse embryogenesis. However, the RNA-editing activities in early human embryonic development have not been investigated. RESULTS: Here, we characterized genome-wide A-to-I RNA-editing activities during human early embryogenesis by profiling 68 single cells from 29 human embryos spanning from oocyte to morula stages. We demonstrate dynamic changes in genome-wide RNA-editing during early human embryogenesis in a stage-specific fashion. In parallel with ADAR expression level changes, the genome-wide A-to-I RNA-editing levels in cells remained relatively stable until 4-cell stage, but dramatically decreased at 8-cell stage, continually decreased at morula stage. We detected 37 non-synonymously RNA-edited genes, of which 5 were frequently found in cells of multiple embryonic stages. Moreover, we found that A-to-I editings in miRNA-targeted regions of a substantial number of genes preferably occurred in one or two sequential stages. CONCLUSIONS: Our single-cell analysis reveals dynamic changes in genome-wide RNA-editing during early human embryogenesis in a stage-specific fashion, and provides important insights into early human embryogenesis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3115-2) contains supplementary material, which is available to authorized users

X chromosome dosage of histone demethylase KDM5C determines sex differences in adiposity

Males and females differ in body composition and fat distribution. Using a mouse model that segregates gonadal sex (ovaries and testes) from chromosomal sex (XX and XY), we showed that XX chromosome complement in combination with a high-fat diet led to enhanced weight gain in the presence of male or female gonads. We identified the genomic dosage of Kdm5c, an X chromosome gene that escapes X chromosome inactivation, as a determinant of the X chromosome effect on adiposity. Modulating Kdm5c gene dosage in XX female mice to levels that are normally present in males resulted in reduced body weight, fat content, and food intake to a degree similar to that seen with altering the entire X chromosome dosage. In cultured preadipocytes, the levels of KDM5C histone demethylase influenced chromatin accessibility (ATAC-Seq), gene expression (RNA-Seq), and adipocyte differentiation. Both in vitro and in vivo, Kdm5c dosage influenced gene expression involved in extracellular matrix remodeling, which is critical for adipocyte differentiation and adipose tissue expansion. In humans, adipose tissue KDM5C mRNA levels and KDM5C genetic variants were associated with body mass. These studies demonstrate that the sex-dependent dosage of Kdm5c contributes to male/female differences in adipocyte biology and highlight X-escape genes as a critical component of female physiology

Prenatal diagnosis and postnatal verification in fetuses with total anomalous pulmonary venous connection

ObjectiveTo systematically verify the accuracy of a four-step prenatal ultrasonography in diagnosing fetal total anomalous pulmonary venous connection (TAPVC).MethodsA total of 62 TAPVC fetuses received prenatal ultrasonography and were confirmed by postnatal echocardiography, surgery, or postabortion autopsy. The suspected TAPVC fetuses were further screened by a four-step prenatal ultrasonography for TAPVC classification, pulmonary venous obstruction, and the associated malformations, and followed postpartum. The sonographic features, clinical data, and prognosis of the TAPVC fetuses were retrospectively analyzed.ResultsOf the 62 TAPVC fetuses, supracardiac TAPVC was found in 20 cases, intracardiac TAPVC in 12, infracardiac TAPVC in 21, and mixed TAPVC in 9. A total of 30 cases with right atrium isomerism were correctly diagnosed. Of the 11 cases with other intracardiac and extracardiac malformations, 1 case was missed to be diagnosed. Of the 21 isolated TAPVC cases, 6 were missed prenatally and 1 case was prenatally diagnosed as intracardiac and postnatally proved to be mixed (intracardiac type + supracardiac type) by echocardiography. Of the 13 TAPVC live births, 4 infants died in the neonatal period without operation. Of the nine infants undergoing the operation, five recuperated and survived; one survived but had complications with superior vena cava obstruction and collateral circulation formation, and three died postoperatively.ConclusionThe four-step prenatal ultrasound procedure can comprehensively and systematically evaluate fetal TAPVC, detailing the classification, potential obstruction, and associated malformations. It provides substantial support for subsequent prenatal counseling and neonatal assessment. The retrospective analysis also reveals that isolated TAPVC is more prone to be missed in diagnosis

Prenatal Diagnosis of Recurrent Distal 1q21.1 Duplication in Three Fetuses With Ultrasound Anomalies

Background: The phenotype of duplication of 1q21.1 region is variable, ranging from macrocephaly, autism spectrum disorder, congenital anomalies, to a normal phenotype. Few cases have been reported in the literature regarding prenatal diagnosis of 1q21.1 duplication syndrome. The current study presents prenatal diagnosis of 1q21.1 duplication syndrome in three fetuses with ultrasound anomalies.Case presentation: Three fetuses from three unrelated families were included in the study. The prenatal routine ultrasound examination showed nasal bone loss in Fetus 1 and Fetus 3, as well as duodenal atresia in Fetus 2. Chromosomal microarray analysis was performed to provide genetic analysis of amniotic fluid and parental blood samples. The CMA results revealed two de novo duplications of 1.34 and 2.69 Mb at distal 1q21.1 region in two fetuses with absent nasal bone, as well as a maternal inherited 1.35-Mb duplication at distal 1q21.1 in one fetus with duodenal atresia.Conclusions: The phenotype of 1q21.1 duplication syndrome in prenatal diagnosis is variable. The fetuses with nasal bone loss or duodenal atresia may be related to 1q21.1 duplication and chromosomal microarray analysis should be performed

Characterization of ultrasound and postnatal pathology in fetuses with heterotaxy syndrome

BackgroundTo explore the diagnostic clues and abnormality spectrum of heterotaxy syndrome by prenatal ultrasonography and postnatal verification.MethodsThe prenatal ultrasonic data of 88 heterotaxy syndrome fetuses were analyzed retrospectively as left isomerism (LI) and right isomerism (RI). Prenatal ultrasound compared with the anatomical casting of the fetal body after labor induction, and the confirmatory postnatal diagnosis after delivery.ResultsFetal LI showed typical malformations of gastric vesicles on different sides from the heart, absence of hepatic segment of the inferior vena cava (IVC), abdominal aorta (AO) parallel with the azygos vein (AV), bilateral left bronchus, bilateral left atrial appendages, and polysplenia; intracardiac malformations of AV septal defects (AVSD), single atrium (SA), left ventricular outflow tract obstruction (LVOTO), and double-outlet right ventricle (DORV); and cardiac conduction abnormalities of sinus bradycardia and AV blockage. Fetal RI reported typical malformations of gastric vesicles on different sides from the heart, juxtaposition of the IVC with AO, anomalous pulmonary venous connection (APVC), asplenia, and bilateral right atrial appendages; intracardiac malformations of AVSD, SA, single ventricle, pulmonary atresia and stenosis, and DORV. The postnatal verification revealed 3 malformations misdiagnoses and 4 malformations missed diagnoses in LI fetuses and 10 misdiagnoses and 8 missed diagnoses in RI fetuses.ConclusionsThe proposed five-step prenatal ultrasonography has an important diagnostic value for the identification and classification of heterotaxy syndrome. The different sides of gastric vesicles and cardiac apex are important diagnostic clues for heterotaxy syndrome, featuring disconnected or hypoplastic IVC, typical complex cardiac malformation, and atrioventricular block in fetal LI, and shown APVC, juxtaposition of IVC and AO, and intracardiac malformations such as AVSD, DORV, and LVOTO in fetal RI

Overexpression of LCMR1 is significantly associated with clinical stage in human NSCLC

<p>Abstract</p> <p>Background</p> <p>Lung cancer is one of the most common human cancers and the leading cause of cancer death worldwide. The identification of lung cancer associated genes is essential for lung cancer diagnosis and treatment.</p> <p>Methods</p> <p>Differential Display-PCR technique was used to achieve the novel cDNA, which were then verified by real-time PCR. Northern blot was utilized to observe the expression of LCMR1 in different human tissues. 84 cases human NSCLC tissues and normal counterparts were analyzed for the expression of LCMR1 by immunohistochemistry.</p> <p>Results</p> <p>A novel 778-bp cDNA fragment from human large cell lung carcinoma cell lines 95C and 95D was obtained, and named <it>LCMR1 </it>(Lung Cancer Metastasis Related protein 1). LCMR1 was differentially expressed in different human tissues. LCMR1 was strongly overexpressed in NSCLC and its expression was significantly associated with clinical stage.</p> <p>Conclusion</p> <p>Our data indicated that <it>LCMR1</it>, strongly overexpressed in NSCLC, might have applications in the clinical diagnosis and treatment of lung cancer.</p

Structure and Evolution of Glycogen Branching Enzyme N-Termini From Bacteria

In bacteria, glycogen plays important roles in carbon and energy storage. Its structure has recently been linked with bacterial environmental durability. Among the essential genes for bacterial glycogen metabolism, the glgB-encoded branching enzyme GBE plays an essential role in forming α-1,6-glycosidic branching points, and determines the unique branching patterns in glycogen. Previously, evolutionary analysis of a small sets of GBEs based on their N-terminal domain organization revealed that two types of GBEs might exist: (1) Type 1 GBE with both N1 and N2 (also known as CBM48) domains and (2) Type 2 GBE with only the N2 domain. In this study, we initially analyzed N-terminal domains of 169 manually reviewed bacterial GBEs based on hidden Markov models. A previously unreported group of GBEs (Type 3) with around 100 amino acids ahead of the N1 domains was identified. Phylogenetic analysis found clustered patterns of GBE types in certain bacterial phyla, with the shorter, Type 2 GBEs predominantly found in Gram-positive species, while the longer Type 1 GBEs are found in Gram-negative species. Several in vitro studies have linked N1 domain with transfer of short oligosaccharide chains during glycogen formation, which could lead to small and compact glycogen structures. Compact glycogen degrades more slowly and, as a result, may serve as a durable energy reserve, contributing to the enhanced environmental persistence for bacteria. We were therefore interested in classifying GBEs based on their N-terminal domain via large-scale sequence analysis. In addition, we set to understand the evolutionary patterns of different GBEs through phylogenetic analysis at species and sequence levels. Three-dimensional modeling of GBE N-termini was also performed for structural comparisons. A further study of 9,387 GBE sequences identified 147 GBEs that might belong to a possibly novel group of Type 3 GBE, most of which fall into the phylum of Actinobacteria. We also attempted to correlate glycogen average chain length (ACL) with GBE types. However, no significant conclusions were drawn due to limited data availability. In sum, our study systematically investigated bacterial GBEs in terms of domain organizations from evolutionary point of view, which provides guidance for further experimental study of GBE N-terminal functions in glycogen structure and bacterial physiology

Mapping adipose and muscle tissue expression quantitative trait loci in African Americans to identify genes for type 2 diabetes and obesity

Relative to European Americans, type 2 diabetes (T2D) is more prevalent in African Americans (AAs). Genetic variation may modulate transcript abundance in insulin-responsive tissues and contribute to risk; yet published studies identifying expression quantitative trait loci (eQTLs) in African ancestry populations are restricted to blood cells. This study aims to develop a map of genetically regulated transcripts expressed in tissues important for glucose homeostasis in AAs, critical for identifying the genetic etiology of T2D and related traits. Quantitative measures of adipose and muscle gene expression, and genotypic data were integrated in 260 non-diabetic AAs to identify expression regulatory variants. Their roles in genetic susceptibility to T2D, and related metabolic phenotypes were evaluated by mining GWAS datasets. eQTL analysis identified 1,971 and 2,078 cis-eGenes in adipose and muscle, respectively. Cis-eQTLs for 885 transcripts including top cis-eGenes CHURC1, USMG5, and ERAP2, were identified in both tissues. 62.1% of top cis-eSNPs were within ±50kb of transcription start sites and cis-eGenes were enriched for mitochondrial transcripts. Mining GWAS databases revealed association of cis-eSNPs for more than 50 genes with T2D (e.g. PIK3C2A, RBMS1, UFSP1), gluco-metabolic phenotypes, (e.g. INPP5E, SNX17, ERAP2, FN3KRP), and obesity (e.g. POMC, CPEB4). Integration of GWAS meta-analysis data from AA cohorts revealed the most significant association for cis-eSNPs of ATP5SL and MCCC1 genes, with T2D and BMI, respectively. This study developed the first comprehensive map of adipose and muscle tissue eQTLs in AAs (publically accessible at https://mdsetaa.phs.wakehealth.edu) and identified genetically-regulated transcripts for delineating genetic causes of T2D, and related metabolic phenotypes