scholarly journals A Set of Genes Differentially Expressed Between Avirulent and Virulent Meloidogyne incognita Near-Isogenic Lines Encode Secreted Proteins

2003 ◽  
Vol 16 (12) ◽  
pp. 1077-1084 ◽  
Author(s):  
Cédric Neveu ◽  
Stéphanie Jaubert ◽  
Pierre Abad ◽  
Philippe Castagnone-Sereno
Keyword(s):  
Meloidogyne Incognita ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Near Isogenic Lines ◽  
Root Knot Nematode ◽  
Significant Similarity ◽  
Cdna Sequences ◽  
Isogenic Lines ◽  
Esophageal Gland

A cDNA-amplification fragment length polymorphism (AFLP)-based strategy has been used to identify genes differentially expressed between two pairs of near-isogenic lines (NIL) of the root-knot nematode Meloidogyne incognita either avirulent or virulent against the tomato Mi resistance gene. Gene expression profiles from infective second-stage juveniles (J2) were compared, and 22 of the 24,025 transcript-derived fragments (TDF) generated proved to be differential, i.e., present in both avirulent NIL and absent in both virulent NIL. Fourteen of the TDF sequences did not show any significant similarity to known proteins, while eight matched reported sequences from nematodes and other invertebrates. The differential expression of nine genes was confirmed by reverse transcription-polymerase chain reaction (RT-PCR) experiments. In situ hybridization conducted with five of the sequences showed that two were specifically expressed in the intestinal cells (HM10 and PM1), one in the subventral esophageal glands (HM1), and two in the dorsal esophageal gland of J2 (HM7 and HM12). Analysis of full-length cDNA sequences revealed the presence of a signal peptide for HM1, HM10, and HM12, indicating that the encoded proteins are putatively secreted. Since secreted products in general and esophageal gland secretions in particular are thought to be among the main M. incognita pathogenicity factors, this result suggests a possible dual role for some of the genes encoding such secretions, i.e., they could be involved in both pathogenicity and virulence or avirulence of these biotrophic parasites.

scholarly journals Transcriptome Analysis of Eggplant Root in Response to Root-Knot Nematode Infection

Pathogens ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 470
Author(s):  
Min Zhang ◽  
Hongyuan Zhang ◽  
Jie Tan ◽  
Shuping Huang ◽  
Xia Chen ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Expression Profiles ◽  
Resistance Mechanism ◽  
Solanum Melongena ◽  
Enrichment Analysis ◽  
Nematode Resistance ◽  
Differentially Expressed ◽  
Root Knot Nematode ◽  
Solanum Torvum ◽  
Plant Nematode

Eggplant (Solanum melongena L.), which belongs to the Solanaceae family, is an important vegetable crop. However, its production is severely threatened by root-knot nematodes (RKNs) in many countries. Solanum torvum, a wild relative of eggplant, is employed worldwide as rootstock for eggplant cultivation due to its resistance to soil-borne diseases such as RKNs. In this study, to identify the RKN defense mechanisms, the transcriptomic profiles of eggplant and Solanum torvum were compared. A total of 5360 differentially expressed genes (DEGs) were identified for the response to RKN infection. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that these DEGs are mainly involved in the processes of response to stimulus, protein phosphorylation, hormone signal transduction, and plant-pathogen interaction pathways. Many phytohormone-related genes and transcription factors (MYB, WRKY, and NAC) were differentially expressed at the four time points (ck, 7, 14, and 28 days post-infection). The abscisic acid signaling pathway might be involved in plant-nematode interactions. qRT-PCR validated the expression levels of some of the DEGs in eggplant. These findings demonstrate the nematode-induced expression profiles and provide some insights into the nematode resistance mechanism in eggplant.

4 Molecularly guided multiplexed digital spatial analysis reveals differential gene expression profiles in the WNT-β-catenin pathway between melanoma and prostate tumors

2020 ◽  
Vol 8 (Suppl 3) ◽  
pp. A4-A4
Author(s):  
Anushka Dikshit ◽  
Dan Zollinger ◽  
Karen Nguyen ◽  
Jill McKay-Fleisch ◽  
Kit Fuhrman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Single Molecule ◽  
Spatial Information ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Fluorescence Assay ◽  
Differentially Expressed ◽  
Tumor Type ◽  
Prostate Tumors

BackgroundThe canonical WNT-β-catenin signaling pathway is vital for development and tissue homeostasis but becomes strongly tumorigenic when dysregulated. and alter the transcriptional signature of a cell to promote malignant transformation. However, thorough characterization of these transcriptomic signatures has been challenging because traditional methods lack either spatial information, multiplexing, or sensitivity/specificity. To overcome these challenges, we developed a novel workflow combining the single molecule and single cell visualization capabilities of the RNAscope in situ hybridization (ISH) assay with the highly multiplexed spatial profiling capabilities of the GeoMx™ Digital Spatial Profiler (DSP) RNA assays. Using these methods, we sought to spatially profile and compare gene expression signatures of tumor niches with high and low CTNNB1 expression.MethodsAfter screening 120 tumor cores from multiple tumors for CTNNB1 expression by the RNAscope assay, we identified melanoma as the tumor type with the highest CTNNB1 expression while prostate tumors had the lowest expression. Using the RNAscope Multiplex Fluorescence assay we selected regions of high CTNNB1 expression within 3 melanoma tumors as well as regions with low CTNNB1 expression within 3 prostate tumors. These selected regions of interest (ROIs) were then transcriptionally profiled using the GeoMx DSP RNA assay for a set of 78 genes relevant in immuno-oncology. Target genes that were differentially expressed were further visualized and spatially assessed using the RNAscope Multiplex Fluorescence assay to confirm GeoMx DSP data with single cell resolution.ResultsThe GeoMx DSP analysis comparing the melanoma and prostate tumors revealed that they had significantly different gene expression profiles and many of these genes showed concordance with CTNNB1 expression. Furthermore, immunoregulatory targets such as ICOSLG, CTLA4, PDCD1 and ARG1, also demonstrated significant correlation with CTNNB1 expression. On validating selected targets using the RNAscope assay, we could distinctly visualize that they were not only highly expressed in melanoma compared to the prostate tumor, but their expression levels changed proportionally to that of CTNNB1 within the same tumors suggesting that these differentially expressed genes may be regulated by the WNT-β-catenin pathway.ConclusionsIn summary, by combining the RNAscope ISH assay and the GeoMx DSP RNA assay into one joint workflow we transcriptionally profiled regions of high and low CTNNB1 expression within melanoma and prostate tumors and identified genes potentially regulated by the WNT- β-catenin pathway. This novel workflow can be fully automated and is well suited for interrogating the tumor and stroma and their interactions.GeoMx Assays are for RESEARCH ONLY, not for diagnostics.

Effects of MiR-451a on the Phagocytosis and Polarization of Macrophages

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 42-42
Author(s):  
Xiaoli Liu ◽  
Dongyue Zhang ◽  
Hao Wang ◽  
Qian Ren ◽  
Lina Wang ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Conflicts Of Interest ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Microrna Expression ◽  
Differentially Expressed ◽  
Proliferation Capacity ◽  
Microrna Sequencing ◽  
Differentiation Marker

Macrophages are important member in tissue microenvironments and play diverse physiologic and pathologic roles. Leukemia associated macrophages (LAM) are a kind of specifically activated macrophages in leukemia microenvironment, which are different from M1, M2 and TAMs. We have reported the heterogeneities in gene expression profiles of LAMs. However, MicroRNA expression profiles of LAMs and regulatory mechanism are still unknown. Here, a MLL-AF9 induced mouse acute myeloid leukemia (AML) model was used, and LAMs in the spleen and bone marrow were sorted for microRNA sequencing. The microRNA expression profiles of LAMs in bone marrow and spleen in AML mice were different from macrophages from control mice. Based on the volcano plot, more than 100 microRNAs were differentially expressed in LAMs compared with macrophages in control mice. Next, five differentially expressed microRNAs were selected and verified by qRT-PCR in LAMs from spleen. The results showed that miR-451a and miR-155-5p in spleen LAMs were significantly upregulated in LAMs from spleen. Overexpression of miR-451a altered the morphology of macrophages, enhanced the phagocytic ability of macrophages, and promotes the expression of macrophage differentiation marker CD11b. Furthermore, overexpression of miR-451a had little effect on M0 macrophages, but increased the proliferation capacity of macrophages upon stimulation toward M1 or M2 phenotype. MiR-451a overexpressed-macrophages had higher level of iNOS when stimulated with LPS or IL-4 whereas there was no difference in the expression of IL-1β, IL-6, CD206 and Arg-1 between MiR-451a overexpressed-macrophages and control macrophage. Therefore, our data revealed the characteristics of the microRNA expression profile of LAMs for the first time, and verified the effect of miR-451a on macrophage in vitro. Disclosures No relevant conflicts of interest to declare.

171 THE EFFECT OF TRICHOSTATIN A ON THE DEVELOPMENT AND THE GLOBAL GENE EXPRESSION PATTERNS IN MOUSE EMBRYOS DEVELOPING IN VITRO

2008 ◽  
Vol 20 (1) ◽  
pp. 165
Author(s):  
X. S. Cui ◽  
X. Y. Li ◽  
T. Kim ◽  
N.-H. Kim
Keyword(s):  
Gene Expression ◽  
Trichostatin A ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Mouse Embryos ◽  
Differentially Expressed ◽  
Gene Expression Patterns ◽  
Cell Stage

Trichostatin A (TSA) is an inhibitor of histone deacetylase and is able to alter gene expression patterns by interfering with the removal of acetyl groups from histones. The aim of this study was to determine the effect of TSA treatment on the development and gene expression patterns of mouse zygotes developing in vitro. The addition of 100 nm TSA to the culture medium did not affect the cleavage of mouse embryos (TSA treatment, 148/150 (99%) v. control, 107/107 (100%)); however, embryos that were treated with TSA arrested at the 2-cell stage (145/148, 98%). We estimated the number of nuclei in control and TSA-treated embryos by propidium iodide staining, taking into account the presence of any cells with two or more nuclei. At 62–63 h post-hCG stimulation, control zygotes had developed to the 4-cell stage and exhibited one nucleus in each blastomere, indicative of normal development. In contrast, we observed tetraploid nuclei in at least one blastomere in 20.8% (11/53) of the embryos that had been treated with TSA. At 28–29 h post-hCG stimulation (metaphase of the 1-cell stage), there was no difference in the mitotic index (as determined by analyzing the microtubule configuration) in the TSA group compared to the control group. At the 2-cell stage, however, we did not observe mitotic spindles and metaphase chromatin in embryos in the TSA treatment group compared to the controls. Interestingly, when embryos were cultured in TSA-free medium from 35 h post-hCG stimulation (S- or early G2-phase of the 2-cell stage) onward, almost all of them (47/50) developed to the blastocyst stage. In contrast, when embryos were cultured in TSA-free medium from 42 h post-hCG stimulation (middle G2-phase of the 2-cell stage) onward, they did not develop to the 4-cell stage. We used Illumina microarray technology to analyze the gene expression profiles in control and TSA-treated late 2-cell-stage embryos. Applied Biosystems Expression System software was used to extract assay signals and assay signal-to-noise ratio values from the microarray images. Our data showed that 897 genes were significantly (P < 0.05; 2-sample t-test) up- or down-regulated by TSA treatment compared to controls. Analysis using the PANTHER classification system (https://panther.appliedbiosystems.com) revealed that the 575 genes that were differentially expressed in the TSA group compared to the control were classified as being associated with putative biological processes or molecular function. Overall, in terms of putative biological processes, more nucleoside, nucleotide, and nucleic acid metabolism, protein metabolism and modification, signal transduction, developmental process, and cell cycle genes were differentially expressed between the TSA and control groups. In terms of putative molecular function, more nucleic acid-binding transcription factor and transferase genes were differentially expressed between the groups. The results collectively suggest that inhibition of histone acetylation in mouse embryos affects gene expression profiles at the time of zygotic genome activation, and this subsequently affects further development.

Integrated Transcriptomic Analysis of Necrosis-related Gene in Diffuse Gliomas

2019 ◽  
Vol 80 (04) ◽  
pp. 240-249
Author(s):  
Jiajia Wang ◽  
Jie Ma
Keyword(s):  
Gene Expression ◽  
High Risk ◽  
Differentially Expressed Genes ◽  
Expression Profiles ◽  
Prognostic Index ◽  
Gene Expression Profiles ◽  
Risk Groups ◽  
Low Risk ◽  
Differentially Expressed ◽  
Low Grade

Glioblastoma multiforme (GBM), an aggressive brain tumor, is characterized histologically by the presence of a necrotic center surrounded by so-called pseudopalisading cells. Pseudopalisading necrosis has long been used as a prognostic feature. However, the underlying molecular mechanism regulating the progression of GBMs remains unclear. We hypothesized that the gene expression profiles of individual cancers, specifically necrosis-related genes, would provide objective information that would allow for the creation of a prognostic index. Gene expression profiles of necrotic and nonnecrotic areas were obtained from the Ivy Glioblastoma Atlas Project (IVY GAP) database to explore the differentially expressed genes.A robust signature of seven genes was identified as a predictor for glioblastoma and low-grade glioma (GBM/LGG) in patients from The Cancer Genome Atlas (TCGA) cohort. This set of genes was able to stratify GBM/LGG and GBM patients into high-risk and low-risk groups in the training set as well as the validation set. The TCGA, Repository for Molecular Brain Neoplasia Data (Rembrandt), and GSE16011 databases were then used to validate the expression level of these seven genes in GBMs and LGGs. Finally, the differentially expressed genes (DEGs) in the high-risk and low-risk groups were subjected to gene ontology enrichment, Kyoto Encyclopedia of Genes and Genomes pathway, and gene set enrichment analyses, and they revealed that these DEGs were associated with immune and inflammatory responses. In conclusion, our study identified a novel seven-gene signature that may guide the prognostic prediction and development of therapeutic applications.

The RNA-seq approach to discriminate gene expression profiles in response to Beauveria bassiana and Micrococcus luteus microbial pathogens on Actias selene (Lepidoptera: Saturniidae)

Zootaxa ◽  
2019 ◽  
Vol 4591 (1) ◽  
pp. 1
Author(s):  
DAN LIANG ◽  
PEI WANG ◽  
LINGLING WU ◽  
XIAOLI JIANG ◽  
GUOQING WEI ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Beauveria Bassiana ◽  
Bacterial Infections ◽  
Micrococcus Luteus ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Microbial Pathogens ◽  
Pcr Analysis ◽  
Immune Mechanism

Actias selene (Hübner) is an important silk-spinning moth. Like other moths, it has innate immunity but no acquired immunity. However, there are few studies on immune-related genes of A. selene. Here, differential expression RNAseq experiment was employed to examine the genes related to different metabolic pathways and to explore the immune mechanism of the A. selene post Beauveria bassiana (Bb) and Micrococcus luteus (ML) stimuli. A total of 64,372,921 clean reads were obtained and 39,057 differentially expressed genes (DEGs) were identified. In the Bb vs. PBS group (PBS as the control), 9,092 genes were up-regulated and 4,438 genes were down-regulated; in the ML vs. PBS group, 5,903 genes were up-regulated and 5,175 genes were down-regulated. The KEGG (Kyoto Encyclopedia of Genes and Genomes) and GO (Gene Ontology) analyses of DEGs confirmed that many DEGs were associated with "Metabolism pathway", "cellular process", "cell" and "catalytic activity". Among them, 194 and 149 differentially expressed genes were related to immunity in the Bb vs. PBS group and ML vs. PBS group, respectively. We verified the reliability of the data with reverse transcription quantitative real-time PCR analysis of randomly selected genes. Furthermore, the phylogenetic tree results showed that HSP90, PGRP and MyD88 genes of A. selene were most closely related to Antheraea pernyi (Guérin-Méneville). These results will provide an overview of the molecular mechanism of A. selene resistance to fungal and bacterial infections as well as an evolutionary aspect of these genes. Moreover, the interrelated trophic mechanisms among different groups of organisms are vital to explore, thus this study will lay a foundation for further studies on the innate immune mechanism of saturniid moths, and provide important theoretical basis for studying the relationship between A. selene and other species.

scholarly journals Integrated analysis of the aging brain transcriptome and proteome in tauopathy

2020 ◽  
Vol 15 (1) ◽  
Author(s):  
Carl Grant Mangleburg ◽  
Timothy Wu ◽  
Hari K. Yalamanchili ◽  
Caiwei Guo ◽  
Yi-Chen Hsieh ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Brain ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Mutant Form ◽  
Brain Gene Expression ◽  
Brain Transcriptome ◽  
Age Dependent

Abstract Background Tau neurofibrillary tangle pathology characterizes Alzheimer’s disease and other neurodegenerative tauopathies. Brain gene expression profiles can reveal mechanisms; however, few studies have systematically examined both the transcriptome and proteome or differentiated Tau- versus age-dependent changes. Methods Paired, longitudinal RNA-sequencing and mass-spectrometry were performed in a Drosophila model of tauopathy, based on pan-neuronal expression of human wildtype Tau (TauWT) or a mutant form causing frontotemporal dementia (TauR406W). Tau-induced, differentially expressed transcripts and proteins were examined cross-sectionally or using linear regression and adjusting for age. Hierarchical clustering was performed to highlight network perturbations, and we examined overlaps with human brain gene expression profiles in tauopathy. Results TauWT induced 1514 and 213 differentially expressed transcripts and proteins, respectively. TauR406W had a substantially greater impact, causing changes in 5494 transcripts and 697 proteins. There was a ~ 70% overlap between age- and Tau-induced changes and our analyses reveal pervasive bi-directional interactions. Strikingly, 42% of Tau-induced transcripts were discordant in the proteome, showing opposite direction of change. Tau-responsive gene expression networks strongly implicate innate immune activation. Cross-species analyses pinpoint human brain gene perturbations specifically triggered by Tau pathology and/or aging, and further differentiate between disease amplifying and protective changes. Conclusions Our results comprise a powerful, cross-species functional genomics resource for tauopathy, revealing Tau-mediated disruption of gene expression, including dynamic, age-dependent interactions between the brain transcriptome and proteome.

scholarly journals Genomewide Expression Profile Analysis of the Candida glabrata Pdr1 Regulon

2010 ◽  
Vol 10 (3) ◽  
pp. 373-383 ◽  
Author(s):  
Kelly E. Caudle ◽  
Katherine S. Barker ◽  
Nathan P. Wiederhold ◽  
Lijing Xu ◽  
Ramin Homayouni ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Candida Glabrata ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Resistant Isolate ◽  
Content Type ◽  
Activating Mutations ◽  
Zinc Cluster

ABSTRACTThe ABC transportersCandida glabrataCdr1 (CgCdr1), CgPdh1, and CgSnq2 are known to mediate azole resistance in the pathogenic fungusC. glabrata. Activating mutations inCgPDR1, a zinc cluster transcription factor, result in constitutive upregulation of these ABC transporter genes but to various degrees. We examined the genomewide gene expression profiles of two matched azole-susceptible and -resistantC. glabrataclinical isolate pairs. Of the differentially expressed genes identified in the gene expression profiles for these two matched pairs, there were 28 genes commonly upregulated withCgCDR1in both isolate sets includingYOR1,LCB5,RTA1,POG1,HFD1, and several members of theFLOgene family of flocculation genes. We then sequencedCgPDR1from each susceptible and resistant isolate and found two novel activating mutations that conferred increased resistance when they were expressed in a common background strain in whichCgPDR1had been disrupted. Microarray analysis comparing these reengineered strains to their respective parent strains identified a set of commonly differentially expressed genes, includingCgCDR1,YOR1, andYIM1, as well as genes uniquely regulated by specific mutations. Our results demonstrate that while CgPdr1 activates a broad repertoire of genes, specific activating mutations result in the activation of discrete subsets of this repertoire.

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