Comparison of lncRNA and mRNA expression in mouse brains infected by a wild-type and a lab-attenuated Rabies lyssavirus

Rabies is a lethal disease caused by Rabies lyssavirus, commonly known as rabies virus (RABV), and results in nearly 100 % death once clinical symptoms occur in human and animals. Long non-coding RNAs (lncRNAs) have been reported to be associated with viral infection. But the role of lncRNAs involved in RABV infection is still elusive. In this study, we performed global transcriptome analysis of both of lncRNA and mRNA expression profiles in wild-type (WT) and lab-attenuated RABV-infected mouse brains by using next-generation sequencing. The differentially expressed lncRNAs and mRNAs were analysed by using the edgeR package. We identified 1422 differentially expressed lncRNAs and 4475 differentially expressed mRNAs by comparing WT and lab-attenuated RABV-infected brains. Then we predicted the enriched biological pathways by the Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) database based on the differentially expressed lncRNAs and mRNAs. Our analysis revealed the relationships between lncRNAs and RABV-infection-associated immune response and ion transport-related pathways, which provide a fresh insight into the potential role of lncRNA in immune evasion and neuron injury induced by WT RABV.

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Long Noncoding RNA Expression Profiling By Microarray in Diffuse Large B-Cell Lymphoma and Preliminary Bioinformatics Study

Blood ◽

10.1182/blood.v128.22.5286.5286 ◽

2016 ◽

Vol 128 (22) ◽

pp. 5286-5286

Author(s):

Honghui Huang ◽

Fei Xiao ◽

Lijing Shen ◽

Xiaofeng Han ◽

Fangyuan Chen ◽

...

Keyword(s):

Mrna Expression ◽

Expression Profiling ◽

Kegg Pathway ◽

Expression Profiles ◽

B Cell Lymphoma ◽

Differentially Expressed ◽

Newly Diagnosed ◽

Disease States ◽

Mrna Expression Profiling

Abstract Objective: Application of high-throughput genomics technology to analysis the differences in lncRNA/mRNA expression profiles between the patients with diffuse large B cell lymphoma (DLBCL) and reactive hyperplasia of lymph node (RLN), and between different disease states of DLBCL, in order to explore the role of the aberrantly expressed lncRNAs in the pathogenesis of DLBCL. Materials and methods: Tumor tissue samples from five newly diagnosed DLBCL, 3 relapsed DLBCL patients and 4 samples of RLN were collected. Agilent Human lncRNA/mRNA Microarray (4×180K) was used to profile differentially expression of lncRNA/mRNAs. Bioinformatics methods were performed for data analysis, including screening of differentially expressed lncRNA/mRNAs, gene ontology (GO) and KEGG pathway enrichment analysis, and lncRNA/mRNA co-expression network construction. Portion of dysregulated lncRNAs from the microarray data analysis was selected for validation using quantitative real-time polymerase chain reaction (qRT-PCR). Results: (1) In patients with newly diagnosed DLBCL, compared to RLN, a total of 5,806 dysregulated lncRNAs were identified (P<0.05, FC≥2-fold). Among these, 2,650 lncRNAs were significantly upregulated, while 3,156 lncRNAs were significantly downregulated. From the mRNA expression profiling data, 5,628 differently expressed mRNAs were found (P<0.05, FC≥2-fold). Among them, 2,045 were significantly upregulated and 3,583 downregulated. The most enriched GO term and KEGG pathway annotation associated with DLBCL was cell cycle regulation. The coding and non-coding gene expression network construction showed the significantly correlation between lnc-FAM27B-22:1 and mRNAs, including CDCA7L, CEBPB, CHRDL1 and SMIM9. We speculated that lnc-FAM27B-22:1 might have a critical function in pathogenesis of DLBCL. (2) In patients with primary refractory DLBCL, compared with chemo-sensitive patients, a total of 425 dysregulated lncRNAs were identified(P<0.05, FC≥2-fold). Among these, 124 lncRNAs were significantly upregulated, while 301 lncRNAs were significantly downregulated. From the mRNA expression profiling data, 251 differently expressed mRNAs were found(P<0.05, FC≥2-fold). Among them, 90 were significantly upregulated and 106 downregulated. The most enriched GO terms targeted by dysregulated transcripts were involved in a variety of functions. KEGG pathway analysis showed that 25 pathways corresponded to dysregulated transcripts and the most enriched networks correlated with tumor were Wnt and P53 signaling pathway. (3) In patients with relapsed DLBCL, compared with newly diagnosed patients, a total of 605 dysregulated lncRNAs were identified(P<0.05, FC≥2-fold). Among these, 169 lncRNAs were significantly upregulated, while 436 lncRNAs were significantly downregulated. From the mRNA expression profiling data, 365 differently expressed mRNAs were found(P<0.05, FC≥2-fold). Among them, 201 were significantly upregulated and 164 downregulated. The most enriched GO terms targeted by dysregulated transcripts were involved in a variety of functions. KEGG pathway analysis showed that 24 pathways corresponded to dysregulated transcripts and the most enriched network correlated with tumor was JAK-STAT signaling pathway. (4) Fourteen dysregulated lncRNAs expressions were analyzed in the same sample series using qRT-PCR to validate the microarray analysis results. In all but one lncRNA, consistent trend of expression changes was observed in two methods. Conclusions: In patients with newly diagnosed DLBCL versus RLN, and between different disease states of DLBCL, the lncRNA/mRNA expression profiles were significantly altered. Differentially expressed mRNAs are involved in a number of biological functions and signaling pathways. It prompt lncRNA may play an important role in the mechanism of occurrence, drug resistance and relapse of DLBCL. The above results provide the theory basis for the further study on the role of differentially expressed lncRNA in the development of DLBCL and its potential application as the possible biomarkers of early diagnosis and prognosis. Disclosures No relevant conflicts of interest to declare.

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Molecular Comparison of Imatinib-Naïve and Resistant Gastrointestinal Stromal Tumors: Differentially Expressed microRNAs and mRNAs

Cancers ◽

10.3390/cancers11060882 ◽

2019 ◽

Vol 11 (6) ◽

pp. 882 ◽

Cited By ~ 2

Author(s):

Amirnasr ◽

Gits ◽

van Kuijk ◽

Smid ◽

Vriends ◽

...

Keyword(s):

Mrna Expression ◽

Cellular Proliferation ◽

Expression Profiles ◽

Differentially Expressed ◽

Imatinib Resistance ◽

Network Analyses ◽

Biochemical Pathways ◽

Imatinib Resistant ◽

Differentially Expressed Mirnas ◽

Insight Into

Despite the success of imatinib in advanced gastrointestinal stromal tumor (GIST) patients, 50% of the patients experience resistance within two years of treatment underscoring the need to get better insight into the mechanisms conferring imatinib resistance. Here the microRNA and mRNA expression profiles in primary (imatinib-naïve) and imatinib-resistant GIST were examined. Fifty-three GIST samples harboring primary KIT mutations (exon 9; n = 11/exon 11; n = 41/exon 17; n = 1) and comprising imatinib-naïve (IM-n) (n = 33) and imatinib-resistant (IM-r) (n = 20) tumors, were analyzed. The microRNA expression profiles were determined and from a subset (IM-n, n = 14; IM-r, n = 15) the mRNA expression profile was established. Ingenuity pathway analyses were used to unravel biochemical pathways and gene networks in IM-r GIST. Thirty-five differentially expressed miRNAs between IM-n and IM-r GIST samples were identified. Additionally, miRNAs distinguished IM-r samples with and without secondary KIT mutations. Furthermore 352 aberrantly expressed genes were found in IM-r samples. Pathway and network analyses revealed an association of differentially expressed genes with cell cycle progression and cellular proliferation, thereby implicating genes and pathways involved in imatinib resistance in GIST. Differentially expressed miRNAs and mRNAs between IM-n and IM-r GIST were identified. Bioinformatic analyses provided insight into the genes and biochemical pathways involved in imatinib-resistance and highlighted key genes that may be putative treatment targets.

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Circular RNA expression profiles in cisplatin-induced acute kidney injury in mice

Epigenomics ◽

10.2217/epi-2018-0167 ◽

2019 ◽

Vol 11 (10) ◽

pp. 1191-1207 ◽

Cited By ~ 2

Author(s):

Can-Ming Li ◽

Ming Li ◽

Zeng-Chun Ye ◽

Jia-Yan Huang ◽

Yin Li ◽

...

Keyword(s):

Acute Kidney Injury ◽

Bioinformatics Analysis ◽

Expression Profiles ◽

Kidney Injury ◽

Circular Rna ◽

Differentially Expressed ◽

Cancer Pathways ◽

Polymerase Chain ◽

Generation Sequencing

Aim: This study was carried out to identify the expression profile and role of circRNAs in cisplatin-induced acute kidney injury (AKI). Materials & methods: In this study, an AKI model was established in cisplatin-treated mice, and the expression of circRNAs was profiled by next-generation sequencing. The differential expression levels of selected circRNAs were determined by quantitative real-time polymerase chain reaction. Bioinformatics analysis was conducted to predict the functions. Results: In total, 368 circRNAs were detected to be differentially expressed in response to cisplatin treatment. Bioinformatics analysis indicated that the parental genes of the differentially expressed circRNAs were predominantly implicated in the cell and cell part, cellular process and cancer pathways. Conclusion: CircRNAs might be differentially expressed in AKI, which are potentially involved in pathophysiology of cisplatin-induced nephrotoxicity.

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LncRNA and mRNA Expression Profiles in Methylprednisolone Stimulated Neural Stem Cells

Frontiers in Neuroscience ◽

10.3389/fnins.2021.669224 ◽

2021 ◽

Vol 15 ◽

Author(s):

Yong Tang ◽

Zhongyu Xie ◽

Mengjun Ma ◽

Kaidi Duan ◽

Yuxi Li ◽

...

Keyword(s):

Stem Cells ◽

Neural Stem Cells ◽

Mrna Expression ◽

Expression Profiles ◽

Differentially Expressed ◽

Akt Signaling Pathway ◽

External Stimulation ◽

Cord Injury ◽

And Migration ◽

Insight Into

Spinal cord injury (SCI) is a devastating neurological disorder that affects thousands of individuals each year. Previously, our study in non-human primates with SCI demonstrated that methylprednisolone (MP) resulted in the dysfunction of neural stem cells (NSCs), which may help to explain the controversial roles of MP in SCI. However, the detailed mechanism is still unclear. In this manuscript, we investigated the LncRNA and mRNA expression profiles of NSCs treated with MP. A total of 63 differentially expressed LncRNAs and 174 differentially expressed mRNAs were identified. Gene ontology (GO) analysis showed that differentially expressed mRNAs were highly associated with terms related to regulation of external stimulation, secretion, and migration. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis results indicated that the PI3K–Akt signaling pathway contributed to the functions of MP treated NSCs. Besides, 3899 co-expression pairs were constructed among the differentially expressed LncRNA and mRNA, among which five predicted target mRNAs with the differentially expressed LncRNAs were identified. These results provide greater insight into the precise mechanisms of MP mediating NSC dysfunction in SCI.

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Salicylic Acid Accumulation Controlled by LSD1 Is Essential in Triggering Cell Death in Response to Abiotic Stress

Cells ◽

10.3390/cells10040962 ◽

2021 ◽

Vol 10 (4) ◽

pp. 962

Author(s):

Maciej Jerzy Bernacki ◽

Anna Rusaczonek ◽

Weronika Czarnocka ◽

Stanisław Karpiński

Keyword(s):

Cell Death ◽

Salicylic Acid ◽

Abiotic Stress ◽

Wild Type ◽

Pr Genes ◽

Genes Expression ◽

Salicylic Acid Accumulation ◽

Cell Death Phenotype ◽

Insight Into

Salicylic acid (SA) is well known hormonal molecule involved in cell death regulation. In response to a broad range of environmental factors (e.g., high light, UV, pathogens attack), plants accumulate SA, which participates in cell death induction and spread in some foliar cells. LESION SIMULATING DISEASE 1 (LSD1) is one of the best-known cell death regulators in Arabidopsis thaliana. The lsd1 mutant, lacking functional LSD1 protein, accumulates SA and is conditionally susceptible to many biotic and abiotic stresses. In order to get more insight into the role of LSD1-dependent regulation of SA accumulation during cell death, we crossed the lsd1 with the sid2 mutant, caring mutation in ISOCHORISMATE SYNTHASE 1(ICS1) gene and having deregulated SA synthesis, and with plants expressing the bacterial nahG gene and thus decomposing SA to catechol. In response to UV A+B irradiation, the lsd1 mutant exhibited clear cell death phenotype, which was reversed in lsd1/sid2 and lsd1/NahG plants. The expression of PR-genes and the H2O2 content in UV-treated lsd1 were significantly higher when compared with the wild type. In contrast, lsd1/sid2 and lsd1/NahG plants demonstrated comparability with the wild-type level of PR-genes expression and H2O2. Our results demonstrate that SA accumulation is crucial for triggering cell death in lsd1, while the reduction of excessive SA accumulation may lead to a greater tolerance toward abiotic stress.

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NMR and LC-MS-Based Metabolomics to Study Osmotic Stress in Lignan-Deficient Flax

Molecules ◽

10.3390/molecules26030767 ◽

2021 ◽

Vol 26 (3) ◽

pp. 767

Author(s):

Kamar Hamade ◽

Ophélie Fliniaux ◽

Jean-Xavier Fontaine ◽

Roland Molinié ◽

Elvis Otogo Nnang ◽

...

Keyword(s):

Stress Response ◽

Osmotic Stress ◽

Biosynthetic Pathway ◽

Potential Role ◽

Plant Secondary Metabolites ◽

Wild Type ◽

Osmotic Stress Response ◽

Transgenic Flax ◽

Insight Into

Lignans, phenolic plant secondary metabolites, are derived from the phenylpropanoid biosynthetic pathway. Although, being investigated for their health benefits in terms of antioxidant, antitumor, anti-inflammatory and antiviral properties, the role of these molecules in plants remains incompletely elucidated; a potential role in stress response mechanisms has been, however, proposed. In this study, a non-targeted metabolomic analysis of the roots, stems, and leaves of wild-type and PLR1-RNAi transgenic flax, devoid of (+) secoisolariciresinol diglucoside ((+) SDG)—the main flaxseed lignan, was performed using 1H-NMR and LC-MS, in order to obtain further insight into the involvement of lignan in the response of plant to osmotic stress. Results showed that wild-type and lignan-deficient flax plants have different metabolic responses after being exposed to osmotic stress conditions, but they both showed the capacity to induce an adaptive response to osmotic stress. These findings suggest the indirect involvement of lignans in osmotic stress response.

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Integrative Analysis of miRNA and mRNA Expression Profiles in Mammary Glands of Holstein Cows Artificially Infected with Staphylococcus aureus

Pathogens ◽

10.3390/pathogens10050506 ◽

2021 ◽

Vol 10 (5) ◽

pp. 506

Author(s):

Xiaolong Wang ◽

Yongliang Fan ◽

Yifan He ◽

Ziyin Han ◽

Zaicheng Gong ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Mrna Expression ◽

Calcium Binding ◽

Expression Profiles ◽

Bovine Mastitis ◽

Mammary Glands ◽

Integrative Analysis ◽

Differentially Expressed ◽

Future Application ◽

Collagen Type Iv

Staphylococcus aureus- induced mastitis is one of the most intractable problems for the dairy industry, which causes loss of milk yield and early slaughter of cows worldwide. Few studies have used a comprehensive approach based on the integrative analysis of miRNA and mRNA expression profiles to explore molecular mechanism in bovine mastitis caused by S. aureus. In this study, S. aureus (A1, B1 and C1) and sterile phosphate buffered saline (PBS) (A2, B2 and C2) were introduced to different udder quarters of three individual cows, and transcriptome sequencing and microarrays were utilized to detected miRNA and gene expression in mammary glands from the challenged and control groups. A total of 77 differentially expressed microRNAs (DE miRNAs) and 1625 differentially expressed genes (DEGs) were identified. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that multiple DEGs were enriched in significant terms and pathways associated with immunity and inflammation. Integrative analysis between DE miRNAs and DEGs proved that miR-664b, miR-23b-3p, miR-331-5p, miR-19b and miR-2431-3p were potential factors regulating the expression levels of CD14 Molecule (CD14), G protein subunit gamma 2 (GNG2), interleukin 17A (IL17A), collagen type IV alpha 1 chain (COL4A1), microtubule associated protein RP/EB family member 2 (MAPRE2), member of RAS oncogene family (RAP1B), LDOC1 regulator of NFKB signaling (LDOC1), low-density lipoprotein receptor (LDLR) and S100 calcium binding protein A9 (S100A9) in bovine mastitis caused by S. aureus. These findings could enhance the understanding of the underlying immune response in bovine mammary glands against S. aureus infection and provide a useful foundation for future application of the miRNA–mRNA-based genetic regulatory network in the breeding cows resistant to S. aureus.

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Regulation of hair follicle development by the TNF signal ectodysplasin and its receptor Edar

Development ◽

10.1242/dev.129.10.2541 ◽

2002 ◽

Vol 129 (10) ◽

pp. 2541-2553 ◽

Cited By ~ 4

Author(s):

Johanna Laurikkala ◽

Johanna Pispa ◽

Han-Sung Jung ◽

Pekka Nieminen ◽

Marja Mikkola ◽

...

Keyword(s):

Signaling Pathway ◽

Hair Follicles ◽

Wild Type ◽

Mutant Mouse Embryos ◽

Anhidrotic Ectodermal Dysplasia ◽

Embryonic Morphogenesis ◽

Hair Follicle Development ◽

And Function ◽

Insight Into

X-linked and autosomal forms of anhidrotic ectodermal dysplasia syndromes (HED) are characterized by deficient development of several ectodermal organs, including hair, teeth and exocrine glands. The recent cloning of the genes that underlie these syndromes, ectodysplasin (ED1) and the ectodysplasin A receptor (EDAR), and their identification as a novel TNF ligand-receptor pair suggested a role for TNF signaling in embryonic morphogenesis. In the mouse, the genes of the spontaneous mutations Tabby (Ta) and downless (dl) were identified as homologs of ED1 and EDAR, respectively. To gain insight into the function of this signaling pathway in development of skin and hair follicles, we analyzed the expression and regulation of Eda and Edar in wild type as well as Tabby and Lef1 mutant mouse embryos. We show that Eda and Edar expression is confined to the ectoderm and occurs in a pattern that suggests a role of ectodysplasin/Edar signaling in the interactions between the ectodermal compartments and the formation and function of hair placodes. By using skin explant cultures, we further show that this signaling pathway is intimately associated with interactions between the epithelial and mesenchymal tissues. We also find that Ta mutants lack completely the placodes of the first developing tylotrich hairs, and that they do not show patterned expression of placodal genes, including Bmp4, Lef1, Shh, Ptch and Edar, and the genes for β-catenin and activin A. Finally, we identified activin as a mesenchymal signal that stimulates Edar expression and WNT as a signal that induces Eda expression, suggesting a hierarchy of distinct signaling pathways in the development of skin and hair follicles. In conclusion, we suggest that Eda and Edar are associated with the onset of ectodermal patterning and that ectodysplasin/edar signaling also regulates the morphogenesis of hair follicles.

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Uncontrolled Diabetes Mellitus Has No Major Influence on the Platelet Transcriptome

BioMed Research International ◽

10.1155/2018/8989252 ◽

2018 ◽

Vol 2018 ◽

pp. 1-9 ◽

Cited By ~ 2

Author(s):

Thomas G. Nührenberg ◽

Marco Cederqvist ◽

Federico Marini ◽

Christian Stratz ◽

Björn A. Grüning ◽

...

Keyword(s):

Diabetes Mellitus ◽

Next Generation Sequencing ◽

Platelet Reactivity ◽

Platelet Rich Plasma ◽

Expression Profiles ◽

Bioinformatic Analysis ◽

Differentially Expressed ◽

Major Influence ◽

Next Generation ◽

Generation Sequencing

Background. Diabetes mellitus (DM) has been associated with increased platelet reactivity as well as increased levels of platelet RNAs in plasma. Here, we sought to evaluate whether the platelet transcriptome is altered in the presence of uncontrolled DM. Methods. Next-generation sequencing (NGS) was performed on platelet RNA for 5 patients with uncontrolled DM (HbA1c 9.0%) and 5 control patients (HbA1c 5.5%) with otherwise similar clinical characteristics. RNA was isolated from leucocyte-depleted platelet-rich plasma. Libraries of platelet RNAs were created separately for long RNAs after ribosomal depletion and for small RNAs from total RNA, followed by next-generation sequencing. Results. Platelets in both groups demonstrated RNA expression profiles characterized by absence of leukocyte-specific transcripts, high expression of well-known platelet transcripts, and in total 6,343 consistently detectable transcripts. Extensive statistical bioinformatic analysis yielded 12 genes with consistently differential expression at a lenient FDR < 0.1, thereof 8 protein-coding genes and 2 genes with known expression in platelets (MACF1 and ITGB3BP). Three of the four differentially expressed noncoding genes were YRNAs (RNY1, RNY3, and RNY4) which were all downregulated in DM. 23 miRNAs were differentially expressed between the two groups. Of the 13 miRNAs with decreased expression in the diabetic group, 8 belonged to the DLK1–DIO3 gene region on chromosome 14q32.2. Conclusions. In this study, uncontrolled DM had a remote impact on different components of the platelet transcriptome. Increased expression of MACF1, together with supporting predicted mRNA-miRNA interactions as well as reduced expression of RNYs in platelets, may reflect subclinical platelet activation in uncontrolled DM.

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Genomic Expression Profiling of Colorectal Cancer in Silico

10.21203/rs.3.rs-310514/v1 ◽

2021 ◽

Author(s):

Feifei Liu ◽

Yu Wang ◽

Wenxue Li ◽

Diancheng Li ◽

Yuwei Xin ◽

...

Keyword(s):

Colorectal Cancer ◽

Survival Analysis ◽

Mrna Expression ◽

Differentially Expressed Genes ◽

Expression Profiles ◽

Functional Enrichment ◽

Differentially Expressed ◽

Analysis Tool ◽

Hub Genes ◽

Normal Tissues

Abstract Background: Colorectal cancer (CRC) is one of the most common malignancies of the digestive system; the progression and prognosis of which are affected by a complicated network of genes and pathways. The aim of this study was to identify potential hub genes associated with the progression and prognosis of colorectal cancer (CRC).Methods: We obtained gene expression profiles from GEO database to search differentially expressed genes (DEGs) between CRC tissues and normal tissue. Subsequently, we conducted a functional enrichment analysis, generated a protein–protein interaction (PPI) network to identify the hub genes, and analyzed the expression validation of the hub genes. Kaplan–Meier plotter survival analysis tool was performed to evaluate the prognostic value of hub genes expression in CRC patients.Results: A total of 370 samples, involving CRC and normal tissues were enrolled in this article. 283 differentially expressed genes (DEGs), including 62 upregulated genes and 221 downregulated genes between CRC and normal tissues were selected. We finally filtered out 6 hub genes, including INSL5, MTIM, GCG, SPP1, HSD11B2, and MAOB. In the database of TCGA-COAD, the mRNA expression of INSL5, MT1M, HSD11B2, MAOB in tumor is lower than that in normal; the mRNA expression of SPP1 in tumor is higher than that in normal. In the HPA database, the expression of INSL5, GCG, HSD11B2, MAOB in tumor is lower than that in normal tissues; the expression of SPP1 in the tumor is higher than that in normal tissues. Survival analysis revealed that INSL5, GCG, SPP1 and MT1M may serve as prognostic biomarkers in CRC. Conclusions: We screened out six hub genes to predict the occurrence and prognosis of patients with CRC using bioinformatics methods, which may provide new targets and ideas for diagnosis, prognosis and individualized treatment for CRC.

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