Genome-Wide Transcriptome Profiling of Human Trabecular Meshwork Cells Treated with TGF-β2.

2021 ◽  
Author(s):  
Breedge Callaghan ◽  
Karen Lester ◽  
Brian Lane ◽  
Xiaochen Fan ◽  
Katarzyna Goljanek-Whysall ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Pathology ◽  
Trabecular Meshwork ◽  
Transforming Growth Factor Beta ◽  
Molecular Mechanisms ◽  
Transforming Growth Factor ◽  
Open Angle Glaucoma ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Trabecular Meshwork Cells

Abstract Glaucoma is a complex neurodegenerative disease resulting in progressive optic neuropathy and is a leading cause of irreversible blindness worldwide. Primary open angle glaucoma (POAG) is the predominant form affecting 65.5 million people globally. Despite the prevalence of POAG and the identification of over 120 glaucoma related genetic loci, the underlaying molecular mechanisms are still poorly understood. The transforming growth factor beta (TGF-β) signalling pathway is implicated in the molecular pathology of POAG. To gain a better understanding of the role TGF-β2 plays in the glaucomatous changes to the molecular pathology in the trabecular meshwork, we employed RNA-Seq to delineate the TGF-β2 induced changes in the transcriptome of normal primary human trabecular meshwork cells (HTM). We identified a significant number of differentially expressed genes and associated pathways that contribute to the pathogenesis of POAG. The differentially expressed genes were predominantly enriched in ECM regulation, TGF-β signalling, proliferation/apoptosis, inflammation/wound healing, MAPK signalling, oxidative stress and RHO signalling. Canonical pathway analysis confirmed the enrichment of RhoA signalling, inflammatory-related processes, ECM and cytoskeletal organisation in HTM cells in response to TGF-β2. We also identified novel genes and pathways that were affected after TGF-β2 treatment in the HTM, suggesting additional pathways are activated, including Nrf2, PI3K-Akt, MAPK and HIPPO signalling pathways. The identification and characterisation of TGF-β2 dependent differentially expressed genes and pathways in HTM cells is essential to understand the patho-physiology of glaucoma and to develop new therapeutic agents.

scholarly journals Exploring the Roles of Fecundity-related mRNAs and Long Non-coding RNAs in the Adrenal Glands of Small-tailed Han Sheep

2020 ◽  
Author(s):  
Qing Xia ◽  
Qiuling Li ◽  
Shangquan Gan ◽  
Xiaofei Guo ◽  
Xiaosheng Zhang ◽  
...  
Keyword(s):  
Adrenal Gland ◽  
Signaling Pathways ◽  
Transforming Growth Factor Beta ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Transforming Growth Factor ◽  
Differentially Expressed ◽  
Mitogen Activated Protein Kinase ◽  
Gene Expressions ◽  
Non Coding Rnas

Abstract Background Long non-coding RNAs (lncRNAs) can play important roles in uterine and ovarian functions. However, little researches have been done on the role of lncRNAs in the adrenal gland of sheep. Herein, RNA sequencing was used to compare and analyze gene expressions in adrenal tissues between FecB ++ (WW) and FecB BB (MM) sheep in the follicular and luteal phases and key lncRNAs and genes associated with reproduction were identified. Results In MM sheep, 38 lncRNAs and 545 mRNAs were differentially expressed in the adrenal gland between the luteal and follicular phases; In WW sheep, 30 differentially expressed lncRNAs and 210 mRNAs were identified. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that differentially expressed lncRNAs and their target genes are mainly involved in the circadian rhythm, the mitogen activated protein kinase, thyroid, ovarian steroidogenesis and transforming growth factor beta signaling pathways. Key lncRNAs can regulate reproduction by modulating genes involved in these signaling pathways and biological processes. Specifically, XLOC_254761 , XLOC_357966 , 105614839 and XLOC_212877 targeting CREB1 , PER3 , SMAD1 and TGFBR2 , respectively, appear to play key regulatory roles. Conclusion These results broaden our understanding of lncRNAs in adrenal gland of sheep and provide new insights into the molecular mechanisms underlying sheep reproduction.

scholarly journals Comprehensive analysis of differential expression profiles via transcriptome sequencing in SH-SY5Y cells infected with CV-A16

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0241174
Author(s):  
Yajie Hu ◽  
Zhen Yang ◽  
Shenglan Wang ◽  
Danxiong Sun ◽  
Mingmei Zhong ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Transcriptome Sequencing ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Control Group ◽  
Protein Coding ◽  
Qrt Pcr ◽  
Protein Coding Genes

Coxsackievirus A16 (CV-A16) is one of the viruses that is most frequently associated with hand-foot-and-mouth disease (HFMD). Previous studies have shown that CV-A16 infections are mostly self-limiting, but in recent years, it has been gradually found that CV-A16 infections can also induce neurological complications and eventually cause death in children with HFMD. Moreover, no curative drugs or preventative vaccines have been developed for CV-A16 infection. Therefore, it is particularly important to investigate the mechanism of CV-A16 infection-induced neuropathy. In the current study, transcriptome sequencing technology was used to identify changes in the transcriptome of SH-SY5Y cells infected with CV-A16, which might hide the mechanism of CV-A16-induced neuropathology. The transcriptome profiling showed that 82,406,974, 108,652,260 and 97,753,565 clean reads were obtained in the Control, CV-A16-12 h and CV-A16-24 h groups, respectively. And it was further detected that a total of 136 and 161 differentially expressed genes in CV-A16-12 h and CV-A16-24 h groups, respectively, when compared with Control group. Then, to explore the mechanism of CV-A16 infection, we focused on the common differentially expressed genes at different time points of CV-A16 infection and found that there were 34 differentially expressed genes based on which clustering analysis and functional category enrichment analysis were performed. The results indicated that changes in oxidation levels were particularly evident in the GO term analysis, while only the “Gonadotropin-releasing hormone receptor pathway” was enriched in the KEGG pathway analysis, which might be closely related to the neurotoxicity caused by CV-A16 infection. Meanwhile, the ID2 closely related to nervous system has been demonstrated to be increased during CV-A16 infection. Additionally, the data on differentially expressed non-protein-coding genes of different types within the transcriptome sequencing results were analyzed, and it was speculated that these dysregulated non-protein-coding genes played a pivotal role in CV-A16 infection. Ultimately, qRT-PCR was utilized to validate the transcriptome sequencing findings, and the results of qRT-PCR were in agreement with the transcriptome sequencing data. In conclusion, transcriptome profiling was carried out to analyze response of SH-SY5Y cells to CV-A16 infection. And our findings provide important information to elucidate the possible molecular mechanisms which were linked to the neuropathogenesis of CV-A16 infection.

scholarly journals Exploring the Roles of Fecundity-related Long Non-coding RNAs and mRNAs in the Adrenal Glands of Small-tailed Han Sheep

2020 ◽  
Author(s):  
Qing Xia ◽  
Qiuling Li ◽  
Shangquan Gan ◽  
Xiaofei Guo ◽  
Xiaosheng Zhang ◽  
...  
Keyword(s):  
Adrenal Gland ◽  
Signaling Pathways ◽  
Transforming Growth Factor Beta ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Transforming Growth Factor ◽  
Differentially Expressed ◽  
Mitogen Activated Protein Kinase ◽  
Gene Expressions ◽  
Non Coding Rnas

Abstract Background: Long non-coding RNAs (lncRNAs) can play important roles in uterine and ovarian functions. However, little researches have been done on the role of lncRNAs in the adrenal gland of sheep. Herein, RNA sequencing was used to compare and analyze gene expressions in adrenal tissues between follicular phases and luteal phases in FecBBB (MM) and FecB++ (WW) sheep, respectively, and differentially expressed lncRNAs and genes associated with reproduction were identified.Results: In MM sheep, 38 lncRNAs and 545 mRNAs were differentially expressed in the adrenal gland between the luteal and follicular phases; In WW sheep, 513 differentially expressed lncRNAs and 2481 mRNAs were identified. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that differentially expressed lncRNAs and their target genes are mainly involved in the circadian rhythm, the mitogen activated protein kinase, thyroid, ovarian steroidogenesis and transforming growth factor beta signaling pathways. Differentially expressed lncRNAs can regulate reproduction by modulating genes involved in these signaling pathways and biological processes. Specifically, XLOC_254761, XLOC_357966, 105614839 and XLOC_212877 targeting CREB1, PER3, SMAD1 and TGFBR2, respectively, appear to play key regulatory roles. Conclusion: These results broaden our understanding of lncRNAs in adrenal gland of sheep and provide new insights into the molecular mechanisms underlying sheep reproduction.

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.

scholarly journals Transcriptome Profiling Reveals Potential Genes Involved in Browning of Fresh-cut Eggplant (Solanum Melongena L.)

2020 ◽  
Author(s):  
Xiaohui Liu ◽  
Jing Shang ◽  
Aidong Zhang ◽  
Zongwen Zhu ◽  
Dingshi Zha ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Fruits And Vegetables ◽  
Molecular Mechanisms ◽  
Solanum Melongena ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Enzymatic Browning ◽  
Fruit Samples ◽  
Phenylpropanoid Biosynthesis ◽  
Fresh Cut

Abstract Background: Fresh-cut processing promotes enzymatic browning of fresh fruits and vegetables, which negatively affects the appearance of products and impacts their nutrition. We used the RNA-Seq technique to analyze the transcriptomic changes occurring during the browning of fresh-cut eggplant (Solanum melongena L.) fruit samples from a browning-sensitive cultivar and a browning-resistant cultivar to investigate the genes and molecular mechanisms involved in browning. Results: A total of 111.55 GB of high-quality reads were generated, the genomes of each sample were compared, and 83.50%–95.14% of the data was mapped to the eggplant reference genome. Furthermore, a total of 19631 differentially expressed genes were identified, among which 12 genes and two WRKY transcription factors were identified as potentially involved in enzymatic browning in fresh-cut eggplant fruit. Moreover, the 14 differentially expressed genes associated with browning were verified using qRT-PCR. Conclusions: Several genes associated with phenolic oxidation, phenylpropanoid biosynthesis, and flavonoid biosynthesis were found to be differentially regulated between the eggplant cultivars with different browning sensitivities. This work is of great theoretical significance, as it provides a basis for future molecular studies and improvement of eggplants, and lays a theoretical foundation for the development of browning-resistant fresh-cut fruits and vegetables.

scholarly journals Extracellular matrix stiffness and TGFβ2 regulate YAP/TAZ activity in human trabecular meshwork cells

2021 ◽  
Author(s):  
Haiyan Li ◽  
VijayKrishna Raghunathan ◽  
W. Daniel Stamer ◽  
Preethi S. Ganapathy ◽  
Samuel Herberg
Keyword(s):  
Extracellular Matrix ◽  
Nuclear Localization ◽  
Trabecular Meshwork ◽  
Transforming Growth Factor Beta ◽  
Transcriptional Activity ◽  
Transforming Growth Factor ◽  
Open Angle Glaucoma ◽  
Focal Adhesions ◽  
Binding Motif ◽  
Cell Dysfunction

AbstractPrimary open-angle glaucoma progression is associated with increased human trabecular meshwork (HTM) stiffness and elevated transforming growth factor beta 2 (TGFβ2) levels in aqueous humor. Increased transcriptional activity of Yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ), central players in mechanotransduction, are implicated in glaucomatous HTM cell dysfunction. Yet, the detailed mechanisms underlying YAP/TAZ modulation in HTM cells in response to alterations in extracellular matrix (ECM) stiffness and TGFβ2 levels are not well understood. Using biomimetic ECM hydrogels with tunable stiffness, here we show that increased ECM stiffness elevates YAP/TAZ transcriptional activity potentially through modulating focal adhesions and cytoskeletal rearrangement. Furthermore, TGFβ2 increased YAP/TAZ nuclear localization in both normal and glaucomatous HTM cells, which was prevented by inhibiting extracellular-signal-regulated kinase and Rho-associated kinase signaling pathways to varying degrees. Filamentous (F)-actin depolymerization reversed TGFβ2-induced YAP/TAZ nuclear localization. YAP/TAZ depletion using siRNA or verteporfin decreased focal adhesions, ECM remodeling and cell contractile properties. Similarly, YAP/TAZ inactivation with simvastatin or verteporfin partially blocked TGFβ2-induced HTM hydrogel contraction and stiffening. Collectively, our data provide strong evidence for a pathologic role of aberrant YAP/TAZ signaling in glaucomatous HTM cell dysfunction, and may help inform strategies for the development of novel multifactorial approaches to prevent progressive ocular hypertension in glaucoma.

scholarly journals Exploring the Roles of Fecundity-related mRNAs and Long Non-coding RNAs in the Adrenal Glands of Small-tailed Han Sheep

2019 ◽  
Author(s):  
Qing Xia ◽  
Qiuling Li ◽  
Shangquan Gan ◽  
Xiaofei Guo ◽  
Xiaosheng Zhang ◽  
...  
Keyword(s):  
Adrenal Gland ◽  
Signaling Pathways ◽  
Transforming Growth Factor Beta ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Transforming Growth Factor ◽  
Differentially Expressed ◽  
Mitogen Activated Protein Kinase ◽  
Gene Expressions ◽  
Non Coding Rnas

Abstract Background Long non-coding RNAs (lncRNAs) can play important roles in uterine and ovarian functions. However, little researches have been done on the role of lncRNAs in the adrenal gland of sheep. Herein, RNA sequencing was used to compare and analyze gene expressions in adrenal tissues between FecB ++ (WW) and FecB BB (MM) sheep in the follicular and luteal phases and key lncRNAs and genes associated with reproduction were identified.Results In MM sheep, 38 lncRNAs and 545 mRNAs were differentially expressed in the adrenal gland between the luteal and follicular phases; In WW sheep, 30 differentially expressed lncRNAs and 210 mRNAs were identified. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that differentially expressed lncRNAs and their target genes are mainly involved in the circadian rhythm, the mitogen activated protein kinase, thyroid, ovarian steroidogenesis and transforming growth factor beta signaling pathways. Key lncRNAs can regulate reproduction by modulating genes involved in these signaling pathways and biological processes. Specifically, XLOC_254761 , XLOC_357966 , 105614839 and XLOC_212877 targeting CREB1 , PER3 , SMAD1 and TGFBR2 , respectively, appear to play key regulatory roles.Conclusion These results broaden our understanding of lncRNAs in adrenal gland of sheep and provide new insights into the molecular mechanisms underlying sheep reproduction.

scholarly journals Differential gene expression profiles in foetal skin of Rex rabbits with different wool density

2016 ◽  
Vol 24 (3) ◽  
pp. 223
Author(s):  
L. Liu ◽  
B. Li ◽  
Y.L. Zhu ◽  
C.Y. Wang ◽  
F.C. Li
Keyword(s):  
Gene Expression ◽  
Hair Follicle ◽  
Differentially Expressed Genes ◽  
Transforming Growth Factor Beta ◽  
Transforming Growth Factor ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Signalling Pathways ◽  
Rex Rabbit

<p>This study investigated the mechanisms controlling hair follicle development in the Rex rabbit. The Agilent rabbit gene expression microarray was used to determine differentially expressed genes in Rex rabbit foetuses with different wool densities. The expression patterns of selected differentially-expressed genes were further investigated by quantitative real-time PCR. Compared to low wool density rabbits, 1342 differentially expressed probes were identified in high wool density rabbits, including 950 upregulated probes and 392 downregulated probes. Gene ontology analysis revealed that the most upregulated differentially expressed probes belonged to receptors and the most downregulated differentially expressed probes belonged to DNA binding molecules. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the differentially expressed probes were mainly involved in the sonic hedgehog (Shh) and Eph signalling pathways. The results also suggest that transforming growth factor-beta 1, growth hormone receptor, and the keratin-associated protein 6.1 genes, as well as the Shh and Eph signalling pathways, may be involved in the regulation of hair follicle developmental in Rex rabbits.</p>

scholarly journals Exploring the Roles of Fecundity-related Long Non-coding RNAs and mRNAs in the Adrenal Gland of Small-tailed Han Sheep

2020 ◽  
Author(s):  
Qing Xia ◽  
Qiuling Li ◽  
Shangquan Gan ◽  
Xiaofei Guo ◽  
Xiaosheng Zhang ◽  
...  
Keyword(s):  
Adrenal Gland ◽  
Signaling Pathways ◽  
Transforming Growth Factor Beta ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Transforming Growth Factor ◽  
Differentially Expressed ◽  
Mitogen Activated Protein Kinase ◽  
Gene Expressions ◽  
Non Coding Rnas

Abstract Background: Long non-coding RNAs (lncRNAs) can play important roles in uterine and ovarian functions. However, little researches have been done on the role of lncRNAs in the adrenal gland of sheep. Herein, RNA sequencing was used to compare and analyze gene expressions in adrenal tissue between follicular phase and luteal phase in FecBBB (MM) and FecB++ (WW) sheep, respectively, and differentially expressed lncRNAs and genes associated with reproduction were identified.Results: In MM sheep, 38 lncRNAs and 545 mRNAs were differentially expressed in the adrenal gland between the luteal and follicular phases; In WW sheep, 513 differentially expressed lncRNAs and 2481 mRNAs were identified. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that differentially expressed lncRNAs and their target genes are mainly involved in the circadian rhythm, the mitogen activated protein kinase, thyroid, ovarian steroidogenesis and transforming growth factor beta signaling pathways. Differentially expressed lncRNAs can regulate reproduction by modulating genes involved in these signaling pathways and biological processes. Specifically, XLOC_254761, XLOC_357966, 105614839 and XLOC_212877 targeting CREB1, PER3, SMAD1 and TGFBR2, respectively, appear to play key regulatory roles. Conclusion: These results broaden our understanding of lncRNAs in adrenal gland of sheep and provide new insights into the molecular mechanisms underlying sheep reproduction.

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