scholarly journals Host gene expression at an early stage of virus resistance induction

2017 ◽  
Vol 38 (SI 2 - 6th Conf EFPP 2002) ◽  
pp. 502-503
Author(s):  
E. Gammelgård ◽  
M.L. Mohan ◽  
R.A. Andersson ◽  
J.P.T. Valkonen
Keyword(s):  
Gene Expression ◽  
Virus Resistance ◽  
Early Stage ◽  
Blot Hybridization ◽  
Systemic Infection ◽  
Subtractive Hybridization ◽  
Differentially Expressed ◽  
Host Gene Expression ◽  
Resistance Induction ◽  
Potato Virus A

Suppression subtractive hybridization (SSH) was carried out to detect genes differentially expressed in plants expressing resistance to systemic infection with Potato virus A (PVA), genus Potyvirus. Differential screening has up to now revealed 19 putative differentially expressed genes. Nothern blot hybridization has confirmed the differential expression of seven genes. Three of them were only induced by the virus, but four genes were also wound-induced.

scholarly journals Integrative transcriptome data mining for identification of core lncRNAs in breast cancer

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7821 ◽  
Author(s):  
Xiaoming Zhang ◽  
Jing Zhuang ◽  
Lijuan Liu ◽  
Zhengguo He ◽  
Cun Liu ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Prognostic Value ◽  
Early Stage ◽  
Expression Profiles ◽  
Diagnostic Value ◽  
The Cancer Genome Atlas ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Data Set

Background Cumulative evidence suggests that long non-coding RNAs (lncRNAs) play an important role in tumorigenesis. This study aims to identify lncRNAs that can serve as new biomarkers for breast cancer diagnosis or screening. Methods First, the linear fitting method was used to identify differentially expressed genes from the breast cancer RNA expression profiles in The Cancer Genome Atlas (TCGA). Next, the diagnostic value of all differentially expressed lncRNAs was evaluated using a receiver operating characteristic (ROC) curve. Then, the top ten lncRNAs with the highest diagnostic value were selected as core genes for clinical characteristics and prognosis analysis. Furthermore, core lncRNA-mRNA co-expression networks based on weighted gene co-expression network analysis (WGCNA) were constructed, and functional enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID). The differential expression level and diagnostic value of core lncRNAs were further evaluated by using independent data set from Gene Expression Omnibus (GEO). Finally, the expression status and prognostic value of core lncRNAs in various tumors were analyzed based on Gene Expression Profiling Interactive Analysis (GEPIA). Results Seven core lncRNAs (LINC00478, PGM5-AS1, AL035610.1, MIR143HG, RP11-175K6.1, AC005550.4, and MIR497HG) have good single-factor diagnostic value for breast cancer. AC093850.2 has a prognostic value for breast cancer. AC005550.4 and MIR497HG can better distinguish breast cancer patients in early-stage from the advanced-stage. Low expression of MAGI2-AS3, LINC00478, AL035610.1, MIR143HG, and MIR145 may be associated with lymph node metastasis in breast cancer. Conclusion Our study provides candidate biomarkers for the diagnosis and prognosis of breast cancer, as well as a bioinformatics basis for the further elucidation of the molecular pathological mechanism of breast cancer.

scholarly journals Screening of Differentially Expressed Microsporidia Genes from Nosema ceranae Infected Honey Bees by Suppression Subtractive Hybridization

Insects ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 199
Author(s):  
Zih-Ting Chang ◽  
Chong-Yu Ko ◽  
Ming-Ren Yen ◽  
Yue-Wen Chen ◽  
Yu-Shin Nai
Keyword(s):  
Gene Expression ◽  
Real Time ◽  
Differentially Expressed Genes ◽  
Honey Bees ◽  
Physiological Mechanism ◽  
Subtractive Hybridization ◽  
Infection Process ◽  
Nosema Ceranae ◽  
Differentially Expressed ◽  
Suppressive Subtractive Hybridization

The microsporidium Nosema ceranae is a high prevalent parasite of the European honey bee (Apis mellifera). This parasite is spreading across the world into its novel host. The developmental process, and some mechanisms of N. ceranae-infected honey bees, has been studied thoroughly; however, few studies have been carried out in the mechanism of gene expression in N. ceranae during the infection process. We therefore performed the suppressive subtractive hybridization (SSH) approach to investigate the candidate genes of N. ceranae during its infection process. All 96 clones of infected (forward) and non-infected (reverse) library were dipped onto the membrane for hybridization. A total of 112 differentially expressed sequence tags (ESTs) had been sequenced. For the host responses, 20% of ESTs (13 ESTs, 10 genes, and 1 non-coding RNA) from the forward library and 93.6% of ESTs (44 ESTs, 28 genes) from the reverse library were identified as differentially expressed genes (DEGs) of the hosts. A high percentage of DEGs involved in catalytic activity and metabolic processes revealed that the host gene expression change after N. ceranae infection might lead to an unbalance of physiological mechanism. Among the ESTs from the forward library, 75.4% ESTs (49 ESTs belonged to 24 genes) were identified as N. ceranae genes. Out of 24 N. ceranae genes, nine DEGs were subject to real-time quantitative reverse transcription PCR (real-time qRT-PCR) for validation. The results indicated that these genes were highly expressed during N. ceranae infection. Among nine N. ceranae genes, one N. ceranae gene (AAJ76_1600052943) showed the highest expression level after infection. These identified differentially expressed genes from this SSH could provide information about the pathological effects of N. ceranae. Validation of nine up-regulated N. ceranae genes reveal high potential for the detection of early nosemosis in the field and provide insight for further applications.

Stress-induced gene expression profiling in the black tiger shrimp Penaeus monodon

2007 ◽  
Vol 31 (1) ◽  
pp. 126-138 ◽  
Author(s):  
Enrique de la Vega ◽  
Michael R. Hall ◽  
Kate J. Wilson ◽  
Antonio Reverter ◽  
Rick G. Woods ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sequence Similarity ◽  
Expression Profiles ◽  
Penaeus Monodon ◽  
Gene Expression Profiles ◽  
Subtractive Hybridization ◽  
Long Terminal Repeat Retrotransposons ◽  
Differentially Expressed ◽  
Specific Gene ◽  
Immune Related Genes

Cultured shrimp are continuously exposed to variable environmental conditions that have been associated with stress and subsequent outbreaks of disease. To investigate the effect of environmental stress on Penaeus monodon gene expression, a 3,853 random cDNA microarray chip was generated with clones originating from six stress-enriched hemocyte libraries generated by suppression subtractive hybridization and a normal hemocyte cDNA library. Changes in temporal gene expression were analyzed from shrimp exposed to hypoxic, hyperthermic, and hypoosmotic conditions; 3.1% of the cDNAs were differentially expressed in response to at least one of the environmental stressors, and 72% of the differentially expressed clones had no significant sequence similarity to previously known genes. Among those genes with high identity to known sequences, the most common functional groups were immune-related genes and non-long terminal repeat retrotransposons. Hierarchical clustering revealed a set of cDNAs with temporal and stress-specific gene expression profiles as well as a set of cDNAs indicating a common stress response between stressors. Hypoxic and hyperthermic stressors induced the most severe short-term response in terms of gene regulation, and the osmotic stress had the least variation in expression profiles relative to the control. These expression data agree with observed differences in shrimp physical appearance and behavior following exposure to stress conditions.

scholarly journals Expression of Retroelements in Cervical Cancer and Their Interplay with HPV Infection and Host Gene Expression

Cancers ◽  
2021 ◽  
Vol 13 (14) ◽  
pp. 3513
Author(s):  
Gislaine Curty ◽  
Albert N. Menezes ◽  
Ayslan C. Brant ◽  
Miguel de Mulder Rougvie ◽  
Miguel Ângelo M. Moreira ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cervical Cancer ◽  
Gene Family ◽  
Dna Methyltransferase ◽  
Hpv Infection ◽  
Host Gene ◽  
Differentially Expressed ◽  
Human Endogenous Retrovirus ◽  
Host Gene Expression ◽  
Hpv Status

Retroelements are expressed in diverse types of cancer and are related to tumorigenesis and to cancer progression. We characterized the expression of retroelements in cervical cancer and explored their interplay with HPV infection and their association with expression of neighboring genes. Forty biopsies of invasive cervical carcinoma (squamous cell carcinomas and adenocarcinomas) with genotyped HPV were selected and analyzed for human endogenous retrovirus (HERV) and long interspersed nuclear element 1 (L1) expression through RNA-seq data. We found 8060 retroelements expressed in the samples and a negative correlation of DNA methyltransferase 1 expression with the two most expressed L1 elements. A total of 103 retroelements were found differentially expressed between tumor histological types and between HPV types, including several HERV families (HERV-K, HERV-H, HERV-E, HERV-I and HERV-L). The comparison between HPV mono- and co-infections showed the highest proportion of differentially expressed L1 elements. The location of retroelements affected neighboring gene expression, such as shown for the interleukin-20 gene family. Three HERVs and seven L1 were located close to this gene family and two L1 showed a positive association with IL20RB expression. This study describes the expression of retroelements in cervical cancer and shows their association with HPV status and host gene expression.

scholarly journals Three-dimensional interactions between integrated HPV genomes and cellular chromatin dysregulate host gene expression in early cervical carcinogenesis

2021 ◽  
Author(s):  
Ian J Groves ◽  
Emma LA Drane ◽  
Marco Michalski ◽  
Jack M Monahan ◽  
Cinzia G Scarpini ◽  
...  
Keyword(s):  
Gene Expression ◽  
Early Stage ◽  
Three Dimensional ◽  
Virus Genome ◽  
Host Gene ◽  
Neoplastic Progression ◽  
Host Gene Expression ◽  
Gene Dysregulation ◽  
Sequence Deletion ◽  
Virus Genomes

AbstractDevelopment of cervical cancer is directly associated with integration of human papillomavirus (HPV) genomes into host chromosomes and subsequent modulation of HPV oncogene expression, which correlates with multi-layered epigenetic changes at the integrated HPV genomes. However, the process of integration itself and dysregulation of host gene expression at sites of integration in our model of HPV16 integrant clone natural selection has remained enigmatic. We now show, using a state-of-the-art ‘HPV integrated site capture’ (HISC) technique, that integration likely occurs through microhomology-mediated repair (MHMR) mechanisms via either a direct process, resulting in host sequence deletion (in our case, partially homozygously) or via a ‘looping’ mechanism by which flanking host regions become amplified. Furthermore, using our ‘HPV16-specific Region Capture Hi-C’ technique, we have determined that three-dimensional (3D) interactions between the integrated virus genome and host chromosomes, both at short- (<500 kbp) and long-range (>500 kbp), appear to drive host gene dysregulation through the disruption of local host:host 3D interactions known as topologically associating domains (TADs). This mechanism of HPV-induced host gene expression modulation indicates that integration of virus genomes near to or within a ‘cancer-causing gene’ is not essential to influence such genes within an entire TAD and that these modifications to 3D interactions could have a major role in selection of HPV integrants at the early stage of cervical neoplastic progression.

scholarly journals Short- and long-range cis interactions between integrated HPV genomes and cellular chromatin dysregulate host gene expression in early cervical carcinogenesis

2021 ◽  
Vol 17 (8) ◽  
pp. e1009875
Author(s):  
Ian J. Groves ◽  
Emma L. A. Drane ◽  
Marco Michalski ◽  
Jack M. Monahan ◽  
Cinzia G. Scarpini ◽  
...  
Keyword(s):  
Gene Expression ◽  
Long Range ◽  
Early Stage ◽  
Virus Genome ◽  
Host Gene ◽  
Neoplastic Progression ◽  
Host Gene Expression ◽  
Local Host ◽  
Genome Interactions ◽  
Virus Genomes

Development of cervical cancer is directly associated with integration of human papillomavirus (HPV) genomes into host chromosomes and subsequent modulation of HPV oncogene expression, which correlates with multi-layered epigenetic changes at the integrated HPV genomes. However, the process of integration itself and dysregulation of host gene expression at sites of integration in our model of HPV16 integrant clone natural selection has remained enigmatic. We now show, using a state-of-the-art ‘HPV integrated site capture’ (HISC) technique, that integration likely occurs through microhomology-mediated repair (MHMR) mechanisms via either a direct process, resulting in host sequence deletion (in our case, partially homozygously) or via a ‘looping’ mechanism by which flanking host regions become amplified. Furthermore, using our ‘HPV16-specific Region Capture Hi-C’ technique, we have determined that chromatin interactions between the integrated virus genome and host chromosomes, both at short- (<500 kbp) and long-range (>500 kbp), appear to drive local host gene dysregulation through the disruption of host:host interactions within (but not exceeding) host structures known as topologically associating domains (TADs). This mechanism of HPV-induced host gene expression modulation indicates that integration of virus genomes near to or within a ‘cancer-causing gene’ is not essential to influence their expression and that these modifications to genome interactions could have a major role in selection of HPV integrants at the early stage of cervical neoplastic progression.

scholarly journals A Bioinformatics Approach to Identifying Potential Biomarkers for Cryptosporidium parvum: A Coccidian Parasite Associated with Fetal Diarrhea

Vaccines ◽  
2021 ◽  
Vol 9 (12) ◽  
pp. 1427
Author(s):  
Mumdooh J. Sabir ◽  
Ross Low ◽  
Neil Hall ◽  
Majid Rasool Kamli ◽  
Md. Zubbair Malik
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Cryptosporidium Parvum ◽  
Early Stage ◽  
Expression Profiles ◽  
Interaction Network ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
Data Sets ◽  
Gene Interaction Network

Cryptosporidium parvum (C. parvum) is a protozoan parasite known for cryptosporidiosis in pre-weaned calves. Animals and patients with immunosuppression are at risk of developing the disease, which can cause potentially fatal diarrhoea. The present study aimed to construct a network biology framework based on the differentially expressed genes (DEGs) of C. parvum infected subjects. In this way, the gene expression profiling analysis of C. parvum infected individuals can give us a snapshot of actively expressed genes and transcripts under infection conditions. In the present study, we have analyzed microarray data sets and compared the gene expression profiles of the patients with the different data sets of the healthy control. Using a network medicine approach to identify the most influential genes in the gene interaction network, we uncovered essential genes and pathways related to C. parvum infection. We identified 164 differentially expressed genes (109 up- and 54 down-regulated DEGs) and allocated them to pathway and gene set enrichment analysis. The results underpin the identification of seven significant hub genes with high centrality values: ISG15, MX1, IFI44L, STAT1, IFIT1, OAS1, IFIT3, RSAD2, IFITM1, and IFI44. These genes are associated with diverse biological processes not limited to host interaction, type 1 interferon production, or response to IL-gamma. Furthermore, four genes (IFI44, IFIT3, IFITM1, and MX1) were also discovered to be involved in innate immunity, inflammation, apoptosis, phosphorylation, cell proliferation, and cell signaling. In conclusion, these results reinforce the development and implementation of tools based on gene profiles to identify and treat Cryptosporidium parvum-related diseases at an early stage.

Subtractive hybridization for differential gene expression in mechanically unloaded rat heart

2006 ◽  
Vol 291 (6) ◽  
pp. H2714-H2722 ◽  
Author(s):  
Heiko Bugger ◽  
Stefanie Leippert ◽  
Daniel Blum ◽  
Peter Kahle ◽  
Bernhard Barleon ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Suppression Subtractive Hybridization ◽  
Respiratory Chain ◽  
Rat Heart ◽  
Complex I ◽  
Subtractive Hybridization ◽  
Differentially Expressed ◽  
Isolated Mitochondria ◽  
Mechanical Unloading

The objective of this study was to identify differentially expressed genes in the mechanically unloaded rat heart by suppression subtractive hybridization. In male Wistar-Kyoto rats, mechanical unloading was achieved by infrarenal heterotopic heart transplantation. Differentially expressed genes were investigated systematically by suppression subtractive hybridization. Selected targets were validated by Northern blot analysis, real-time RT-PCR, and immunoblot analysis. Maximal ADP-stimulated oxygen consumption (state 3) was measured in isolated mitochondria. Transplantation caused atrophy (heart-to-body weight ratio: 1.6 ± 0.1 vs. 2.4 ± 0.1, P < 0.001). We selected 1,880 clones from the subtractive hybridization procedure (940 forward and 940 reverse runs assessing up- or downregulation). The first screen verified 465 forward and 140 reverse clones, and the second screen verified 67 forward and 30 reverse clones. On sequencing of 24 forward and 23 reverse clones, 9 forward and 14 reverse homologies to known genes were found. Specifically, we identified reduced mRNA expression of complex I (−49%, P < 0.05) and complex II (−61%, P < 0.001) of the respiratory chain. Significant reductions were also observed on the respiratory chain protein level: −42% for complex I ( P < 0.01), −57% for complex II ( P < 0.05), and −65% for complex IV ( P < 0.05). Consistent with changes in gene and protein expression, state 3 respiration was significantly decreased in isolated mitochondria of atrophied hearts, with glutamate and succinate as substrates: 85 ± 27 vs. 224 ± 32 natoms O·min−1·mg−1with glutamate ( P < 0.01) and 59 ± 18 vs. 154 ± 30 natoms O·min−1·mg−1with succinate ( P < 0.05). Subtractive hybridization indicates major changes in overall gene expression by mechanical unloading and specifically identified downregulation of respiratory chain genes. This observation is functionally relevant and provides a mechanism for the regulation of respiratory capacity in response to chronic mechanical unloading.

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