scholarly journals Dysregulated BMP2 in the Placenta May Contribute to Early-Onset Preeclampsia by Regulating Human Trophoblast Expression of Extracellular Matrix and Adhesion Molecules

2021 ◽  
Vol 9 ◽  
Author(s):  
Yuyin Yi ◽  
Hua Zhu ◽  
Christian Klausen ◽  
Hsun-Ming Chang ◽  
Amy M. Inkster ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Differentially Expressed Genes ◽  
Early Onset ◽  
Molecular Mechanisms ◽  
Differentially Expressed ◽  
Bone Morphogenetic Protein 2 ◽  
Rna Seq ◽  
Placental Development ◽  
Human Trophoblast ◽  
Early Onset Preeclampsia

Many pregnancy disorders, including early-onset preeclampsia (EOPE), are associated with defects in placental trophoblast cell invasion and differentiation during early placental development. Bone morphogenetic protein 2 (BMP2) belongs to the TGF-β superfamily and controls various physiological and developmental processes. However, the expression of BMP2 in the placenta and underlying molecular mechanisms of how BMP2 regulates trophoblast function remain unclear. In this study, we analyzed several publicly available microarray and RNA-seq datasets and revealed differences in expression of TGF-β superfamily members between gestational age-matched non-preeclamptic control and EOPE placentas. Importantly, BMP2 levels were significantly reduced in EOPE placentas compared with controls, and RNAscope in situ hybridization further demonstrated BMP2 expression was disrupted in EOPE placental villi. To explore the molecular mechanisms of BMP2-regulated early trophoblast differentiation, we examined BMP2 expression in first-trimester human placenta and found it to be localized to all subtypes of trophoblasts and the decidua. RNA-seq analysis on control and BMP2-treated primary human trophoblast cells identified 431 differentially expressed genes, including several canonical TGF-β/BMP signaling targets (BAMBI, ID1, INHBA, IGFBP3). Gene ontology annotations revealed that differentially expressed genes were involved in cell adhesion and extracellular matrix organization. Furthermore, we identified adhesion molecule with IgG-like domain 2 (AMIGO2) as a novel target for BMP2 that contributed to BMP2-induced trophoblast invasion and endothelial-like tube formation. Overall, our findings provide insight into the molecular processes controlled by BMP2 during early placental development that may contribute to the pathogenesis of EOPE.

scholarly journals Landscape of Dysregulated Placental RNA Editing Associated with Preeclampsia

2019 ◽  
Author(s):  
Xiaoxue Yang ◽  
Jing Yang ◽  
Xiaozhen Liang ◽  
Qian Chen ◽  
Sijia Jiang ◽  
...  
Keyword(s):  
Rna Editing ◽  
Differentially Expressed Genes ◽  
Binding Sites ◽  
Early Onset ◽  
Normal Subjects ◽  
Differentially Expressed ◽  
Expression Level ◽  
Trophoblast Cells ◽  
Placental Development ◽  
Gene Set

AbstractDysregulated RNA editing is well documented in several diseases such as cancer. The extent to which RNA editing might be involved in diseases originated in the placenta remains unknown, because RNA editing has rarely been studied in the placenta. Here, we have systematically profiled RNA editome on the placentae from 9 patients with early-onset severe preeclampsia (EOSPE) and 32 normal subjects, and a widespread RNA editing dysregulation in EOSPE has been identified. The mis-edited gene set is enriched with known preeclampsia-associated genes and differentially expressed genes in EOSPE. The “RNA editing events” at two microRNA binding sites in 3’-UTR of the LEP mRNA were generated, which could lead to increased expression level of LEP in trophoblast cells. Upregulation of LEP were also observed in the placentae of PE patients. These results suggest that widespread placental RNA editing may be involved in placental development and dysregulation of RNA editing in the placenta may contribute to the pathogenesis of preeclampsia.

scholarly journals Molecular Mechanisms Underlying Sugarcane Response to Aluminum Stress by RNA-Seq

2020 ◽  
Author(s):  
Thiago Mateus Rosa-Santos ◽  
Renan Gonçalves da Silva ◽  
Poornasree Kumar ◽  
Pratibha Kottapalli ◽  
Chiquito Crasto ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Aluminum Tolerance ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Aluminum Stress ◽  
Physiological Processes ◽  
Aluminum Ions ◽  
Detoxification Mechanism ◽  
Genomic Studies

Sugarcane is an important sugar-source crop. As any other plant, it can be exposed to several abiotic stress conditions. Though some metals contribute to critical physiological processes in plants, the presence of aluminum ions (Al3+) can be very toxic. In order to develop plants that flourish in acidic soils, it is critical to gain insights into the molecular mechanisms of sugarcane response to aluminum stress. To determine the genes involved in sugarcane response to aluminum stress we generated 372 million paired-end RNA sequencing reads, from roots of CTC-2 and RB855453 two contrasting cultivars. Data normalization resulted in 162,161 contigs and 97,335 trinity genes. After the read cutoff, the differentially expressed genes were 4,858 in CTC-2 and 1,307 in the RB855453, Treatment Vs Control, respectively. The differentially expressed genes were annotated into 34 functional categories. The majority of the genes were upregulated in the CTC-2 (tolerant cultivar) and down regulated in RB855453 (sensitive cultivar). Here, we present the first root-transcriptome of sugarcane under aluminum stress. The results and conclusions of this study provide a valuable resource for future genetic and genomic studies in sugarcane. This transcriptome analysis points out that sugarcane tolerance to aluminum may be explained by an efficient detoxification mechanism combined with the lateral root formation and activation of redox enzymes. Following our results, we present here, a hypothetical model for the aluminum tolerance in CTC-2 cultivar.

scholarly journals Insights into the Synthesis, Secretion and Curing of Barnacle Cyprid Adhesive via Transcriptomic and Proteomic Analyses of the Cement Gland

Marine Drugs ◽  
2020 ◽  
Vol 18 (4) ◽  
pp. 186
Author(s):  
Guoyong Yan ◽  
Jin Sun ◽  
Zishuai Wang ◽  
Pei-Yuan Qian ◽  
Lisheng He
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Lysyl Oxidase ◽  
Enrichment Analysis ◽  
Salivary Secretion ◽  
Cement Gland ◽  
Differentially Expressed ◽  
Model Organisms ◽  
Rna Seq ◽  
Secretion Pathway

Barnacles represent one of the model organisms used for antifouling research, however, knowledge regarding the molecular mechanisms underlying barnacle cyprid cementation is relatively scarce. Here, RNA-seq was used to obtain the transcriptomes of the cement glands where adhesive is generated and the remaining carcasses of Megabalanus volcano cyprids. Comparative transcriptomic analysis identified 9060 differentially expressed genes, with 4383 upregulated in the cement glands. Four cement proteins, named Mvcp113k, Mvcp130k, Mvcp52k and Mvlcp1-122k, were detected in the cement glands. The salivary secretion pathway was significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the differentially expressed genes, implying that the secretion of cyprid adhesive might be analogous to that of saliva. Lysyl oxidase had a higher expression level in the cement glands and was speculated to function in the curing of cyprid adhesive. Furthermore, the KEGG enrichment analysis of the 352 proteins identified in the cement gland proteome partially confirmed the comparative transcriptomic results. These results present insights into the molecular mechanisms underlying the synthesis, secretion and curing of barnacle cyprid adhesive and provide potential molecular targets for the development of environmentally friendly antifouling compounds.

Transcriptome profiling of differentially expressed genes of male and female inflorescences in spinach (Spinacia oleracea L.)

Genome ◽  
2021 ◽  
Author(s):  
Zhiyuan Liu ◽  
Haoying Wang ◽  
Zhaosheng Xu ◽  
Helong Zhang ◽  
Guoliang Li ◽  
...  
Keyword(s):  
Sex Determination ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Spinacia Oleracea ◽  
Transcriptome Profiling ◽  
Vital Role ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Male And Female ◽  
Spinacia Oleracea L

Spinach (Spinacia oleracea L.) is commonly considered a dioecious plant with heterogametic (XY) and homogametic (XX) sex chromosomes. The characteristic is also utilized for the production of spinach hybrid seeds. However, the molecular mechanisms of sex determination in spinach are still unclear because of a lack of genomic and transcriptomic information. In this study, RNA-sequencing (RNA-seq) was performed in male and female inflorescences to provide insight into the molecular basis of sex determination in spinach. Comparative transcriptome analyses showed that 2,278 differentially expressed genes (DEGs) were identified between male and female inflorescences. A high correlation between the RNA-Seq and qRT-PCR validation for DEGs was observed. Among these, 182 DEGs were annotated to transcription factors including the MYB family protein, bHLH family, and MADS family, suggesting these factors might play a vital role in sex determination. Moreover, 26 DEGs related to flower development, including nine ABCE class genes, were detected. Expression analyses of hormone pathways showed that brassinosteroids may be key hormones related to sex determination in spinach. Overall, this study provides a large amount of DEGs related to sexual expression and lays a foundation for unraveling the regulatory mechanism of sex determination in spinach.

Identification of key factors associated with early- and late-onset ovarian serous cystadenocarcinoma

2020 ◽  
Vol 16 (34) ◽  
pp. 2821-2833
Author(s):  
Shuang Ma ◽  
Yang Zheng ◽  
Chengwei Fei
Keyword(s):  
Overall Survival ◽  
Differentially Expressed Genes ◽  
Early Onset ◽  
Molecular Mechanisms ◽  
Late Onset ◽  
Differentially Expressed ◽  
Key Factors ◽  
Factors Associated ◽  
Serous Cystadenocarcinoma ◽  
Key Genes

Aim: To uncover the molecular mechanisms of early-onset ovarian serous cystadenocarcinoma (EOOSC; patients <50 years old) and late-onset ovarian serous cystadenocarcinoma (LOOSC; patients ≥50 years old). Materials & methods: Bioinformatics was utilized to identify the key factors. Results: 478 EOOSC and 899 LOOSC individual differentially expressed genes were identified and enriched in different pathways. The expression of key genes LAG3, LRRC63 and MT1B significantly influenced the overall survival of EOOSC patients. The expression of key genes RDH12, NTSR1, ZSCAN16, CT45A3 and EPPIN_WFDC6 significantly affected the overall survival of LOOSC patients. Conclusions: The molecular mechanisms of EOOSC and LOOSC appear to be different, so that patients might be treated individually in respect of age.

scholarly journals Changes in Ovary Transcriptome and Alternative splicing at estrus from Xiang pigs with Large and Small Litter Size

2019 ◽  
Author(s):  
Fuping Zhang ◽  
Liangting Tang ◽  
Xueqin Ran ◽  
Ning Mao ◽  
Yiqi Ruan ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Candidate Genes ◽  
Differentially Expressed Genes ◽  
Litter Size ◽  
Molecular Mechanisms ◽  
Reproductive Traits ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Small Litter ◽  
Small Litter Size

AbstractBackground/AimsLitter size is one of the most important reproductive traits in pig breeding, which is affected by multiple genes and the environment. Ovaries are the most important reproductive organs and have a profound impact on the reproduction efficiency. Therefore, genetic differences in the ovaries may contribute to the observed differences in litter size. Although QTLs and candidate genes have been reported to affect the litter size in many pig breeds, however, the findings cannot elucidate the marked differences of the reproductive traits between breeds. The aim of present work is to elucidate the mechanisms of the differences for the reproductive traits and identify candidate genes associated with litter size in Xiang pig breed.MethodsThe changes in ovary transcriptome and alternative splicing were investigated at estrus between Xiang pigs with large and small litter size by RNA-seq technology. The RNA-seq results were confirmed by RT-qPCR method.ResultsWe detected 16,219 - 16,285 expressed genes and 12 types of alternative splicing (AS) events in Xiang pig samples. A total of 762 differentially expressed genes were identified by XL (Xiang pig group with larger litter size) vs XS (Xiang pig group with small litter size) sample comparisons. A total of 34 genes were upregulated and 728 genes were downregulated in XL ovary samples compared with the XS samples. Alternative splicing (AS) rates in XL samples were slightly lower than that observed in XS samples. Most of differentially expressed genes were differentially regulated on AS level. Eleven candidate genes were potentially identified to be related to Xiang pig fecundity and litter size, which may be closely related to the gonad development, oocyte maturation or embryo quality.ConclusionThe significant changes in the expression of the protein-coding genes and the level of alternative splicing in estrus ovarian transcriptome between XL and XS groups probably are the molecular mechanisms of phenotypic variation in litter size.

scholarly journals Transcriptome analysis of fasting caecotrophy on hepatic lipid metabolism in New Zealand rabbits

2018 ◽  
Author(s):  
yadong wang ◽  
Huifen Xu ◽  
Guirong Sun ◽  
Mingming Xue ◽  
Shuaijie Sun ◽  
...  
Keyword(s):  
Growth Rate ◽  
Lipid Metabolism ◽  
Growth Performance ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Effective Means ◽  
Differentially Expressed ◽  
Control Group ◽  
Rna Seq ◽  
Final Body Weight

Background: Rabbit produce two kinds of feces: hard and soft feces, and they have a preference for consuming the latter. Although this habit of rabbits has been reported for many years, little is known on whether this behavior will impact growth performance and metabolism. The RNA-Seq technology is an effective means of analyzing transcript groups to clarify molecular mechanisms. The aim of the present study was to investigate the effects of fasting caecotrophy on growth performance and lipid metabolism in rabbits. Results: Our results indicated that, compared with the control group, the final body weight, weight gain, liver weight, specific growth rate and feed conversion ratio were all decreased in the experimental group (P<0.05). Oil red staining of the liver tissue indicated that fasting caecotrophy resulted in decrease of lipid droplet accumulation. RNA sequencing (RNA-seq) analysis revealed a total of 301.2 million raw reads approximately 45.06 Gb of high-quality clean data. The data were mapped to the rabbit genome (http://www.ensembl.org/Oryctolagus_cuniculus). After a five step filtering process, 14964 genes were identified, including 444 differentially expressed genes (P<0.05, foldchange≥1). Especially for remarkable changes of genes related to lipid metabolism, RT-PCR further validated the remarkable decrease of these genes in fasting caecotrophy group, including CYP7A1, PPARG, ABCA1, ABCB1, ABCG1, GPAM, SREBP, etc. KEGG annotation of the differentially expressed genes indicated that the main pathways affected were retinol metabolism, pentose and glucuronide interactions, starch and sucrose metabolism, fatty acid degradation, steroid hormone biosynthesis. Conclusion: In conclusion, the present study revealed that banning caecotrophy reduced growth rate and altered lipid metabolism, our results laid instructive basis for rabbit feeding and production. These data also provides a reference for studying the effects of soft feces on other small herbivores.

Exploring differentially expressed genes associated with coat color in goat skin using RNA-seq

2019 ◽  
Vol 99 (2) ◽  
pp. 357-366
Author(s):  
Yongdong Peng ◽  
Yaqi Wang ◽  
Ruining Wang ◽  
Liying Geng ◽  
Ruxue Ma ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Quantitative Polymerase Chain Reaction ◽  
Differentially Expressed ◽  
Rna Seq ◽  
White Skin ◽  
Black And White ◽  
Goat Skin ◽  
Skin Physiology ◽  
Black Goat

Fur color in domestic goats is an important, genetically determined characteristic that is associated with economic value. This study was designed to perform a comprehensive expression profiling of genes expressed in the skin tissues from Laiwu Black goat and Lubei White goat. Comparisons of black and white goat skin transcriptomes revealed 102 differentially expressed genes (DEGs), of which 38 were upregulated and 64 downregulated in black skin compared with white skin. Among the DEGs, we identified six genes involved in pigmentation, including agouti signaling protein (ASIP), CAMP responsive element binding protein 3-like 1 (CREB3L1), dopachrome tautomerase (DCT), premelanosome protein (PMEL), transient receptor potential cation channel subfamily M member 1 (TRPM1), and tyrosinase-related protein 1 (TYRP1). Notably, there were no significant differences in the expression of melanocortin 1 receptor, microphthalmia-associated transcription factor, tyrosinase, and KIT proto-oncogene receptor tyrosine kinase between the black and white skin samples, whereas ASIP expression was detected only in white skin. PMEL, TRPM1, TYRP1, and DCT showed higher expression in black goat skin, but ASIP and CREB3L1 had higher expression in white goat skin. Quantitative polymerase chain reaction results for PMEL, TRPM1, DCT, TYRP1, and CREB3L1 expression were consistent with those for RNA-seq. These results will expand our understanding of the complex molecular mechanisms of skin physiology and melanogenesis in goats, and provide a foundation for future studies.

Identification of Differentially Expressed Genes Associated with Papillary Thyroid Carcinoma

2020 ◽  
Vol 23 (6) ◽  
pp. 546-553
Author(s):  
Hongyuan Cui ◽  
Mingwei Zhu ◽  
Junhua Zhang ◽  
Wenqin Li ◽  
Lihui Zou ◽  
...  
Keyword(s):  
Papillary Thyroid Carcinoma ◽  
Thyroid Carcinoma ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Cellular Proliferation ◽  
Mrna Level ◽  
Thyroid Tissue ◽  
Differentially Expressed ◽  
Thyroid Tumors ◽  
Papillary Thyroid

Objective: Next-generation sequencing (NGS) was performed to identify genes that were differentially expressed between normal thyroid tissue and papillary thyroid carcinoma (PTC). Materials & Methods: Six candidate genes were selected and further confirmed with quantitative real-time polymerase chain reaction (qRT-PCR), and immunohistochemistry in samples from 24 fresh thyroid tumors and adjacent normal tissues. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was used to investigate signal transduction pathways of the differentially expressed genes. Results: In total, 1690 genes were differentially expressed between samples from patients with PTC and the adjacent normal tissue. Among these, SFRP4, ZNF90, and DCN were the top three upregulated genes, whereas KIRREL3, TRIM36, and GABBR2 were downregulated with the smallest p values. Several pathways were associated with the differentially expressed genes and involved in cellular proliferation, cell migration, and endocrine system tumor progression, which may contribute to the pathogenesis of PTC. Upregulation of SFRP4, ZNF90, and DCN at the mRNA level was further validated with RT-PCR, and DCN expression was further confirmed with immunostaining of PTC samples. Conclusion: These results provide new insights into the molecular mechanisms of PTC. Identification of differentially expressed genes should not only improve the tumor signature for thyroid tumors as a diagnostic biomarker but also reveal potential targets for thyroid tumor treatment.

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