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10. Hypoxia/reoxygenation attenuates migration and invasion of human extracellular villus trophoblast cells via DNA methyltransferase pathway

Author

HU Sichen, LAN Xi, and DING Yubin

Subjects
hypoxia/reoxygenation, extravillous trophoblast, dna methyltransferase, epithelial-mesenchymal transition, migration, invasion, Medicine (General), R5-920
Abstract

Objective To explore the regulative mechanism of hypoxia/reoxygen (H/R) for invasion ability of extravillous trophoblast (EVT). Methods Immortalized human EVT cell line HTR-8/SVneo in early pregnancy, primary EVT cells isolated from the villi of placenta in early pregnancy, and villi explants were cultured respectively. A simulation model of H/R environment in EVT cells invading the uterus was established under the conversion conditions of 1% O2 for 24 h to 20% O2 for another 24 h. Western blotting and immunofluorescence assay were used to detect the expression of key factors such as cell invasion, and Transwell chamber test was employed to observe cell migration and invasion. Results After H/R induction, the migration and invasion abilities of HTR-8/SVneo cells were weakened, and the epitaxial ability of cultured villi explants and the migration and invasion abilities of isolated primary EVT cells were also weakened. Under H/R conditions, the expression levels of MMP-2 and MMP-9, integrin-β1 and integrin-α5 were decreased in HTR-8/SVneo cells (P < 0.05), and the protein expression of DNA methyltransferase (DNMTs) was also down-regulated (P < 0.01). In the primary EVT cells under H/R condition, the expression levels of epithelial-mesenchymal transition (EMT) positive regulatory factors, Slug and Snails, were inhibited (P < 0.05), that of epithelial cell marker E-cadherin was increased (P < 0.01), protein levels of MMP-2 and MMP-9, integrin-β1 and integrin-α5 were decreased (P < 0.05), and cell invasion ability was reduced along with decreased DNMT1 and DNMT3A expression (P < 0.05). However, overexpression of DNMT1, DNMT3A and DNMT3B in HTR-8/SVneo cells promoted the up-regulation of interstitial markers N-cadherin, and MMP-2 and MMP-9 (P < 0.05). Conclusion H/R regulates the expression of EMT-related factors such as MMP-2/-9 through DNMTs, and thereby reduces the migration and invasion abilities of EVT cells.

Published
2023
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42. CDEMI: Characterizing differences in microbial composition and function in microbiome data

Author

Wang, Lidan, Liang, Xiao, Chen, Hao, Cao, Lijie, Liu, Lan, Zhu, Feng, Ding, Yubin, Tang, Jing, and Xie, Youlong

Subjects
Software/Web server Article, Structural Biology, Genetics, Biophysics, Biochemistry, Computer Science Applications, Biotechnology
Abstract

Microbial communities influence host phenotypes through microbiota-derived metabolites and interactions between exogenous active substances (EASs) and the microbiota. Owing to the high dynamics of microbial community composition and difficulty in microbial functional analysis, the identification of mechanistic links between individual microbes and host phenotypes is complex. Thus, it is important to characterize variations in microbial composition across various conditions (for example, topographical locations, times, physiological and pathological conditions, and populations of different ethnicities) in microbiome studies. However, no web server is currently available to facilitate such characterization. Moreover, accurately annotating the functions of microbes and investigating the possible factors that shape microbial function are critical for discovering links between microbes and host phenotypes. Herein, an online tool, CDEMI, is introduced to discover microbial composition variations across different conditions, and five types of microbe libraries are provided to comprehensively characterize the functionality of microbes from different perspectives. These collective microbe libraries include (1) microbial functional pathways, (2) disease associations with microbes, (3) EASs associations with microbes, (4) bioactive microbial metabolites, and (5) human body habitats. In summary, CDEMI is unique in that it can reveal microbial patterns in distributions/compositions across different conditions and facilitate biological interpretations based on diverse microbe libraries. CDEMI is accessible at http://rdblab.cn/cdemi/

Published
2023
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48. A critical assessment of clustering algorithms to improve cell clustering and identification in single-cell transcriptome study.

Author

Liang, Xiao, Cao, Lijie, Chen, Hao, Wang, Lidan, Wang, Yangyun, Fu, Lijuan, Tan, Xiaqin, Chen, Enxiang, Ding, Yubin, and Tang, Jing

Subjects
DEEP learning, TRANSCRIPTOMES, RNA sequencing, CLUSTERING algorithms
Abstract

Cell clustering is typically the initial step in single-cell RNA sequencing (scRNA-seq) analyses. The performance of clustering considerably impacts the validity and reproducibility of cell identification. A variety of clustering algorithms have been developed for scRNA-seq data. These algorithms generate cell label sets that assign each cell to a cluster. However, different algorithms usually yield different label sets, which can introduce variations in cell-type identification based on the generated label sets. Currently, the performance of these algorithms has not been systematically evaluated in single-cell transcriptome studies. Herein, we performed a critical assessment of seven state-of-the-art clustering algorithms including four deep learning-based clustering algorithms and commonly used methods Seurat, Cosine-based Tanimoto similarity-refined graph for community detection using Leiden's algorithm (CosTaL) and Single-cell consensus clustering (SC3). We used diverse evaluation indices based on 10 different scRNA-seq benchmarks to systematically evaluate their clustering performance. Our results show that CosTaL, Seurat, Deep Embedding for Single-cell Clustering (DESC) and SC3 consistently outperformed Single-Cell Clustering Assessment Framework and scDeepCluster based on nine effectiveness scores. Notably, CosTaL and DESC demonstrated superior performance in clustering specific cell types. The performance of the single-cell Variational Inference tools varied across different datasets, suggesting its sensitivity to certain dataset characteristics. Notably, DESC exhibited promising results for cell subtype identification and capturing cellular heterogeneity. In addition, SC3 requires more memory and exhibits slower computation speed compared to other algorithms for the same dataset. In sum, this study provides useful guidance for selecting appropriate clustering methods in scRNA-seq data analysis. [ABSTRACT FROM AUTHOR]

Published
2024
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50. Impairment of endometrial decidual reaction in early pregnant mice fed with high fat diet

Author

CHEN, Zixuan, LI, Weike, CHEN, Xuemei, LIU, Xueqing, DING, Yubin, LI, Fangfang, HE, Junlin, WANG, Yingxiong, and GAO, Rufei

Subjects
Boron Compounds, Male, Estradiol, Phalloidine, Body Weight, Palmitic Acid, General Medicine, Diet, High-Fat, Mice, Inbred C57BL, Endometrium, Mice, Cholesterol, Homeobox A10 Proteins, Pregnancy, Prostaglandin-Endoperoxide Synthases, Bone Morphogenetic Proteins, Animals, Female, Collagen, Obesity, Azo Compounds, Progesterone, Triglycerides, Research Article, Oleic Acid
Abstract

OBJECTIVE: To investigate the effect of obesity induced by high fat diet on decidual reaction of endometrium in mice, and the effect of high fat treatment on decidual reaction of endometrial stromal cells. METHODS: Twelve 4-week-old healthy C57BL/6J female mice were randomly divided into high fat diet group and control group with 6 mice in each group. They were fed with high fat diet (22 kJ/g) or normal diet (16 kJ/g) for 12 weeks, respectively. The body weight of mice was measured every week. After feeding for 12 weeks, the body length and width of mice were measured, and the levels of fasting serum triglyceride and total cholesterol were determined. Then the mice were mated with healthy C57BL/6J male mice, and the uterine tissues were collected on the seventh day of pregnancy. The decidual cells and collagen fibers in mouse endometrium was observed by HE staining and Masson staining respectively. The expression of decidual reaction related proteins in mouse endometrium were detected by immunohistochemistry and Western blotting. Mouse endometrial stromal cells (mESCs) were isolated and treated with the oleic acid and palmitic acid in vitro , and the decidual reaction was induced with estradiol and progesterone. The accumulation of lipid droplets in mESCs was observed by oil red O and Bodipy staining. The cytoskeleton of mESCs was observed by phalloidin staining. The levels of decidual reaction related genes and proteins were detected by real-time fluorescence quantitative PCR and Western blotting. RESULTS: After feeding for 12 weeks, the body weight of mice in the high fat group was significantly higher than that in the control group ( P0.05), but the body width of mice in the high fat group was significantly larger than that in the control group ( P

Published
2022
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