scholarly journals Profiling gene expression of the host response to a Plasmodium vivax irradiated sporozoite immunization and infectious challenge

2018 ◽  
Author(s):  
Monica C Rojas-Pena ◽  
Dalia C Arafat ◽  
Juan Manuel Velasquez ◽  
Swetha C Garimalla ◽  
Myriam Arevalo-Herrera ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plasmodium Vivax ◽  
Inflammatory Responses ◽  
Interferon Response ◽  
Global Public Health ◽  
T Cell Signaling ◽  
Blood Samples ◽  
Phase 2 Trial ◽  
Before And After ◽  
Differential Transcription

The development of vaccines that provide sterile protection against human malaria is a major global public health priority requiring a better understanding of the mechanisms involved in natural and vaccine-induced sterile immunity. RNAseq was used to profile gene expression of peripheral blood samples from 12 Duffy positive (Fy+) (Plasmodium vivax susceptible) volunteers enrolled in a phase 2 trial who were vaccinated with radiation attenuated P. vivax sporozoites (RAS; 5 were protected, 7 not) and from 5 Fy- (P. vivax resistant) volunteers exposed to mosquitoes harboring live non-attenuated sporozoites. Blood samples were obtained before and after immunization as well as after controlled infection with live P vivax sporozoites. The most profound changes in gene expression were observed between baseline and post-challenge, with 97 distinct signatures differentiating protected and not protected Fy+ individuals. Differentiation was also observed between Fy- and Fy+ protected individuals, notably with downregulation of multiple inflammatory responses as well as extracellular matrix-related gene activity. Analysis of transcriptional modules shows that both B-cell and T-cell signaling are reduced while cell cycle regulation, interferon response, and other informative signatures are elevated in individuals who are not protected against malaria. An asymptomatic individual had an intermediate profile indicative of differential transcription associated with pathology and symptomology. Systems biology thus provides insight into how whole malaria-attenuated sporozoites prime the immune system to protect against malaria, as well as the transcription responses that are associated with sterile protection.

scholarly journals Leukocyte Gene Expression in Patients with Medication Refractory Depression before and after Treatment with ECT or Isoflurane Anesthesia: A Pilot Study

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
E. Iacob ◽  
S. C. Tadler ◽  
K. C. Light ◽  
H. R. Weeks ◽  
K. W. Smith ◽  
...  
Keyword(s):  
Gene Expression ◽  
Healthy Controls ◽  
Open Label ◽  
Blood Samples ◽  
Refractory Depression ◽  
Isoflurane Anesthesia ◽  
Before And After ◽  
Open Label Trial ◽  
Underlying Mechanisms ◽  
Potential Biomarkers

Objective. To evaluate leukocyte gene expression for 9 selected genes (mRNAs) as biological markers in patients with medication refractory depression before and after treatment with ECT or isoflurane anesthesia (ISO).Methods. In a substudy of a nonrandomized open-label trial comparing effects of ECT to ISO therapy, blood samples were obtained before and after treatment from 22 patients with refractory depression, and leukocyte mRNA was assessed by quantitative PCR. Patients’ mRNAs were also compared to 17 healthy controls.Results. Relative to controls, patients before treatment showed significantly higher IL10 and DBI and lower ADRA2A and ASIC3 mRNA (P<0.025). Both ECT and ISO induced significant decreases after treatment in 4 genes: IL10, NR3C1, DRD4, and Sult1A1. After treatment, patients’ DBI, ASIC3, and ADRA2A mRNA remained dysregulated.Conclusion. Significant differences from controls and/or significant changes after ECT or ISO treatment were observed for 7 of the 9 mRNAs studied. Decreased expression of 4 genes after effective treatment with either ECT or ISO suggests possible overlap of underlying mechanisms. Three genes showing dysregulation before and after treatment may be trait-like biomarkers of medication refractory depression. Gene expression for these patients has the potential to facilitate diagnosis, clarify pathophysiology, and identify potential biomarkers for treatment effects.

scholarly journals Identification of biomarkers associated with clinical severity of chronic obstructive pulmonary disease

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10513
Author(s):  
Jie Zhang ◽  
Changli Zhu ◽  
Hong Gao ◽  
Xun Liang ◽  
Xiaoqian Fan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune Responses ◽  
Inflammatory Responses ◽  
Lymphocyte Activation ◽  
Stage I ◽  
Clinical Severity ◽  
Chronic Obstructive ◽  
Clinical Classification ◽  
Obstructive Pulmonary Disease ◽  
Blood Samples

We sought to identify the biomarkers related to the clinical severity of stage I to stage IV chronic obstructive pulmonary disease (COPD). Gene expression profiles from the blood samples of COPD patients at each of the four stages were acquired from the Gene Expression Omnibus Database (GEO, accession number: GSE54837). Genes showing expression changes among the different stages were sorted by soft clustering. We performed functional enrichment, protein–protein interaction (PPI), and miRNA regulatory network analyses for the differentially expressed genes. The biomarkers associated with the clinical classification of COPD were selected from logistic regression models and the relationships between TLR2 and inflammatory factors were verified in clinical blood samples by qPCR and ELISA. Gene clusters demonstrating continuously rising or falling changes in expression (clusters 1, 2, and 7 and clusters 5, 6, and 8, respectively) from stage I to IV were defined as upregulated and downregulated genes, respectively, and further analyzed. The upregulated genes were enriched in functions associated with defense, inflammatory, or immune responses. The downregulated genes were associated with lymphocyte activation and cell activation. TLR2, HMOX1, and CD79A were hub proteins in the integrated network of PPI and miRNA regulatory networks. TLR2 and CD79A were significantly correlated with clinical classifications. TLR2 was closely associated with inflammatory responses during COPD progression. Functions associated with inflammatory and immune responses as well as lymphocyte activation may play important roles in the progression of COPD from stage I to IV. TLR2 and CD79A may serve as potential biomarkers for the clinical severity of COPD. TLR2 and CD79A may also serve as independent biomarkers in the clinical classification in COPD. TLR2 may play an important role in the inflammatory responses of COPD.

Dietary Changes in Fasting Levels of Factor VII Coagulant Activity (FVII: C) Are Accompanied by Changes in Factor VII Protein and other Vitamin K-dependent Proteins

1995 ◽  
Vol 73 (02) ◽  
pp. 239-242 ◽  
Author(s):  
E M Bladbjerg ◽  
T Tholstrup ◽  
P Marckmann ◽  
B Sandström ◽  
J Jespersen
Keyword(s):  
Fatty Acids ◽  
Vitamin K ◽  
Protein C ◽  
Saturated Fatty Acids ◽  
Factor Vii ◽  
Dietary Regimen ◽  
Blood Samples ◽  
Dietary Changes ◽  
Coagulant Activity ◽  
Before And After

SummaryThe mechanisms behind dietary effects on fasting coagulant activity of factor VII (FVII: C) are not clarified. In the present study of 15 young volunteers, two experimental diets differing in composition of saturated fatty acids (C18:0 [diet S] or C12:0 + C14:0 [diet ML]) were served for 3 weeks each. Fasting blood samples were collected before and after the dietary regimen and analysed for triglycerides, FVII:C, and protein concentrations of FVII, FII, FX, protein C, CRP, albumin, fibrinogen, and F1+2. FVII:C was significantly reduced on diet S compared with diet ML. This was accompanied by a decrease in FVII protein, F1+2 and the vitamin K-dependent proteins FII, FX, and protein C. In contrast, no changes were observed in triglycerides, FVII:C/FVII: Ag, albumin and CRP. Fibrinogen was increased on diet S compared with diet ML. Our findings suggest that the change in fasting FVII:C was part of a general change in concentrations of vitamin K-dependent proteins.

ADRENAL 17-HYDROXYCORTICOSTEROID SECRETION IN THE DOG IN RESPONSE TO ETHANOL

1972 ◽  
Vol 70 (4) ◽  
pp. 736-740 ◽  
Author(s):  
T. Suzuki ◽  
R. Higashi ◽  
T. Hirose ◽  
H. Ikeda ◽  
K. Tamura
Keyword(s):  
Venous Blood ◽  
Secretion Rate ◽  
Conscious Dogs ◽  
Blood Samples ◽  
Before And After

ABSTRACT Conscious dogs were infused intravenously with ethanol in doses of 0.7 and 1.0 g/kg. The adrenal venous blood samples were collected before and after the infusion of ethanol and analysed for 17-hydroxycorticosteroids (17-OHCS). After the infusion of 0.7 g/kg (subanaesthetic dose) of ethanol the adrenal 17-OHCS secretion rate showed either a slight increase or no change. After the infusion of 1.0 g/kg (anaesthetic dose) of ethanol the adrenal 17-OHCS secretion rate increased markedly and reached 1.21±0.15 (mean±sem) μg/kg/min, while it was 0.09±0.023 μg/kg/min before the infusion.

scholarly journals Transcriptomic phases of periodontitis lesions using the nonhuman primate model

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jeffrey L. Ebersole ◽  
Radhakrishnan Nagarajan ◽  
Sreenatha Kirakodu ◽  
Octavio A. Gonzalez
Keyword(s):  
Gene Expression ◽  
Nonhuman Primate ◽  
Gingival Crevicular Fluid ◽  
Inflammatory Responses ◽  
Expression Profiles ◽  
Lesion Detection ◽  
Gingival Tissue ◽  
Specific Gene ◽  
Nonhuman Primate Model ◽  
Primate Model

AbstractWe used a nonhuman primate model of ligature-induced periodontitis to identify patterns of gingival transcriptomic after changes demarcating phases of periodontitis lesions (initiation, progression, resolution). A total of 18 adult Macaca mulatta (12–22 years) had ligatures placed (premolar, 1st molar teeth) in all 4 quadrants. Gingival tissue samples were obtained (baseline, 2 weeks, 1 and 3 months during periodontitis and at 5 months resolution). Gene expression was analyzed by microarray [Rhesus Gene 1.0 ST Array (Affymetrix)]. Compared to baseline, a large array of genes were significantly altered at initiation (n = 6049), early progression (n = 4893), and late progression (n = 5078) of disease, with the preponderance being up-regulated. Additionally, 1918 genes were altered in expression with disease resolution, skewed towards down-regulation. Assessment of the genes demonstrated specific profiles of epithelial, bone/connective tissue, apoptosis/autophagy, metabolism, regulatory, immune, and inflammatory responses that were related to health, stages of disease, and tissues with resolved lesions. Unique transcriptomic profiles occured during the kinetics of the periodontitis lesion exacerbation and remission. We delineated phase specific gene expression profiles of the disease lesion. Detection of these gene products in gingival crevicular fluid samples from human disease may contribute to a better understanding of the biological dynamics of the disease to improve patient management.

scholarly journals Modulation of the Tissue Expression Pattern of Zebrafish CRP-Like Molecules Suggests a Relevant Antiviral Role in Fish Skin

Biology ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 78
Author(s):  
Melissa Bello-Perez ◽  
Mikolaj Adamek ◽  
Julio Coll ◽  
Antonio Figueras ◽  
Beatriz Novoa ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bacterial Infections ◽  
Quantitative Polymerase Chain Reaction ◽  
Tissue Expression ◽  
Interferon Response ◽  
Fish Skin ◽  
Tissue Expression Pattern ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Antiviral Role

Recent studies suggest that short pentraxins in fish might serve as biomarkers for not only bacterial infections, as in higher vertebrates including humans, but also for viral ones. These fish orthologs of mammalian short pentraxins are currently attracting interest because of their newly discovered antiviral activity. In the present work, the modulation of the gene expression of all zebrafish short pentraxins (CRP-like proteins, CRP1-7) was extensively analyzed by quantitative polymerase chain reaction. Initially, the tissue distribution of crp1-7 transcripts and how the transcripts varied in response to a bath infection with the spring viremia of carp virus, were determined. The expression of crp1-7 was widely distributed and generally increased after infection (mostly at 5 days post infection), except for crp1 (downregulated). Interestingly, several crp transcription levels significantly increased in skin. Further assays in mutant zebrafish of recombinant activation gene 1 (rag1) showed that all crps (except for crp2, downregulated) were already constitutively highly expressed in skin from rag1 knockouts and only increased moderately after viral infection. Similar results were obtained for most mx isoforms (a reporter gene of the interferon response), suggesting a general overcompensation of the innate immunity in the absence of the adaptive one.

scholarly journals Challenges with Methods for Detecting and Studying the Transcription Factor Nuclear Factor Kappa B (NF-κB) in the Central Nervous System

Cells ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1335
Author(s):  
Marina Mostafizar ◽  
Claudia Cortes-Pérez ◽  
Wanda Snow ◽  
Jelena Djordjevic ◽  
Aida Adlimoghaddam ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Signaling Pathways ◽  
Quantitative Methods ◽  
Nuclear Factor Kappa B ◽  
Inflammatory Responses ◽  
Nuclear Factor ◽  
Nuclear Factor Kappa ◽  
Regulated Gene Expression ◽  
Transcription Factor Nuclear Factor

The transcription factor nuclear factor kappa B (NF-κB) is highly expressed in almost all types of cells. NF-κB is involved in many complex biological processes, in particular in immunity. The activation of the NF-κB signaling pathways is also associated with cancer, diabetes, neurological disorders and even memory. Hence, NF-κB is a central factor for understanding not only fundamental biological presence but also pathogenesis, and has been the subject of intense study in these contexts. Under healthy physiological conditions, the NF-κB pathway promotes synapse growth and synaptic plasticity in neurons, while in glia, NF-κB signaling can promote pro-inflammatory responses to injury. In addition, NF-κB promotes the maintenance and maturation of B cells regulating gene expression in a majority of diverse signaling pathways. Given this, the protein plays a predominant role in activating the mammalian immune system, where NF-κB-regulated gene expression targets processes of inflammation and host defense. Thus, an understanding of the methodological issues around its detection for localization, quantification, and mechanistic insights should have a broad interest across the molecular neuroscience community. In this review, we summarize the available methods for the proper detection and analysis of NF-κB among various brain tissues, cell types, and subcellular compartments, using both qualitative and quantitative methods. We also summarize the flexibility and performance of these experimental methods for the detection of the protein, accurate quantification in different samples, and the experimental challenges in this regard, as well as suggestions to overcome common challenges.

scholarly journals Correcting for experiment-specific variability in expression compendia can remove underlying signals

GigaScience ◽  
2020 ◽  
Vol 9 (11) ◽  
Author(s):  
Alexandra J Lee ◽  
YoSon Park ◽  
Georgia Doing ◽  
Deborah A Hogan ◽  
Casey S Greene
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Original Signal ◽  
Batch Effects ◽  
Technical Variability ◽  
The Past ◽  
Statistical Correction ◽  
Before And After ◽  
Data Collections ◽  
Biological Patterns

Abstract Motivation In the past two decades, scientists in different laboratories have assayed gene expression from millions of samples. These experiments can be combined into compendia and analyzed collectively to extract novel biological patterns. Technical variability, or "batch effects," may result from combining samples collected and processed at different times and in different settings. Such variability may distort our ability to extract true underlying biological patterns. As more integrative analysis methods arise and data collections get bigger, we must determine how technical variability affects our ability to detect desired patterns when many experiments are combined. Objective We sought to determine the extent to which an underlying signal was masked by technical variability by simulating compendia comprising data aggregated across multiple experiments. Method We developed a generative multi-layer neural network to simulate compendia of gene expression experiments from large-scale microbial and human datasets. We compared simulated compendia before and after introducing varying numbers of sources of undesired variability. Results The signal from a baseline compendium was obscured when the number of added sources of variability was small. Applying statistical correction methods rescued the underlying signal in these cases. However, as the number of sources of variability increased, it became easier to detect the original signal even without correction. In fact, statistical correction reduced our power to detect the underlying signal. Conclusion When combining a modest number of experiments, it is best to correct for experiment-specific noise. However, when many experiments are combined, statistical correction reduces our ability to extract underlying patterns.

scholarly journals Transcriptomic analysis identifies differences in gene expression in actinic keratoses after treatment with imiquimod and between responders and non responders

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Megan H. Trager ◽  
Emanuelle Rizk ◽  
Sharon Rose ◽  
Kuixi Zhu ◽  
Branden Lau ◽  
...  
Keyword(s):  
Gene Expression ◽  
Squamous Cell Carcinoma ◽  
Distinct Pattern ◽  
Study Endpoint ◽  
Inflammatory Gene Expression ◽  
Immune Modulators ◽  
Actinic Keratoses ◽  
Before And After ◽  
Pre Treatment

AbstractThe presence of actinic keratoses (AKs) increases a patient’s risk of developing squamous cell carcinoma by greater than six-fold. We evaluated the effect of topical treatment with imiquimod on the tumor microenvironment by measuring transcriptomic differences in AKs before and after treatment with imiquimod 3.75%. Biopsies were collected prospectively from 21 patients and examined histologically. RNA was extracted and transcriptomic analyses of 788 genes were performed using the nanoString assay. Imiquimod decreased number of AKs by study endpoint at week 14 (p < 0.0001). Post-imiquimod therapy, levels of CDK1, CXCL13, IL1B, GADPH, TTK, ILF3, EWSR1, BIRC5, PLAUR, ISG20, and C1QBP were significantly lower (adjusted p < 0.05). Complete responders (CR) exhibited a distinct pattern of inflammatory gene expression pre-treatment relative to incomplete responders (IR), with alterations in 15 inflammatory pathways (p < 0.05) reflecting differential expression of 103 genes (p < 0.05). Presence of adverse effects was associated with improved treatment response. Differences in gene expression were found between pre-treatment samples in CR versus IR, suggesting that higher levels of inflammation pre-treament may play a part in regression of AKs. Further characterization of the immune micro-environment in AKs may help develop biomarkers predictive of response to topical immune modulators and may guide therapy.

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