Transcriptome-level assessment of the impact of deformed wing virus on honey bee larvae

AbstractDeformed wing virus (DWV) prevalence is high in honey bee (Apis mellifera) populations. The virus infects honey bees through vertical and horizontal transmission, leading to behavioural changes, wing deformity, and early mortality. To better understand the impacts of viral infection in the larval stage of honey bees, artificially reared honey bee larvae were infected with DWV (1.55 × 1010 copies/per larva). No significant mortality occurred in infected honey bee larvae, while the survival rates decreased significantly at the pupal stage. Examination of DWV replication revealed that viral replication began at 2 days post inoculation (d.p.i.), increased dramatically to 4 d.p.i., and then continuously increased in the pupal stage. To better understand the impact of DWV on the larval stage, DWV-infected and control groups were subjected to transcriptomic analysis at 4 d.p.i. Two hundred fifty-five differentially expressed genes (DEGs) (fold change ≥ 2 or ≤ -2) were identified. Of these DEGs, 168 genes were downregulated, and 87 genes were upregulated. Gene Ontology (GO) analysis showed that 141 DEGs (55.3%) were categorized into molecular functions, cellular components and biological processes. One hundred eleven genes (38 upregulated and 73 downregulated) were annotated by KO (KEGG Orthology) pathway mapping and involved metabolic pathways, biosynthesis of secondary metabolites and glycine, serine and threonine metabolism pathways. Validation of DEGs was performed, and the related gene expression levels showed a similar tendency to the DEG predictions at 4 d.p.i.; cell wall integrity and stress response component 1 (wsc1), cuticular protein and myo-inositol 2-dehydrogenase (iolG) were significantly upregulated, and small conductance calcium-activated potassium channel protein (SK) was significantly downregulated at 4 d.p.i. Related gene expression levels at different d.p.i. revealed that these DEGs were significantly regulated from the larval stage to the pupal stage, indicating the potential impacts of gene expression levels from the larval to the pupal stages. Taken together, DWV infection in the honey bee larval stage potentially influences the gene expression levels from larvae to pupae and reduces the survival rate of the pupal stage. This information emphasizes the consequences of DWV prevalence in honey bee larvae for apiculture.

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Codon usage is an important determinant of gene expression levels largely through its effects on transcription

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1606724113 ◽

2016 ◽

Vol 113 (41) ◽

pp. E6117-E6125 ◽

Cited By ~ 122

Author(s):

Zhipeng Zhou ◽

Yunkun Dang ◽

Mian Zhou ◽

Lin Li ◽

Chien-hung Yu ◽

...

Keyword(s):

Gene Expression ◽

Codon Usage ◽

Important Determinant ◽

Mrna Translation ◽

Mrna Levels ◽

Protein Coding ◽

Expression Levels ◽

Highly Expressed Genes ◽

The Impact ◽

Gene Expression Levels

Codon usage biases are found in all eukaryotic and prokaryotic genomes, and preferred codons are more frequently used in highly expressed genes. The effects of codon usage on gene expression were previously thought to be mainly mediated by its impacts on translation. Here, we show that codon usage strongly correlates with both protein and mRNA levels genome-wide in the filamentous fungus Neurospora. Gene codon optimization also results in strong up-regulation of protein and RNA levels, suggesting that codon usage is an important determinant of gene expression. Surprisingly, we found that the impact of codon usage on gene expression results mainly from effects on transcription and is largely independent of mRNA translation and mRNA stability. Furthermore, we show that histone H3 lysine 9 trimethylation is one of the mechanisms responsible for the codon usage-mediated transcriptional silencing of some genes with nonoptimal codons. Together, these results uncovered an unexpected important role of codon usage in ORF sequences in determining transcription levels and suggest that codon biases are an adaptation of protein coding sequences to both transcription and translation machineries. Therefore, synonymous codons not only specify protein sequences and translation dynamics, but also help determine gene expression levels.

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Direct effect of acaricides on pathogen loads and gene expression levels in honey bees Apis mellifera

Journal of Insect Physiology ◽

10.1016/j.jinsphys.2011.12.011 ◽

2012 ◽

Vol 58 (5) ◽

pp. 613-620 ◽

Cited By ~ 134

Author(s):

Humberto Boncristiani ◽

Robyn Underwood ◽

Ryan Schwarz ◽

Jay D. Evans ◽

Jeffery Pettis ◽

...

Keyword(s):

Gene Expression ◽

Apis Mellifera ◽

Direct Effect ◽

Honey Bees ◽

Expression Levels ◽

Gene Expression Levels

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Honey Bee Viruses, Colony Health, and Antiviral Defense

Proceedings ◽

10.3390/proceedings2020050016 ◽

2020 ◽

Vol 50 (1) ◽

pp. 16

Author(s):

Katie F. Daughenbaugh ◽

Alex J. McMenamin ◽

Laura M. Brutscher ◽

Fenali Parekh ◽

Michelle L. Flenniken

Keyword(s):

Gene Expression ◽

Heat Shock ◽

Honey Bee ◽

Honey Bees ◽

Antiviral Defense ◽

Deformed Wing Virus ◽

Antiviral Responses ◽

Model Virus ◽

Virus Abundance

Honey bee colony losses are influenced by multiple abiotic and biotic factors, including viruses. To investigate the effects of RNA viruses on honey bees, we infected bees with a model virus (Sindbis-GFP) in the presence or absence of double-stranded RNA (dsRNA). In honey bees, dsRNA is the substrate for sequence-specific RNA interference (RNAi)-mediated antiviral defense and is a trigger of sequence-independent\antiviral responses. Transcriptome sequencing identified more than 200 differentially expressed genes, including genes in the RNAi, Toll, Imd, JAK-STAT, and heat shock response pathways, and many uncharacterized genes. To confirm the virus limiting role of two genes (i.e., dicer and mf116383) in honey bees, we utilized RNAi to reduce their expression in vivo and determined that the virus abundance increased. To evaluate the role of the heat shock stress response in antiviral defense, bees were heat stressed post-virus infection and the virus abundance and gene expression were assessed. Heat-stressed bees had reduced virus levels and a greater expression of several heat shock protein encoding genes (hsps) compared to the controls. To determine if these genes are universally associated with antiviral defense, bees were infected with another model virus, Flock House virus (FHV), or deformed wing virus and the gene expression was assessed. The expression of dicer was greater in bees infected with either FHV or Sindbis-GFP compared to the mock-infected bees, but not in the deformed wing virus-infected bees. To further investigate honey bee antiviral defense mechanisms and elucidate the function of key genes (dicer, ago-2, mf116383, and hsps) at the cellular level, primary honey bee larval hemocytes were transfected with dsRNA or infected with the Lake Sinai virus 2 (LSV2). These studies indicate that mf116383 and hsps mediate dsRNA detection and that MF116383 is involved in limiting LSV2 infection. Together, these results further our understanding of honey bee antiviral defense, particularly dsRNA-mediated antiviral responses, at both the individual bee and cellular levels.

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Evaluation of UHRF1 and P16INK4A expression levels in newly diagnosed AML patients

Biomedical Research and Therapy ◽

10.15419/bmrat.v5i9.475 ◽

2018 ◽

Vol 5 (9) ◽

pp. 2658-2663 ◽

Cited By ~ 1

Author(s):

Vahid Amiri ◽

Mohamadhossein Mohammadi ◽

Mohammad Reza Khosravi Farsani ◽

Arshia Gharehbaghian ◽

Abbas Hajifathali ◽

...

Keyword(s):

Gene Expression ◽

Negative Correlation ◽

Leukemic Cells ◽

Control Group ◽

Newly Diagnosed ◽

Expression Levels ◽

Age Related ◽

P16ink4a Gene ◽

The Impact ◽

Gene Expression Levels

Introduction: Gene mutation is an infrequent cause of tumor suppressor gene (TSG) defect in de novo AML patients. Instead, it seems that leukemic cells employ epigenetic tricks to attenuate the negative impacts of intact TSGs. Ordinarily, critical TSGs, such as p16INK4A, is hyper-methylated in AML blasts under the impact of master epigenetic regulators, such as UHRF1. In this study, we investigated the correlation between UHRF1 and p16INK4A gene expression levels in newly diagnosed AML patients. Methods: Bone marrow and peripheral blood samples were obtained from 50 newly diagnosed AML patients and 18 healthy normal control subjects. Gene expression levels of UHRF1 and P16INK4A were surveyed using SYBR Green Quantitative Real-time PCR. Statistical analyses were done using SPSS statistical software 21.0. Results: P16INK4A gene expression showed reduced levels in 80.64% of patients above 45 years of age, while only 32% of patients below 45 years had reduced expression levels. The Spearman correlation test also demonstrated a significant negative correlation between UHRF1 and p16INK4A gene expression levels in AML patients, which was not observed in the control group (r=0.343 and P= 0.015). Conclusion: Regarding the age-related patterns of UHRF1 and p16INK4A gene expression, and also the presence of negative correlation between them, we conclude that UHRF1 may potentially be involved in p16INK4A down-regulation in elderly AML patients, which may subsequently facilitate the progression of AML in older ages.

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Multi-tiered Analyses of Honey Bees That Resist or Succumb to Parasitic Mites and Viruses

10.21203/rs.3.rs-291062/v1 ◽

2021 ◽

Author(s):

Daniel B. Weaver ◽

Brandi L. Cantarel ◽

Christine Elsik ◽

Dawn L. Lopez ◽

Jay Evans

Keyword(s):

Gene Expression ◽

Honey Bee ◽

Honey Bees ◽

Host Responses ◽

Negative Effects ◽

Pollination Services ◽

Deformed Wing Virus ◽

Mortality And Morbidity ◽

The Individual ◽

Parasitic Mites

Abstract Background Varroa destructor mites, and the numerous viruses they vector to their honey bee hosts, are among the most serious threats to honey bee populations, causing mortality and morbidity to both the individual honey bee and colony, the negative effects of which convey to the pollination services provided by honey bees worldwide. Here we use a combination of targeted assays and deep RNA sequencing to determine host and microbial changes in resistant and susceptible honey bee lineages. We focus on three study sets. The first involves field sampling of sympatric western bees, some derived from resistant stock and some from stock susceptible to mites. The second experiment contrasts three colonies more deeply, two from susceptible stock from the southeastern U.S. and one from mite-resistant bee stock from Eastern Texas. Finally, to decouple the effects of mites from those of the viruses they vector, we experimentally expose honey bees to DWV in the laboratory, measuring viral growth and host responses. Results We find strong differences between resistant and susceptible bees in terms of both viral loads and bee gene expression. Interestingly, lineages of bees with naturally low levels of the mite-vectored Deformed wing virus, also carried lower levels of viruses not vectored by mites. By mapping gene expression results against current ontologies and other studies, we describe the impacts of mite parasitism, as well as viruses on bee health against two genetic backgrounds. We identify numerous genes and processes seen in other studies of stress and disease in honey bee colonies, though we find novel genes and new patterns of expression too. Conclusions We provide evidence that honey bees surviving in the face of parasitic mites do so through their abilities to resist the presence of devastating viruses vectored by these mites. By revealing responses to viral infection and mite parasitism in different lineages, our data identify candidate proteins for the evolution of mite tolerance and virus resistance.

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Decreased Levels of Microfibril-Associated Glycoprotein (MAGP)-1 in Patients with Colon Cancer and Obesity Are Associated with Changes in Extracellular Matrix Remodelling

International Journal of Molecular Sciences ◽

10.3390/ijms22168485 ◽

2021 ◽

Vol 22 (16) ◽

pp. 8485

Author(s):

Iranzu Gómez de Segura ◽

Patricia Ahechu ◽

Javier Gómez-Ambrosi ◽

Amaia Rodríguez ◽

Beatriz Ramírez ◽

...

Keyword(s):

Gene Expression ◽

Colon Cancer ◽

Extracellular Matrix ◽

Matrix Protein ◽

Extracellular Matrix Protein ◽

Mrna Levels ◽

Expression Levels ◽

The Impact ◽

Ht 29 ◽

Gene Expression Levels

Objective: The protein microfibril-associated glycoprotein (MAGP)-1 constitutes a crucial extracellular matrix protein. We aimed to determine its impact on visceral adipose tissue (VAT) remodelling during obesity-associated colon cancer (CC). Methods: Samples obtained from 79 subjects (29 normoponderal (NP) (17 with CC) and 50 patients with obesity (OB) (19 with CC)) were used in the study. Circulating concentrations of MAGP-1 and its gene expression levels (MFAP2) in VAT were analysed. The impact of inflammation-related factors and adipocyte-conditioned media (ACM) on MFAP2 mRNA levels in colon adenocarcinoma HT-29 cells were further analysed. The effects of MAGP-1 in the expression of genes involved in the extracellular matrix (ECM) remodelling and tumorigenesis in HT-29 cells was also explored. Results: Obesity (p < 0.01) and CC (p < 0.001) significantly decreased MFAP2 gene expression levels in VAT whereas an opposite trend in TGFB1 mRNA levels was observed. Increased mRNA levels of MFAP2 after the stimulation of HT-29 cells with lipopolysaccharide (LPS) (p < 0.01) and interleukin (IL)-4 (p < 0.01) together with a downregulation (p < 0.05) after hypoxia mimicked by CoCl2 treatment was observed. MAGP-1 treatment significantly enhanced the mRNA levels of the ECM-remodelling genes collagen type 6 α3 chain (COL6A3) (p < 0.05), decorin (DCN) (p < 0.01), osteopontin (SPP1) (p < 0.05) and TGFB1 (p < 0.05). Furthermore, MAGP-1 significantly reduced (p < 0.05) the gene expression levels of prostaglandin-endoperoxide synthase 2 (COX2/PTGS2), a key gene controlling cell proliferation, growth and adhesion in CC. Interestingly, a significant decrease (p < 0.01) in the mRNA levels of MFAP2 in HT-29 cells preincubated with ACM from volunteers with obesity compared with control media was observed. Conclusion: The decreased levels of MAGP-1 in patients with obesity and CC together with its capacity to modulate key genes involved in ECM remodelling and tumorigenesis suggest MAGP-1 as a link between AT excess and obesity-associated CC development.

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Genetic variants in R-Spondin/RNF43 complex and gene expression levels to predict efficacy of cetuximab (cet) in patients (pts) with metastatic colorectal cancer (mCRC): Data from the FIRE-3 phase III trial.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.4_suppl.190 ◽

2020 ◽

Vol 38 (4_suppl) ◽

pp. 190-190

Author(s):

Francesca Battaglin ◽

Yi Xiao ◽

Joshua Millstein ◽

Andreas Seeber ◽

Hiroyuki Arai ◽

...

Keyword(s):

Gene Expression ◽

Genetic Variants ◽

Multivariable Analysis ◽

Colorectal Carcinogenesis ◽

Phase Iii ◽

First Line ◽

Tissue Samples ◽

Expression Levels ◽

The Impact ◽

Gene Expression Levels

190 Background: Wnt signaling deregulation is a primary driver of colorectal carcinogenesis. RNF43 is a key suppressor of Wnt activation while R-Spodin inhibits RNF43 activity. RNF43 mutations are associated with the serrated neoplasia pathway, BRAF mutation and MSI. We hypothesized that genetic variants in the R-Spodin/RNF43 complex and corresponding genes expression levels may predict cetuximab efficacy in mCRC pts. Methods: Genomic DNA from blood samples of pts enrolled in the randomized FIRE-3 trial was genotyped through the OncoArray, a custom array manufactured by Illumina. The impact on outcome of 17 functional SNPs within RNF43/ ZNRF3, LGR4/5 and RSPO1/2/3 was analyzed in 129 pts treated with first-line FOLFIRI/cet and 107 pts treated with FOLFIRI/bevacizumab (bev). Gene expression levels were measured from tumor tissue samples from 102 pts in the cet arm by HTG EdgeSeq Oncology Biomarker Panel. False discovery rate (FDR) for gene expression analysis was computed using the Benjamini-Hochberg approach (significant Q < 0.1). Results: In the cet cohort, pts with the C/C genotype of ZNRF3 rs132531 had significantly shorter overall survival compared to any T allele carriers (mOS: 20.3 vs 52 mo) in both univariable (HR 3.61, 95% CI 1.65-7.88, P < .001) and multivariable analysis (adjusted P = .01). Conversely, RSPO1 rs4652964 any G allele carriers showed increased tumor response (TR) rates compared to the A/A genotype (83 vs 66 %, P = .04). These associations were not observed in bev arm. Lower gene expression levels of RNF43 were associated with shorter PFS in pts with right-sided tumors receiving FOLFIRI/cet ( P = .006, Q < 0.1). RSPO1 expression levels were also associated with TR in the same subgroup (70 vs 10% in high vs low; P = .001, Q < .05). RNF43 expression was associated with TR in pts with left-sided tumors (82% in high vs 58% in low, P = .014, Q = 0.1). Conclusions: Our results provide the first evidence that germline polymorphisms and tumor gene expression levels of RNF43/ ZNRF3 and RSPO1 may have a predictive value in mCRC pts receiving first-line cetuximab-based treatment and contribute to modulate anti-EGFRs activity.

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Hepatic gene expression profiling of 5′-AMP-induced hypometabolism in mice

Physiological Genomics ◽

10.1152/physiolgenomics.00174.2010 ◽

2011 ◽

Vol 43 (7) ◽

pp. 325-345 ◽

Cited By ~ 7

Author(s):

Zhaoyang Zhao ◽

Takao Miki ◽

Anita Van Oort-Jansen ◽

Tomoko Matsumoto ◽

David S. Loose ◽

...

Keyword(s):

Gene Expression ◽

Adenosine Monophosphate ◽

Clinical Applications ◽

Hepatic Gene Expression ◽

Expression Levels ◽

Altered Gene Expression ◽

Hypometabolic State ◽

Altered Gene ◽

The Impact ◽

Gene Expression Levels

There is currently much interest in clinical applications of therapeutic hypothermia. Hypothermia can be a consequence of hypometabolism. We have recently established a procedure for the induction of a reversible deep hypometabolic state in mice using 5′-adenosine monophosphate (5′-AMP) in conjunction with moderate ambient temperature. The current study aims at investigating the impact of this technology at the gene expression level in a major metabolic organ, the liver. Our findings reveal that expression levels of the majority of genes in liver are not significantly altered by deep hypometabolism. However, among those affected by hypometabolism, more genes are differentially upregulated than downregulated both in a deep hypometabolic state and in the early arousal state. These altered gene expression levels during 5′-AMP induced hypometabolism are largely restored to normal levels within 2 days of the treatment. Our data also suggest that temporal control of circadian genes is largely stalled during deep hypometabolism.

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The impact of prolonged cold preservation on the graft function and gene expression levels in an experimental lung transplantation model

Surgery Today ◽

10.1007/s00595-012-0234-5 ◽

2012 ◽

Vol 43 (1) ◽

pp. 81-87

Author(s):

Osamu Yoshida ◽

Masaomi Yamane ◽

Sumiharu Yamamoto ◽

Mikio Okazaki ◽

Shinichi Toyooka ◽

...

Keyword(s):

Gene Expression ◽

Lung Transplantation ◽

Graft Function ◽

Cold Preservation ◽

Expression Levels ◽

The Impact ◽

Transplantation Model ◽

Gene Expression Levels

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Impact of RNA degradation on measurements of gene expression

10.1101/002261 ◽

2014 ◽

Cited By ~ 1

Author(s):

Irene Gallego Romero ◽

Athma A. Pai ◽

Jenny Tung ◽

Yoav Gilad

Keyword(s):

Gene Expression ◽

Expression Profiling ◽

Rna Extraction ◽

Rna Degradation ◽

Significant Loss ◽

Whole Genome ◽

Expression Levels ◽

Rna Quality ◽

The Impact ◽

Gene Expression Levels

The use of low quality RNA samples in whole-genome gene expression profiling remains controversial. It is unclear if transcript degradation in low quality RNA samples occurs uniformly, in which case the effects of degradation can be normalized, or whether different transcripts are degraded at different rates, potentially biasing measurements of expression levels. This concern has rendered the use of low quality RNA samples in whole-genome expression profiling problematic. Yet, low quality samples are at times the sole means of addressing specific questions e.g., samples collected in the course of fieldwork. We sought to quantify the impact of variation in RNA quality on estimates of gene expression levels based on RNA-seq data. To do so, we collected expression data from tissue samples that were allowed to decay for varying amounts of time prior to RNA extraction. The RNA samples we collected spanned the entire range of RNA Integrity Number (RIN) values (a quality metric commonly used to assess RNA quality). We observed widespread effects of RNA quality on measurements of gene expression levels, as well as a slight but significant loss of library complexity in more degraded samples. While standard normalizations failed to account for the effects of degradation, we found that a simple linear model that controls for the effects of RIN can correct for the majority of these effects. We conclude that in instances where RIN and the effect of interest are not associated, this approach can help recover biologically meaningful signals in data from degraded RNA samples.

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