De novo assembly and analysis of the transcriptome of the Dermacentor marginatus genes differentially expressed after blood-feeding and long-term starvation

Abstract Background: The ixodid tick Dermacentor marginatus is a vector of many pathogens wide spread in Eurasia. Studies of gene sequence on many tick species have greatly increased the information on tick protective antigen which might have the potential to function as effective vaccine candidates or drug targets for eco-friendly acaricide development. In the current study, RNA-seq was applied to identify D. marginatus sequences and analyze differentially expressed unigenes.Methods: To obtain a broader picture of gene sequences and changes in expression level, RNA-seq was performed to obtain the whole-body transcriptome data of D. marginatus adult female ticks after engorgement and long-term starvation. Subsequently, the real-time quantitative PCR (RT-qPCR) was applied to validate the RNA-seq data.Results: RNA-seq produced 30,251 unigenes, of which 32% were annotated. Gene expression was compared among groups that differed by status as newly molted, starved and engorged female adult ticks. Nearly one third of the unigenes in each group were differentially expressed compared to the other two groups, and the most numerous were genes encoding proteins involved in catalytic and binding activities and apoptosis. Selected up-regulated differentially expressed genes in each group were associated to protein, lipids, carbohydrate and chitin metabolism. Blood-feeding and long-term starvation also caused genes differentially expressed in the defense response and antioxidant response. RT-qPCR results indicated 6 differentially expressed transcripts showed similar trends in expression changes with RNA-seq results confirming that the gene expression profiles in transcriptome data is in consistent with RT-qPCR validation.Conclusions: Obtaining the sequence information of D. marginatus and characterizing the expression pattern of the genes involved in blood-feeding and during starvation would be helpful in understanding molecular physiology of D. marginatus and provides data for anti-tick vaccine and drug development for controlling the tick.

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De novo assembly and analysis of the transcriptome of the Dermacentor marginatus genes differentially expressed after blood feeding and long-term starvation

10.21203/rs.3.rs-57342/v2 ◽

2020 ◽

Author(s):

Ercha Hu ◽

Yuan Meng ◽

Ying Ma ◽

Ruiqi Song ◽

Zhengxiang Hu ◽

...

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Blood Feeding ◽

Differentially Expressed ◽

Whole Body ◽

Sequence Information ◽

Transcriptome Data ◽

Rna Seq ◽

Dermacentor Marginatus

Abstract Background: The ixodid tick Dermacentor marginatus is a vector of many pathogens wide spread in Eurasia. Studies of gene sequence on many tick species have greatly increased the information on tick protective antigen which might have the potential to function as effective vaccine candidates or drug targets for eco-friendly acaricide development. In the current study, RNA-seq was applied to identify D. marginatus sequences and analyze differentially expressed unigenes.Methods: To obtain a broader picture of gene sequences and changes in expression level, RNA-seq was performed to obtain the whole-body transcriptome data of D. marginatus adult female ticks after engorgement and long-term starvation. Subsequently, the real-time quantitative PCR (RT-qPCR) was applied to validate the RNA-seq data.Results: RNA-seq produced 30,251 unigenes, of which 32% were annotated. Gene expression was compared among groups that differed by status as newly molted, starved and engorged female adult ticks. Nearly 1/3 of the unigenes in each group were differentially expressed compared to the other two groups, and the most numerous were genes encoding proteins involved in catalytic and binding activities and apoptosis. Selected up-regulated differentially expressed genes in each group were associated to protein, lipids, carbohydrate and chitin metabolism. Blood-feeding and long-term starvation also caused genes differentially expressed in the defense response and antioxidant response. RT-qPCR results indicated 6 differentially expressed transcripts showed similar trends in expression changes with RNA-seq results confirming that the gene expression profiles in transcriptome data is in consistent with RT-qPCR validation.Conclusions: Obtaining the sequence information of D. marginatus and characterizing the expression pattern of the genes involved in blood feeding and during starvation would be helpful in understanding molecular physiology of D. marginatus and provides data for anti-tick vaccine and drug development for controlling the tick.

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De novo assembly and analysis of the transcriptome of the Dermacentor marginatus genes differentially expressed after blood-feeding and long-term starvation

Parasites & Vectors ◽

10.1186/s13071-020-04442-2 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Ercha Hu ◽

Yuan Meng ◽

Ying Ma ◽

Ruiqi Song ◽

Zhengxiang Hu ◽

...

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Blood Feeding ◽

Differentially Expressed ◽

Whole Body ◽

Sequence Information ◽

Transcriptome Data ◽

Rna Seq ◽

Dermacentor Marginatus

Abstract Background The ixodid tick Dermacentor marginatus is a vector of many pathogens wide spread in Eurasia. Studies of gene sequence on many tick species have greatly increased the information on tick protective antigen which might have the potential to function as effective vaccine candidates or drug targets for eco-friendly acaricide development. In the current study, RNA-seq was applied to identify D. marginatus sequences and analyze differentially expressed unigenes. Methods To obtain a broader picture of gene sequences and changes in expression level, RNA-seq was performed to obtain the whole-body transcriptome data of D. marginatus adult female ticks after engorgement and long-term starvation. Subsequently, the real-time quantitative PCR (RT-qPCR) was applied to validate the RNA-seq data. Results RNA-seq produced 30,251 unigenes, of which 32% were annotated. Gene expression was compared among groups that differed by status as newly molted, starved and engorged female adult ticks. Nearly one third of the unigenes in each group were differentially expressed compared to the other two groups, and the most numerous were genes encoding proteins involved in catalytic and binding activities and apoptosis. Selected up-regulated differentially expressed genes in each group were associated to protein, lipids, carbohydrate and chitin metabolism. Blood-feeding and long-term starvation also caused genes differentially expressed in the defense response and antioxidant response. RT-qPCR results indicated 6 differentially expressed transcripts showed similar trends in expression changes with RNA-seq results confirming that the gene expression profiles in transcriptome data is in consistent with RT-qPCR validation. Conclusions Obtaining the sequence information of D. marginatus and characterizing the expression pattern of the genes involved in blood-feeding and during starvation would be helpful in understanding molecular physiology of D. marginatus and provides data for anti-tick vaccine and drug development for controlling the tick.

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De novo assembly and analysis of the transcriptome of the Dermacentor marginatus genes differentially expressed after blood feeding and long-term starvation

10.21203/rs.3.rs-57342/v3 ◽

2020 ◽

Author(s):

Ercha Hu ◽

Yuan Meng ◽

Ying Ma ◽

Ruiqi Song ◽

Zhengxiang Hu ◽

...

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Blood Feeding ◽

Differentially Expressed ◽

Whole Body ◽

Sequence Information ◽

Transcriptome Data ◽

Rna Seq ◽

Dermacentor Marginatus

Abstract Background: The ixodid tick Dermacentor marginatus is a vector of many pathogens wide spread in Eurasia. Studies of gene sequence on many tick species have greatly increased the information on tick protective antigen which might have the potential to function as effective vaccine candidates or drug targets for eco-friendly acaricide development. In the current study, RNA-seq was applied to identify D. marginatus sequences and analyze differentially expressed unigenes.Methods: To obtain a broader picture of gene sequences and changes in expression level, RNA-seq was performed to obtain the whole-body transcriptome data of D. marginatus adult female ticks after engorgement and long-term starvation. Subsequently, the real-time quantitative PCR (RT-qPCR) was applied to validate the RNA-seq data.Results: RNA-seq produced 30,251 unigenes, of which 32% were annotated. Gene expression was compared among groups that differed by status as newly molted, starved and engorged female adult ticks. Nearly one third of the unigenes in each group were differentially expressed compared to the other two groups, and the most numerous were genes encoding proteins involved in catalytic and binding activities and apoptosis. Selected up-regulated differentially expressed genes in each group were associated to protein, lipids, carbohydrate and chitin metabolism. Blood-feeding and long-term starvation also caused genes differentially expressed in the defense response and antioxidant response. RT-qPCR results indicated 6 differentially expressed transcripts showed similar trends in expression changes with RNA-seq results confirming that the gene expression profiles in transcriptome data is in consistent with RT-qPCR validation.Conclusions: Obtaining the sequence information of D. marginatus and characterizing the expression pattern of the genes involved in blood feeding and during starvation would be helpful in understanding molecular physiology of D. marginatus and provides data for anti-tick vaccine and drug development for controlling the tick.

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De Novo Assembly and Analysis of Transcriptome of the Dermacentor Marginatus Genes Differentially Expressed After Blood Feeding and Long-term Starvation

10.21203/rs.3.rs-57342/v1 ◽

2020 ◽

Author(s):

Ercha Hu ◽

Yuan Meng ◽

Ying Ma ◽

Ruiqi Song ◽

Zhengxiang Hu ◽

...

Keyword(s):

Gene Expression ◽

Drug Development ◽

Blood Feeding ◽

Differentially Expressed ◽

Whole Body ◽

Sequence Information ◽

Transcriptome Data ◽

Rna Seq ◽

Dermacentor Marginatus

Abstract Background The Ixodid tick Dermacentor marginatus is a vector of many pathogens wide spread in Eurasia. Study of gene targets of the tick species provides insight to find novel tick protective antigen for drug development and vaccine targets. Methods To obtain a broader picture of gene sequences and changes in expression level, the RNA-seq was performed to obtain the whole-body transcriptome data of D. marginatus adult female ticks after engorgement and long-term starvation. Subsequently, the real-time quantitative PCR (RT-qPCR) was applied to validate the RNA-seq data. Results The RNA-seq produced 30251 unigenes, of which 32% were annotated using Trinity. Gene expression was compared among groups differed by status as newly molted, starved and engorged female adult ticks. Nearly 1/3 of the unigenes in each group were differentially expressed compared to the other two group, and the most numerous were genes encoding proteins involved in catalytic and binding activities and apoptosis. Selected up-regulated differentially expressed genes in each group associated to protein, lipids, carbohydrate and chitin metabolism. Blood feeding and long-term starvation also caused genes differentially expressed in the defense response and antioxidant response. RT-qPCR results indicated 6 differentially expressed transcripts showed similar trends in expression changes with RNA-seq results confirming that the gene expression profiles in transcriptome data is in consistent with RT-qPCR validation. Conclusions Obtaining the sequence information of D. marginatus and characterizing the expression pattern of the genes involved in blood feeding and during starvation would be helpful in understanding molecular physiology of D. marginatus and provides data for anti-tick vaccine and drug development for controlling the tick.

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HIV-1 Infection Transcriptomics: Meta-Analysis of CD4+ T Cells Gene Expression Profiles

Viruses ◽

10.3390/v13020244 ◽

2021 ◽

Vol 13 (2) ◽

pp. 244 ◽

Cited By ~ 1

Author(s):

Antonio Victor Campos Coelho ◽

Rossella Gratton ◽

João Paulo Britto de Melo ◽

José Leandro Andrade-Santos ◽

Rafael Lima Guimarães ◽

...

Keyword(s):

Gene Expression ◽

T Cells ◽

Differentially Expressed Genes ◽

Cd4 T Cells ◽

Expression Profiles ◽

Meta Analysis ◽

Differentially Expressed ◽

Rna Seq ◽

Infected Cells ◽

Hiv 1

HIV-1 infection elicits a complex dynamic of the expression various host genes. High throughput sequencing added an expressive amount of information regarding HIV-1 infections and pathogenesis. RNA sequencing (RNA-Seq) is currently the tool of choice to investigate gene expression in a several range of experimental setting. This study aims at performing a meta-analysis of RNA-Seq expression profiles in samples of HIV-1 infected CD4+ T cells compared to uninfected cells to assess consistently differentially expressed genes in the context of HIV-1 infection. We selected two studies (22 samples: 15 experimentally infected and 7 mock-infected). We found 208 differentially expressed genes in infected cells when compared to uninfected/mock-infected cells. This result had moderate overlap when compared to previous studies of HIV-1 infection transcriptomics, but we identified 64 genes already known to interact with HIV-1 according to the HIV-1 Human Interaction Database. A gene ontology (GO) analysis revealed enrichment of several pathways involved in immune response, cell adhesion, cell migration, inflammation, apoptosis, Wnt, Notch and ERK/MAPK signaling.

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RNA-seq analysis of non-muscular invasive bladder cancer to reveal different gene expression profiles between smoking and non-smoking patients.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.6_suppl.478 ◽

2021 ◽

Vol 39 (6_suppl) ◽

pp. 478-478

Author(s):

Zhichao Fu ◽

Shenghua Liu ◽

Jianfei Wang ◽

Ning He ◽

Yadong Yang ◽

...

Keyword(s):

Gene Expression ◽

Bladder Cancer ◽

Tumor Progression ◽

Urothelial Carcinoma ◽

Differentially Expressed Genes ◽

Poor Prognosis ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Differentially Expressed ◽

Rna Seq

478 Background: Bladder cancer is the ninth most common malignancy in the world, approximately 75% of patients are diagnosed with non-muscle invasive bladder cancer (NMIBC). Smoking has been established to be a carcinogenic risk factor of bladder cancer. Nevertheless, the detailed relationship between smoking and progression of NMIBC are poorly understood. In this study, we revealed high expressed genes in smoking patients were significantly related to tumor progression in NMIBC patients. Methods: A total of 54 NMIBC patients including 19 never smokers and 35 smokers (current smokers and previous smokers) were enrolled in this study.The gene expression profiles were obtained by RNA-seq and the differentially expressed genes between smoking and non-smoking patients were identified using DESeq2 .The further analysis of the association between genes expression and patient survival in NMIBC cohorts(Jakob et al., 2016)and IMvigor 210 cohorts(Jonathan et al., 2016)by Kaplan-Meier survival estimate. Results: We identified 46 differentially expressed genes (p<0.05) in smoking and non-somking NMIBC patients. IDO1 and KRT14 gene, which related to bladder cancer progression and poor prognosis, was identified significantly higher expressed in somking group compared with non-smoking and they have a logFC of 2.6,3.9 with FDR 1.83E-5,3.40E-5 respectively. The expression of other genes, including KRT6A, CASP14, SERPINA1, MYO3A and IL20RB, were significantly higher in smoking patients compared to non-somking. Notably, survival data analysis from 476 NMIBC cohorts showed that IL20RB had a significant relationship with poor PFS(p = 0.021) and in the Mvigor 210 Cohort including 310 advanced or metastatic urothelial carcinoma patients treated with atezolizumab, we found that the high expression of IL20RB was significantly related to poor OS(p = 0.002). Conclusions: We identified 14 genes related to tumor progression were significantly higher in smoking NMIBC patients than in non-smoking. Among these genes, the expression of IL20RB was related to the poor prognosis of NMIBC, and it may correlates with reduced clinical benefit of immunotherapeutic in patients with urothelial carcinoma.

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The G-CSF Produces Long-Term Changes in Gene and Mirnas Expression Profiles in CD34+ From Healthy Donors

Blood ◽

10.1182/blood.v120.21.588.588 ◽

2012 ◽

Vol 120 (21) ◽

pp. 588-588

Author(s):

Alicia Báez ◽

Concepción Prats-Martín ◽

Isabel Álvarez-Laderas ◽

Estefania Garcia ◽

Luis Ignacio Sanchez-Abarca ◽

...

Keyword(s):

Gene Expression ◽

Conflicts Of Interest ◽

Reference Group ◽

Expression Profiles ◽

Differentially Expressed ◽

Long Term Effects ◽

Time Points ◽

Healthy Donors ◽

Mirnas Expression

Abstract Abstract 588 Introduction: The G-CSF (granulocyte colony-stimulating factor) is the cytokine most commonly used for the mobilization of hematopoietic progenitor cells (HPCs) from healthy donors used in allogenic transplantation (allo-HSCT). Although the administration of G-CSF is considered safe, the knowledge about its long-term effects, especially in HPCs, is limited. The aim of this study was to analyze whether G-CSF induces changes in gene and miRNAs expression profiles in HPCs from healthy donors, and determine whether or not these changes persist at the long term. Materials and Method: CD34 + cells were isolated by immunomagnetic separation and sorting from 5 healthy donors before mobilization with G-CSF and at afterwards at 5, 30 and 365 days after mobilization. A pool of samples from PB not mobilized was used as reference group. We analyzed the expression of 375 miRNAs using TaqMan MicroRNA Arrays Human v2.0 (Applied Biosystems), and the gene expression profile using Whole Human Genome Oligo microarray kit 4×44K (Agilent). The expression levels of genes and miRNAs were obtained by the 2-ΔΔCTmethod. From expression data hierarchical clustering was performed using the Euclidean distance. To identify genes and miRNAs differentially expressed due to the effect of G-CSF at different time-points a cut-off value of level expression 2,5 above or below the control values was used and non-parametric Mann-Whitney test was applied. All analysis were performed using the Multi-experiment Viewer 4.7.1. The function of the miRNAs and genes of interest was determined from the various databases available online (TAM database, Gene Ontology, TargetScan Human). Results: Seven miRNAs were differentially expressed in HPCs at 5, 30 and 365 days after mobilization with G-CSF, as compared to HPCs obtained from not mobilized PB. In addition, 67 genes were also differentially expressed after administration of G-CSF, whose expression profiles remained abnormal 1 year after mobilization. These genes are involved in biological processes such as hematopoietic cell proliferation, ribosomal protein synthesis, cell metabolism and transmembrane transportation. Interestingly, 8 of these genes are target of the miRNAs also identified in the current study, which suggests that their expression might be regulated by these miRNAs. Conclusion: The G-CSF modifies gene expression profiles and miRNAs in HPCs from healthy donors. Remarkably, these changes were observed from early time-points and persisted at least 1 year after exposure to the drug. This effect of G-CSF on HPCs have not been previously reported and might be clinically relevant. Disclosures: No relevant conflicts of interest to declare.

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Meta-Analysis of Hypoxic Transcriptomes from Public Databases

Biomedicines ◽

10.3390/biomedicines8010010 ◽

2020 ◽

Vol 8 (1) ◽

pp. 10 ◽

Cited By ~ 1

Author(s):

Hidemasa Bono ◽

Kiichi Hirota

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Meta Analysis ◽

Gene Expression Profiles ◽

Data Driven ◽

Transcriptome Data ◽

Rna Seq ◽

Experimental Conditions ◽

Oxygen Homeostasis ◽

Before And After

Hypoxia is the insufficiency of oxygen in the cell, and hypoxia-inducible factors (HIFs) are central regulators of oxygen homeostasis. In order to obtain functional insights into the hypoxic response in a data-driven way, we attempted a meta-analysis of the RNA-seq data from the hypoxic transcriptomes archived in public databases. In view of methodological variability of archived data in the databases, we first manually curated RNA-seq data from appropriate pairs of transcriptomes before and after hypoxic stress. These included 128 human and 52 murine transcriptome pairs. We classified the results of experiments for each gene into three categories: upregulated, downregulated, and unchanged. Hypoxic transcriptomes were then compared between humans and mice to identify common hypoxia-responsive genes. In addition, meta-analyzed hypoxic transcriptome data were integrated with public ChIP-seq data on the known human HIFs, HIF-1 and HIF-2, to provide insights into hypoxia-responsive pathways involving direct transcription factor binding. This study provides a useful resource for hypoxia research. It also demonstrates the potential of a meta-analysis approach to public gene expression databases for selecting candidate genes from gene expression profiles generated under various experimental conditions.

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Different gene expression profiles in iPSC-derived motor neurons from ALS8 patients with variable clinical courses suggest mitigating pathways for neurodegeneration

Human Molecular Genetics ◽

10.1093/hmg/ddaa069 ◽

2020 ◽

Vol 29 (9) ◽

pp. 1465-1475 ◽

Cited By ~ 1

Author(s):

Danyllo Oliveira ◽

David A Morales-Vicente ◽

Murilo S Amaral ◽

Livia Luz ◽

Andrea L Sertié ◽

...

Keyword(s):

Gene Expression ◽

Cell Death ◽

Differentially Expressed Genes ◽

Motor Neurons ◽

Oxidative Metabolism ◽

Protein Targeting ◽

Expression Profiles ◽

Protein Translation ◽

Differentially Expressed ◽

Rna Seq

Abstract Amyotrophic lateral sclerosis type 8 (ALS8) is an autosomal dominant form of ALS, which is caused by pathogenic variants in the VAPB gene. Here we investigated five ALS8 patients, classified as ‘severe’ and ‘mild’ from a gigantic Brazilian kindred, carrying the same VAPB mutation but displaying different clinical courses. Copy number variation and whole exome sequencing analyses in such individuals ruled out previously described genetic modifiers of pathogenicity. After deriving induced pluripotent stem cells (iPSCs) for each patient (N = 5) and controls (N = 3), motor neurons were differentiated, and high-throughput RNA-Seq gene expression measurements were performed. Functional cell death and oxidative metabolism assays were also carried out in patients’ iPSC-derived motor neurons. The degree of cell death and mitochondrial oxidative metabolism were similar in iPSC-derived motor neurons from mild patients and controls and were distinct from those of severe patients. Similar findings were obtained when RNA-Seq from such cells was performed. Overall, 43 genes were upregulated and 66 downregulated in the two mild ALS8 patients when compared with severe ALS8 individuals and controls. Interestingly, significantly enriched pathways found among differentially expressed genes, such as protein translation and protein targeting to the endoplasmic reticulum (ER), are known to be associated with neurodegenerative processes. Taken together, the mitigating mechanisms here presented appear to maintain motor neuron survival by keeping translational activity and protein targeting to the ER in such cells. As ALS8 physiopathology has been associated with proteostasis mechanisms in ER–mitochondria contact sites, such differentially expressed genes appear to relate to the bypass of VAPB deficiency.

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Contrasting patterns of divergence at the regulatory and sequence level in European Daphnia galeata natural populations

10.1101/374991 ◽

2018 ◽

Cited By ~ 1

Author(s):

Suda Parimala Ravindran ◽

Maike Herrmann ◽

Mathilde Cordellier

Keyword(s):

Gene Expression ◽

Local Adaptation ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Differentially Expressed ◽

Population Divergence ◽

Sequence Information ◽

Snp Analysis ◽

Daphnia Galeata ◽

Key Species

ABSTRACTUnderstanding the genetic basis of local adaptation has long been a focus of evolutionary biology. Recently there has been increased interest in deciphering the evolutionary role of Daphnia’s plasticity and the molecular mechanisms of local adaptation. Using transcriptome data, we assessed the differences in gene expression profiles and sequences in four European Daphnia galeata populations. In total, ~33% of 32,903 transcripts were differentially expressed between populations. Among 10,280 differentially expressed transcripts, 5,209 transcripts deviated from neutral expectations and their population-specific expression pattern is likely the result of local adaptation processes. Furthermore, a SNP analysis allowed inferring population structure and distribution of genetic variation. The population divergence at the sequence-level was comparatively higher than the gene expression level by several orders of magnitude and consistent with strong founder effects and lack of gene flow between populations. Using sequence information, the candidate transcripts were annotated using a comparative genomics approach. Thus, we identified candidate transcriptomic regions for local adaptation in a key species of aquatic ecosystems in the absence of any laboratory induced stressor.

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