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Phenotypic spectrum and genetic analysis in the fatal cases of Schaaf-Yang syndrome: Two case reports and literature review.
Chen, X, Ma, X, Zou, C
Medicine. 2020;(29):e20574
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Abstract
RATIONALE Schaaf-Yang syndrome, a rare imprinted hereditary disease caused by MAGEL2 variants, manifests as developmental delay/intellectual disability, neonatal hypotonia, feeding difficulties, contractures, and autism spectrum disorder. PATIENT CONCERNS Patient 1 and 2 were infant girls presenting facial dysmorphisms, contractures of interphalangeal joints, neonatal hypotonia, feeding difficulties, congenital heart diseases, and respiratory complications. Besides, Patient 2 presented with delayed psychomotor development. DIAGNOSIS Whole-exome sequencing was performed and heterozygous mutations of the MAGEL2 gene were detected in the patients. They were diagnosed as Schaaf-Yang syndrome. INTERVENTIONS The patients received supportive treatment including mechanical ventilation, parenteral nutrition and gastric tube feeding. OUTCOMES Whole-exome sequencing revealed de novo heterozygous c.1996dupC pathogenic mutations in the MAGEL2 gene in the 2 patients. They died due to respiratory failure at the age of 20 days and 98 days, respectively. LESSONS Our results indicate that MAGEL2 variants can cause congenital heart disease and fatal respiratory complications, broadening the phenotypic spectrum and adding to the fatal cases of Schaaf-Yang syndrome. We highly suggest that the MAGEL2 gene should be added to gene-panels or gene-filters in next-generation sequencing-based diagnostics, which is of great significance for early diagnosis and early intervention of Schaaf-Yang syndrome patients.
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Strategies and industrial perspectives to improve oral absorption of biological macromolecules.
Liu, C, Kou, Y, Zhang, X, Cheng, H, Chen, X, Mao, S
Expert opinion on drug delivery. 2018;(3):223-233
Abstract
INTRODUCTION Therapeutic proteins have become a highly attractive drug of choice due to minimal toxicity, high activity and exquisite specificity. Oral delivery of protein drugs is a very interesting area for research, and, naturally, numerous technologies are required to improve the oral bioavailability of therapeutic proteins. AREAS COVERED This review article systemically generalized the major physiological barriers facing oral macromolecule delivery as well as the current approaches and novel developments in the field, including permeation enhancers, enzyme inhibitors, particulate drug delivery system, ligand delivery system, mucoadhesive delivery system, mucus penetration delivery system and other strategies. EXPERT OPINION The development of composite formulation methods need to meet regulatory requirements for reproducibility, manufacturing cost, and bioavailability. So far, oral delivery of protein and peptide drugs is still facing immense challenges despite of the fact that some clinical studies are undergoing. The most advanced clinical strategies for therapeutic proteins are co-administration of absorption enhancers or protease inhibitors. Besides, rising new technologies in the field also provides a growing opportunity, such as nanotechnology, mucoadhesive and mucus penetration particulate delivery system.
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PredHydroxy: computational prediction of protein hydroxylation site locations based on the primary structure.
Shi, SP, Chen, X, Xu, HD, Qiu, JD
Molecular bioSystems. 2015;(3):819-25
Abstract
Compared to well-known and extensively studied protein phosphorylation, protein hydroxylation attracts much less attention and the molecular mechanism of the hydroxylation is still incompletely understood. And yet annotation of hydroxylation in proteomes is a first-critical step toward decoding protein function and understanding their physiological roles that have been implicated in the pathological processes and providing useful information for the drug designs of various diseases related with hydroxylation. In this work, we present a novel method called PredHydroxy to automate the prediction of the proline and lysine hydroxylation sites based on position weight amino acids composition, 8 high-quality amino acid indices and support vector machines. The PredHydroxy achieved a promising performance with an area under the receiver operating characteristic curve (AUC) of 82.72% and a Matthew's correlation coefficient (MCC) of 69.03% for hydroxyproline as well as an AUC of 87.41% and a MCC of 66.68% for hydroxylysine in jackknife cross-validation. The results obtained from both the cross validation and independent tests suggest that the PredHydroxy might be a powerful and complementary tool for further experimental investigation of protein hydroxylation. Feature analyses demonstrate that hydroxylation and non-hydroxylation have distinct location-specific differences; alpha and turn propensity is of importance for the hydroxylation of proline and lysine residues. A user-friendly server is freely available on the web at: .
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Quantitative prediction of the thermal motion and intrinsic disorder of protein cofactors in crystalline state: a case study on halide anions.
Ren, Y, Chen, X, Li, X, Lai, H, Wang, Q, Zhou, P, Chen, G
Journal of theoretical biology. 2010;(2):291-8
Abstract
The thermal motion and intrinsic disorder of protein cofactors are highly correlated with their biological functions and can be at least in part measured by atomic temperature factor or B-factor. However, this crystallographic parameter, which actually shares the equal importance with the atomic coordinate in describing the complete profile of crystal structures, has long been underappreciated in the field of biology. In the present study, we attempt to put the first step towards the quantitative prediction of the B-factor values of halide anions, which were recently found to play a fundamental role in conferring stability and specificity to the architecture of proteins and their complexes with nucleic acids and small ligands. In this procedure, the local nonbonding landscapes of halide anions bound in proteins are characterized by electrostatic and dispersion potentials, and then the resulting descriptors of the characterization are statistically correlated with experimentally measured B-factors by using both linear and nonlinear machine learning approaches. From the modeling results and the comparison of these results to those obtained previously for predicting protein B-factors, we demonstrate that the dynamic behavior of halide anions in protein crystals is primarily governed by the local features of nonbonding potential landscapes and, owing to the non-ignorable noise existing in experimental data, the relationship between the B-factor values and the local nonbonding landscapes can only be modeled at a moderate level of accuracy even using the complicated nonlinear methods. These findings are consistent well with that concluding from previous studies of protein B-factors.
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An improved Gibbs sampling method for motif discovery via sequence weighting.
Chen, X, Jiang, T
Computational systems bioinformatics. Computational Systems Bioinformatics Conference. 2006;:239-47
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Abstract
The discovery of motifs in DNA sequences remains a fundamental and challenging problem in computational molecular biology and regulatory genomics, although a large number of computational methods have been proposed in the past decade. Among these methods, the Gibbs sampling strategy has shown great promise and is routinely used for finding regulatory motif elements in the promoter regions of co-expressed genes. In this paper, we present an enhancement to the Gibbs sampling method when the expression data of the concerned genes is given. A sequence weighting scheme is proposed by explicitly taking gene expression variation into account in Gibbs sampling. That is, every putative motif element is assigned a weight proportional to the fold change in the expression level of its downstream gene under a single experimental condition, and a position specific scoring matrix (PSSM) is estimated from these weighted putative motif elements. Such an estimated PSSM might represent a more accurate motif model since motif elements with dramatic fold changes in gene expression are more likely to represent true motifs. This weighted Gibbs sampling method has been implemented and successfully tested on both simulated and biological sequence data. Our experimental results demonstrate that the use of sequence weighting has a profound impact on the performance of a Gibbs motif sampling algorithm.