scholarly journals Changes in N6-Methyladenosine Modification Modulate Diabetic Cardiomyopathy by Reducing Myocardial Fibrosis and Myocyte Hypertrophy

2021 ◽  
Vol 9 ◽  
Author(s):  
Wenhao Ju ◽  
Kai Liu ◽  
Shengrong Ouyang ◽  
Zhuo Liu ◽  
Feng He ◽  
...  
Keyword(s):  
Myocardial Fibrosis ◽  
Diabetic Cardiomyopathy ◽  
High Throughput Sequencing ◽  
Cardiac Fibrosis ◽  
Kegg Pathway ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Myocyte Hypertrophy ◽  
Rna Immunoprecipitation ◽  
Pathway Analyses

In this study, we aimed to systematically profile global RNA N6-methyladenosine (m6A) modification patterns in a mouse model of diabetic cardiomyopathy (DCM). Patterns of m6A in DCM and normal hearts were analyzed via m6A-specific methylated RNA immunoprecipitation followed by high-throughput sequencing (MeRIP-seq) and RNA sequencing (RNA-seq). m6A-related mRNAs were validated by quantitative real-time PCR analysis of input and m6A immunoprecipitated RNA samples from DCM and normal hearts. A total of 973 new m6A peaks were detected in DCM samples and 984 differentially methylated sites were selected for further study, including 295 hypermethylated and 689 hypomethylated m6A sites (fold change (FC) > 1.5, P < 0.05). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway analyses indicated that unique m6A-modified transcripts in DCM were closely linked to cardiac fibrosis, myocardial hypertrophy, and myocardial energy metabolism. Total m6A levels were higher in DCM, while levels of the fat mass and obesity-associated (FTO) protein were downregulated. Overexpression of FTO in DCM model mice improved cardiac function by reducing myocardial fibrosis and myocyte hypertrophy. Overall, m6A modification patterns were altered in DCM, and modification of epitranscriptomic processes, such as m6A, is a potentially interesting therapeutic approach.

scholarly journals Chorionic villus-derived mesenchymal stem cell-mediated autophagy promotes proliferation and invasiveness of trophoblasts under hypoxia by activating the JAK2/STAT3 signalling pathway

2020 ◽  
Author(s):  
Yijing Chu ◽  
Chongyu Yue ◽  
Wei Peng ◽  
Weiping Chen ◽  
Yan Zhang ◽  
...  
Keyword(s):  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Chorionic Villus ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Protein Levels ◽  
Hypoxic Conditions ◽  
Upstream Regulator ◽  
Pathway Analyses ◽  
Stat3 Signalling

Abstract Objectives Trophoblast dysfunction during pregnancy is fundamentally involved in preeclampsia. The aim of this study was to understand how human chorionic villous mesenchymal stem cells (CV-MSCs) operate in regulation of trophoblast function.Materials and Methods We treated trophoblasts with CV-MSC supernatant under hypoxic conditions, and transcriptome and pathway analyses of trophoblasts were performed. Western blotting and PCR analysis were used to examine the JAK2, STAT3 and autophagy associated protein expression levels in trophoblasts.Results The CV-MSC supernatant treatment markedly enhanced proliferation, invasion and autophagy. The RNA-seq revealed JAK2/STAT3 signalling as an upstream regulator, and STAT3 mRNA and protein levels increased during CV-MSC treatment. Inhibition of JAK2/STAT3 signalling reduced autophagy, survival and invasion of trophoblasts even in the presence of CV-MSCs, and blocking autophagy did not affect STAT3 activation in trophoblasts treated with CV-MSCs. Importantly, overexpression of STAT3 increased the levels of autophagy in trophoblasts; thus, it regulated positively autophagy in hypoxic trophoblasts. Human placental explants also proved our finding, in which STAT3 was activated and LC3B-II levels were increased by CV-MSC treatment.Conclusions Our data suggest that CV-MSC-dependent activation of JAK2/STAT3 signalling is a prerequisite for upregulation of autophagy in trophoblasts.

scholarly journals High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute

2015 ◽  
Vol 2015 ◽  
pp. 1-14 ◽  
Author(s):  
Md. Tariqul Islam ◽  
Ahlan Sabah Ferdous ◽  
Rifat Ara Najnin ◽  
Suprovath Kumar Sarker ◽  
Haseena Khan
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Kegg Pathway ◽  
Translational Repression ◽  
Biological Processes ◽  
Rt Pcr ◽  
Stem Loop ◽  
Evolutionarily Conserved ◽  
Pathway Analyses ◽  
Species Specific

MicroRNAs play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. A group of plant microRNAs are evolutionarily conserved; however, others are expressed in a species-specific manner. Jute is an agroeconomically important fibre crop; nonetheless, no practical information is available for microRNAs in jute to date. In this study, Illumina sequencing revealed a total of 227 known microRNAs and 17 potential novel microRNA candidates in jute, of which 164 belong to 23 conserved families and the remaining 63 belong to 58 nonconserved families. Among a total of 81 identified microRNA families, 116 potential target genes were predicted for 39 families and 11 targets were predicted for 4 among the 17 identified novel microRNAs. For understanding better the functions of microRNAs, target genes were analyzed by Gene Ontology and their pathways illustrated by KEGG pathway analyses. The presence of microRNAs identified in jute was validated by stem-loop RT-PCR followed by end point PCR and qPCR for randomly selected 20 known and novel microRNAs. This study exhaustively identifies microRNAs and their target genes in jute which will ultimately pave the way for understanding their role in this crop and other crops.

scholarly journals Analysis of the Defence Responses to Tomato Spotted Wilt Orthotospovirus (TSWV) and Hippeastrum Chlorotic Ringspot Orthotospovirus (HCRV) Infection in Capsicum Annuum Based on Transcriptome

2020 ◽  
Author(s):  
Zhiqiang Jia ◽  
Xue Gao ◽  
Ye Xu ◽  
Hongzheng Tao ◽  
Baoju Yang ◽  
...  
Keyword(s):  
Capsicum Annuum ◽  
Plant Pathogen ◽  
Crop Production ◽  
High Throughput Sequencing ◽  
Plant Hormone ◽  
Plant Responses ◽  
Rna Seq ◽  
Tomato Spotted Wilt ◽  
Wide Range ◽  
Pathway Analyses

Abstract Background: Orthotospovirus has a wide range of hosts, widely distributed in southwestern China and have serious harm to crop production. Tomato spotted wilt orthotospovirus (TSWV) and Hippeastrum chlorotic ringspot orthotospovirus (HCRV) are seriously harms the quality of pepper (Capsicum annuum L.). However, the detailed molecular mechanism of pepper disease caused by TSWV and HCRV remains obscure.Method: Transcriptome analysis (RNA-seq) based on high-throughput sequencing, with TSVV, HCRV and mock-inoculated plants as controls, to investigate and compare the gene expression changes in pepper leaves, and analyze the plants invaded by orthotospoviruses defensive response.Results: The RNA-Seq results of pepper 1 day after inoculation (1 dpi) showed that the number of differentially expressed genes(DEG) after HCRV infection was greater than that after TSWV infection. Gene Ontology enrichment and KEGG pathway analyses were performed on the two viruses, and the KEGG results showed that DEG were mainly enriched in plant-pathogen interactions, plant hormone signal transduction, and defence processes.Conclusion: The conclusion of this study is that after orthotospovirus infects pepper, the DEG changes in the processes of plant-pathogen interaction, plant hormone and phenylpropanoid synthesis. In addition, transcription factors such as WRKY and MYB changed significantly. These factors comprehensively affect the plant's defence response and ultimately enhance the plant's resistance to viruses. Findings of present study will significantly help enhance our understanding of the complicated defense process of plant responses to orthotospoviruses infection.

scholarly journals MicroRNA expression profiles in peri-miniscrew implant crevicular fluid in orthodontics: a pilot study

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Wendan He ◽  
Yanru Yang ◽  
Longgan Cai ◽  
Qiaoling Lei ◽  
Zhongdong Wang ◽  
...  
Keyword(s):  
Mirna Expression ◽  
Kegg Pathway ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Expression Levels ◽  
Qrt Pcr ◽  
Miniscrew Implant ◽  
Pathway Analyses ◽  
Crevicular Fluid

Abstract Background This study systematically evaluated microRNA (miRNA) expression patterns in peri-miniscrew implant crevicular fluid (PMICF) in orthodontic patients. Methods Next-generation sequencing (NGS) was performed to obtain miRNA profiles in PMICF or gingival crevicular fluid (GCF) collected from 3 healthy volunteers (H), 3 peri-implantitis patients (PMSII) and 5 periodontitis patients (P). MiRNA expression patterns were compared between normal and orthodontic PMICF and GCF. Differentially expressed miRNAs were estimated by quantitative real-time PCR (qRT-PCR). Enrichment analyses of the gene targets controlled by these miRNAs were conducted by Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Results Compared with healthy donors, in PMSII patients, a total of 206 upregulated miRNAs and 152 downregulated miRNAs were detected in PMICF, while periodontitis patients had 333 upregulated miRNAs and 318 downregulated miRNAs. MiR-544a, miR-1245b-3p, miR-1825, miR-4291, miR-3689e, and miR-4477a were chosen randomly for further examination. qRT-PCR examination confirmed that the expression levels of miR-1245b-3p and miR-4291 were higher in PMSII than in H samples and that the expression levels of miR-1825 were higher in PMSII than in P samples. However, contrary to the NGS results, qRT-PCR analysis showed decreased expression of miR544a in PMSII. MiR3689e and miR4477a expression did not differ significantly among all samples. According to GO and KEGG pathway analyses of miR-1825, miR-4291, and miR-1245b-3p high enrichment of target genes involved in the PI3K-AKT signalling pathway was observed. Conclusions The NGS analysis of normal and orthodontic PMICF/CGF showed different miRNA profiles, which may lay the foundation for future research on the molecular mechanism of PMSII. miR-4291, miR-1245b-3p and miR-1825 may be used as diagnostic markers and potential therapeutic targets for PMSII.

scholarly journals Chorionic villus-derived mesenchymal stem cell-mediated autophagy promotes proliferation and invasiveness of trophoblasts under hypoxia by activating the JAK2/STAT3 signalling pathway

2020 ◽  
Author(s):  
Yijing Chu ◽  
Chongyu Yue ◽  
Wei Peng ◽  
Weiping Chen ◽  
Yan Zhang ◽  
...  
Keyword(s):  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Chorionic Villus ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Protein Levels ◽  
Hypoxic Conditions ◽  
Upstream Regulator ◽  
Pathway Analyses ◽  
Stat3 Signalling

Abstract Objectives Trophoblast dysfunction during pregnancy is fundamentally involved in preeclampsia. The aim of this study was to understand how human chorionic villous mesenchymal stem cells (CV-MSCs) operate in regulation of trophoblast function. Materials and Methods We treated trophoblasts with CV-MSC supernatant under hypoxic conditions, and transcriptome and pathway analyses of trophoblasts were performed. Western blotting and PCR analysis were used to examine the JAK2, STAT3 and autophagy associated protein expression levels in trophoblasts. Results The CV-MSC supernatant treatment markedly enhanced proliferation, invasion and autophagy. The RNA-seq revealed JAK2/STAT3 signalling as an upstream regulator, and STAT3 mRNA and protein levels increased during CV-MSC treatment. Inhibition of JAK2/STAT3 signalling reduced autophagy, survival and invasion of trophoblasts even in the presence of CV-MSCs, and blocking autophagy did not affect STAT3 activation in trophoblasts treated with CV-MSCs. Importantly, overexpression of STAT3 increased the levels of autophagy in trophoblasts; thus, it regulated positively autophagy in hypoxic trophoblasts. Human placental explants also proved our finding, in which STAT3 was activated and LC3B-II levels were increased by CV-MSC treatment. Conclusions Our data suggest that CV-MSC-dependent activation of JAK2/STAT3 signalling is a prerequisite for upregulation of autophagy in trophoblasts.

scholarly journals Pyrroloquinoline quinone ameliorates diabetic cardiomyopathy by inhibiting the pyroptosis signaling pathway in C57BL/6 mice and AC16 cells

2022 ◽  
Author(s):  
Xue-feng Qu ◽  
Bing-zhong Zhai ◽  
Wen-li Hu ◽  
Min-han Lou ◽  
Yi-hao Chen ◽  
...  
Keyword(s):  
Myocardial Fibrosis ◽  
Diabetic Cardiomyopathy ◽  
Nlrp3 Inflammasome ◽  
High Glucose ◽  
Cardiac Fibrosis ◽  
Myocardial Hypertrophy ◽  
Underlying Mechanism ◽  
Pyrroloquinoline Quinone ◽  
Ros Generation ◽  
Protective Effects

Abstract Purpose Diabetic cardiomyopathy (DCM), a common complication of diabetes mellitus and is characterized by myocardial hypertrophy and myocardial fibrosis. Pyrroloquinoline quinone (PQQ), a natural nutrient, exerts strong protection against various myocardial diseases. Pyroptosis, a type of inflammation-related programmed cell death, is vital to the development of DCM. However, the protective effects of PQQ against DCM and the associated mechanisms are not clear. This study aimed to investigate whether PQQ protected against DCM and to determine the underlying molecular mechanism. Methods Diabetes was induced in mice by intraperitoneal injection of streptozotocin, after which the mice were administered PQQ orally (10, 20, or 40 mg/kg body weight/day) for 12 weeks. AC16 human myocardial cells were divided into the following groups and treated accordingly: control (5.5 mmol/L glucose), high glucose (35 mmol/L glucose), and HG + PQQ groups (1 and 10 nmol/L PQQ). Cells were treated for 24 h. Results PQQ reduced myocardial hypertrophy and the area of myocardial fibrosis, which was accompanied by an increase in antioxidant function and a decrease in inflammatory cytokine levels. Moreover, myocardial hypertrophy—(ANP and BNP), myocardial fibrosis—(collagen I and TGF-β1), and pyroptosis-related protein levels decreased in the PQQ treatment groups. Furthermore, PQQ abolished mitochondrial dysfunction and the activation of NF-κB/IκB, and decreased NLRP3 inflammation-mediated pyroptosis in AC16 cells under high-glucose conditions. Conclusion PQQ improved DCM in diabetic mice by inhibiting NF-κB/NLRP3 inflammasome-mediated cell pyroptosis. Long-term dietary supplementation with PQQ may be greatly beneficial for the treatment of DCM. Graphical abstract Diagram of the underlying mechanism of the effects of PQQ on DCM. PQQ inhibits ROS generation and NF-κB activation, which stimulates activation of the NLRP3 inflammasome and regulates the expression of caspase-1, IL-1β, and IL-18. The up-regulated inflammatory cytokines trigger myocardial hypertrophy and cardiac fibrosis and promote the pathological process of DCM.

Overexpression of miR-340-5p Inhibits Skin Fibroblast Proliferation by Targeting Kruppel-like Factor 2

2019 ◽  
Vol 20 (13) ◽  
pp. 1147-1154 ◽  
Author(s):  
Ling Chen ◽  
Qian Li ◽  
Xun Lu ◽  
Xiaohua Dong ◽  
Jingyun Li
Keyword(s):  
Gene Ontology ◽  
Skin Fibroblast ◽  
Kegg Pathway ◽  
Normal Skin ◽  
Skin Fibroblasts ◽  
Differentially Expressed ◽  
Luciferase Reporter ◽  
Fibroblast Proliferation ◽  
Pathway Analyses ◽  
Normal Skin Fibroblast

<P>Objective: MicroRNA (miR)-340-5p has been identified to play a key role in several cancers. However, the function of miR-340-5p in skin fibroblasts remains largely unknown. </P><P> Methods: Gain of function experiments were performed by infecting normal skin fibroblast cells with a lentivirus carrying 22-bp miR-340-5p. Cell proliferation was detected by Cell Counting Kit-8 (CCK-8) assay. To uncover the mechanisms, mRNA-seq was used. Differentially expressed mRNAs were further determined by Gene Ontology and KEGG pathway analyses. The protein levels were analysed by Western blotting. A dual-luciferase reporter assay was used to detect the direct binding of miR-340-5p with the 3&#039;UTR of Kruppel-like factor 2 (KLF2). </P><P> Results: MiR-340-5p lentivirus infection suppressed normal skin fibroblast proliferation. The mRNAseq data revealed that 41 mRNAs were differentially expressed, including 22 upregulated and 19 downregulated transcripts in the miR-340-5p overexpression group compared with those in the control group. Gene Ontology and KEGG pathway analyses revealed that miR-340-5p overexpression correlated with the macromolecule biosynthetic process, cellular macromolecule biosynthetic process, membrane, and MAPK signalling pathway. Bioinformatics analysis and luciferase reporter assays showed that miR-340-5p binds to the 3&#039;UTR of KLF2. Forced expression of miR-340-5p decreased the expression of KLF2 in normal skin fibroblasts. Overexpression of KLF2 restored skin fibroblast proliferation in the miR-340-5p overexpression group. </P><P> Conclusion: This study demonstrates that miR-340-5p may suppress skin fibroblast proliferation, possibly through targeting KLF2. These findings could help us understand the function of miR-340-5p in skin fibroblasts. miR-340-5p could be a therapeutic target for preventing scarring.</P>

scholarly journals Transcriptome Profile Alterations with Carbon Nanotubes, Quantum Dots, and Silver Nanoparticles: A Review

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 794
Author(s):  
Cullen Horstmann ◽  
Victoria Davenport ◽  
Min Zhang ◽  
Alyse Peters ◽  
Kyoungtae Kim
Keyword(s):  
Carbon Nanotubes ◽  
Quantum Dots ◽  
High Throughput Sequencing ◽  
The Body ◽  
Rna Seq ◽  
Mechanisms Of Toxicity ◽  
Promising Tool ◽  
Engineered Nanomaterial ◽  
Next Generation Sequencing Ngs ◽  
Transcriptomic Changes

Next-generation sequencing (NGS) technology has revolutionized sequence-based research. In recent years, high-throughput sequencing has become the method of choice in studying the toxicity of chemical agents through observing and measuring changes in transcript levels. Engineered nanomaterial (ENM)-toxicity has become a major field of research and has adopted microarray and newer RNA-Seq methods. Recently, nanotechnology has become a promising tool in the diagnosis and treatment of several diseases in humans. However, due to their high stability, they are likely capable of remaining in the body and environment for long periods of time. Their mechanisms of toxicity and long-lasting effects on our health is still poorly understood. This review explores the effects of three ENMs including carbon nanotubes (CNTs), quantum dots (QDs), and Ag nanoparticles (AgNPs) by cross examining publications on transcriptomic changes induced by these nanomaterials.

scholarly journals Genome-Wide Identification and Characterization of Hsf and Hsp Gene Families and Gene Expression Analysis under Heat Stress in Eggplant (Solanum melongema L.)

Horticulturae ◽  
2021 ◽  
Vol 7 (6) ◽  
pp. 149
Author(s):  
Chao Gong ◽  
Qiangqiang Pang ◽  
Zhiliang Li ◽  
Zhenxing Li ◽  
Riyuan Chen ◽  
...  
Keyword(s):  
Heat Stress ◽  
Gene Families ◽  
High Temperature Stress ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Genome Wide ◽  
Motif Composition ◽  
Hsp Genes ◽  
Identification And Characterization

Under high temperature stress, a large number of proteins in plant cells will be denatured and inactivated. Meanwhile Hsfs and Hsps will be quickly induced to remove denatured proteins, so as to avoid programmed cell death, thus enhancing the thermotolerance of plants. Here, a comprehensive identification and analysis of the Hsf and Hsp gene families in eggplant under heat stress was performed. A total of 24 Hsf-like genes and 117 Hsp-like genes were identified from the eggplant genome using the interolog from Arabidopsis. The gene structure and motif composition of Hsf and Hsp genes were relatively conserved in each subfamily in eggplant. RNA-seq data and qRT-PCR analysis showed that the expressions of most eggplant Hsf and Hsp genes were increased upon exposure to heat stress, especially in thermotolerant line. The comprehensive analysis indicated that different sets of SmHsps genes were involved downstream of particular SmHsfs genes. These results provided a basis for revealing the roles of SmHsps and SmHsp for thermotolerance in eggplant, which may potentially be useful for understanding the thermotolerance mechanism involving SmHsps and SmHsp in eggplant.

scholarly journals Dynamic alteration in miRNA and mRNA expression profiles at different stages of chronic arsenic exposure-induced carcinogenesis in a human cell culture model of skin cancer

2021 ◽  
Author(s):  
Mayukh Banerjee ◽  
Ana Ferragut Cardoso ◽  
Laila Al-Eryani ◽  
Jianmin Pan ◽  
Theodore S. Kalbfleisch ◽  
...  
Keyword(s):  
Skin Cancer ◽  
Mrna Expression ◽  
Hacat Cell ◽  
Arsenic Exposure ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Mesenchymal Transition ◽  
Chronic Arsenic Exposure ◽  
Pathway Analyses ◽  
Time Point

AbstractChronic arsenic exposure causes skin cancer, although the underlying molecular mechanisms are not well defined. Altered microRNA and mRNA expression likely play a pivotal role in carcinogenesis. Changes in genome-wide differential expression of miRNA and mRNA at 3 strategic time points upon chronic sodium arsenite (As3+) exposure were investigated in a well-validated HaCaT cell line model of arsenic-induced cutaneous squamous cell carcinoma (cSCC). Quadruplicate independent HaCaT cell cultures were exposed to 0 or 100 nM As3+ for up to 28-weeks (wk). Cell growth was monitored throughout the course of exposure and epithelial-mesenchymal transition (EMT) was examined employing immunoblot. Differentially expressed miRNA and mRNA profiles were generated at 7, 19, and 28-wk by RNA-seq, followed by identification of differentially expressed mRNA targets of differentially expressed miRNAs through expression pairing at each time point. Pathway analyses were performed for total differentially expressed mRNAs and for the miRNA targeted mRNAs at each time point. RNA-seq predictions were validated by immunoblot of selected target proteins. While the As3+-exposed cells grew slower initially, growth was equal to that of unexposed cells by 19-wk (transformation initiation), and exposed cells subsequently grew faster than passage-matched unexposed cells. As3+-exposed cells had undergone EMT at 28-wk. Pathway analyses demonstrate dysregulation of carcinogenesis-related pathways and networks in a complex coordinated manner at each time point. Immunoblot data largely corroborate RNA-seq predictions in the endoplasmic reticulum stress (ER stress) pathway. This study provides a detailed molecular picture of changes occurring during the arsenic-induced transformation of human keratinocytes.

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