scholarly journals Aberrant Whole Blood Gene Expression in the Lumen of Human Intracranial Aneurysms

Diagnostics ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1442
Author(s):  
Vincent M. Tutino ◽  
Yongjun Lu ◽  
Daizo Ishii ◽  
Kerry E. Poppenberg ◽  
Hamidreza Rajabzadeh-Oghaz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Whole Blood ◽  
Quantitative Polymerase Chain Reaction ◽  
Expression Patterns ◽  
Transcriptome Profiling ◽  
Circulating Biomarkers ◽  
Post Contrast ◽  
Blood Gene Expression ◽  
Transcriptional Changes ◽  
Polymerase Chain

The rupture of an intracranial aneurysm (IA) causes devastating hemorrhagic strokes. Yet, most IAs remain asymptomatic and undetected until they rupture. In the search for circulating biomarkers of unruptured IAs, we previously performed transcriptome profiling on whole blood and identified an IA-associated panel of 18 genes. In this study, we seek to determine if these genes are also differentially expressed within the IA lumen, which could provide a mechanistic link between the disease and the observed circulating gene expression patterns. To this end, we collected blood from the lumen of 37 IAs and their proximal parent vessels in 31 patients. The expression levels of 18 genes in the lumen and proximal vessel were then measured by quantitative polymerase chain reaction. This analysis revealed that the expression of 6/18 genes (CBWD6, MT2A, MZT2B, PIM3, SLC37A3, and TNFRSF4) was significantly higher in intraluminal blood, while the expression of 3/18 genes (ST6GALNAC1, TCN2, and UFSP1) was significantly lower. There was a significant, positive correlation between intraluminal and proximal expression of CXCL10, MT2A, and MZT2B, suggesting local increases of these genes is reflected in the periphery. Expression of ST6GALNAC1 and TIFAB was significantly positively correlated with IA size, while expression of CCDC85B was significantly positively correlated with IA enhancement on post-contrast MRI, a metric of IA instability and risk. In conclusion, intraluminal expression differences in half of the IA-associated genes observed in this study provide evidence for IA tissue-mediated transcriptional changes in whole blood. Additionally, some genes may be informative in assessing IA risk, as their intraluminal expression was correlated to IA size and aneurysmal wall enhancement.

scholarly journals Biosensor of inflammation biomarkers based on electrical bioimpedance analysis on immobilized DNA without chemical modification

2020 ◽  
Vol 11 (1) ◽  
pp. 31-37
Author(s):  
Modesto Gómez-López ◽  
Ángel Miliar-García ◽  
Nadia Mabel Pérez-Vielma ◽  
Eleazar Lara-Padilla ◽  
César Antonio González-Díaz
Keyword(s):  
Gene Expression ◽  
Dna Sequences ◽  
Deoxyribonucleic Acid ◽  
Quantitative Polymerase Chain Reaction ◽  
Expression Patterns ◽  
New Techniques ◽  
Detection Techniques ◽  
Electrical Bioimpedance ◽  
Polymerase Chain ◽  
Inexpensive Technique

AbstractThe development of biosensors to identify molecular markers or specific genes is fundamental for the implementation of new techniques that allow the detection of specific Deoxyribonucleic acid (DNA) sequences in a fast, economic and simple way. Different detection techniques have been proposed in the development of biosensors. Electrical Bioimpedance Spectroscopy (EBiS) has been used for diagnosis and monitoring of human pathologies, and is recognized as a safe, fast, reusable, easy and inexpensive technique. This study proves the development of a complementary DNA (cDNA) biosensor based on measurements of EBiS and DNA's immobilization with no chemical modifications. The evaluation of its potential utility in the detection of the gene expression of three inflammation characteristic biomarkers (NLRP3, IL-1β and Caspase 1) is presented. The obtained results demonstrate that EBiS can be used to identify different gene expression patterns, measurements that were validated by Quantitative Polymerase Chain Reaction (qPCR). These results indicate the technical feasibility for a biosensor of specific genes through bioimpedance measurements on the immobilization of cDNA.

Microarray Assay Reveals Ciliary Abnormalities of the Allergic Nasal Mucosa

2019 ◽  
Vol 34 (1) ◽  
pp. 50-58 ◽  
Author(s):  
Yang Peng ◽  
Wei-jie Guan ◽  
Zhen-chao Zhu ◽  
Kai Sen Tan ◽  
Zhuo Chen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Polymerase Chain Reaction ◽  
Nasal Mucosa ◽  
Quantitative Polymerase Chain Reaction ◽  
Expression Patterns ◽  
Paraffin Section ◽  
Related Gene ◽  
Chain Reaction ◽  
Control Subjects ◽  
Polymerase Chain

Background Gene expression patterns (particularly, cilia-associated genes) of nasal mucosa, the first-line defense system, in allergic rhinitis (AR) are not well understood. Objective We sought to screen for AR-associated genes in inferior turbinate (IT) from patients with AR, and to validate the expression of common cilia-related genes and ciliary shedding. Methods Prime View™ Human Gene Expression Array, which consisted of more than 530 000 probes covering more than 36 000 transcripts and variants, was employed to compare individual gene expression of ITs from control subjects (n = 11) and patients with AR (n = 19). Gene ontology (GO) analysis was performed with Cytoscape software. Eight of the common cilia-related genes were validated with quantitative polymerase chain reaction. We applied a semiquantitative scoring system for immunofluorescence assay to demonstrate ciliary shedding in 5 areas per paraffin section, with individual sections being scored between 0 (normal ciliary distribution) and 1 (ciliary shedding). Results Compared with control subjects, 160 (38 upregulated and 122 downregulated) genes were differentially expressed for at least 2 folds (all P < .05) in AR. Seven GO categories were significantly enriched, 4 of which were related to cilium assembly and motility. Quantitative polymerase chain reaction validated the predicted direction of change for common cilia-related gene expression. The ciliary distribution score was significantly higher (more prominent ciliary shedding) in AR than in controls ( P < .05). Conclusion The significant aberrant cilia-related gene expression, revealed by microarray assays, might be the critical driver of AR where ciliary shedding is prominent.

scholarly journals A novel whole blood gene expression signature for asthma, dermatitis, and rhinitis multimorbidity in children and adolescents

Allergy ◽  
2020 ◽  
Vol 75 (12) ◽  
pp. 3248-3260 ◽  
Author(s):  
Nathanaël Lemonnier ◽  
Erik Melén ◽  
Yale Jiang ◽  
Stéphane Joly ◽  
Camille Ménard ◽  
...  
Keyword(s):  
Gene Expression ◽  
Children And Adolescents ◽  
Whole Blood ◽  
Gene Expression Signature ◽  
Blood Gene Expression ◽  
Expression Signature

scholarly journals Epigenome-wide association study of whole blood gene expression in Framingham Heart Study participants provides molecular insight into the potential role of CHRNA5 in cigarette smoking-related lung diseases

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Chen Yao ◽  
Roby Joehanes ◽  
Rory Wilson ◽  
Toshiko Tanaka ◽  
Luigi Ferrucci ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Dna Methylation ◽  
Cigarette Smoking ◽  
Association Study ◽  
Whole Blood ◽  
Lung Diseases ◽  
Epigenetic Modification ◽  
Blood Gene Expression ◽  
Increased Risk

Abstract Background DNA methylation is a key epigenetic modification that can directly affect gene regulation. DNA methylation is highly influenced by environmental factors such as cigarette smoking, which is causally related to chronic obstructive pulmonary disease (COPD) and lung cancer. To date, there have been few large-scale, combined analyses of DNA methylation and gene expression and their interrelations with lung diseases. Results We performed an epigenome-wide association study of whole blood gene expression in ~ 6000 individuals from four cohorts. We discovered and replicated numerous CpGs associated with the expression of cis genes within 500 kb of each CpG, with 148 to 1,741 cis CpG-transcript pairs identified across cohorts. We found that the closer a CpG resided to a transcription start site, the larger its effect size, and that 36% of cis CpG-transcript pairs share the same causal genetic variant. Mendelian randomization analyses revealed that hypomethylation and lower expression of CHRNA5, which encodes a smoking-related nicotinic receptor, are causally linked to increased risk of COPD and lung cancer. This putatively causal relationship was further validated in lung tissue data. Conclusions Our results provide a large and comprehensive association study of whole blood DNA methylation with gene expression. Expression platform differences rather than population differences are critical to the replication of cis CpG-transcript pairs. The low reproducibility of trans CpG-transcript pairs suggests that DNA methylation regulates nearby rather than remote gene expression. The putatively causal roles of methylation and expression of CHRNA5 in relation to COPD and lung cancer provide evidence for a mechanistic link between patterns of smoking-related epigenetic variation and lung diseases, and highlight potential therapeutic targets for lung diseases and smoking cessation.

scholarly journals Whole blood gene expression within days after total-body irradiation predicts long term survival in Gottingen minipigs

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sunita Chopra ◽  
Maria Moroni ◽  
Jaleal Sanjak ◽  
Laurel MacMillan ◽  
Bernadette Hritzo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Total Body Irradiation ◽  
Whole Blood ◽  
Radiation Effects ◽  
Expression Profiles ◽  
Mass Casualty ◽  
Machine Learning Algorithms ◽  
Term Survival ◽  
Blood Gene Expression ◽  
Total Body

AbstractGottingen minipigs mirror the physiological radiation response observed in humans and hence make an ideal candidate model for studying radiation biodosimetry for both limited-sized and mass casualty incidents. We examined the whole blood gene expression profiles starting one day after total-body irradiation with increasing doses of gamma-rays. The minipigs were monitored for up to 45 days or time to euthanasia necessitated by radiation effects. We successfully identified dose- and time-agnostic (over a 1–7 day period after radiation), survival-predictive gene expression signatures derived using machine-learning algorithms with high sensitivity and specificity. These survival-predictive signatures fare better than an optimally performing dose-differentiating signature or blood cellular profiles. These findings suggest that prediction of survival is a much more useful parameter for making triage, resource-utilization and treatment decisions in a resource-constrained environment compared to predictions of total dose received. It should hopefully be possible to build such classifiers for humans in the future.

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 Characterization of microglial transcriptomes in the brain and spinal cord of mice in early and late experimental autoimmune encephalomyelitis using a RiboTag strategy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shaona Acharjee ◽  
Paul M. K. Gordon ◽  
Benjamin H. Lee ◽  
Justin Read ◽  
Matthew L. Workentine ◽  
...  
Keyword(s):  
Gene Expression ◽  
Spinal Cord ◽  
Experimental Autoimmune Encephalomyelitis ◽  
Expression Patterns ◽  
Immune Functions ◽  
Autoimmune Encephalomyelitis ◽  
Transcriptional Changes ◽  
Brain And Spinal Cord ◽  
The Brain ◽  
Experimental Autoimmune

AbstractMicroglia play an important role in the pathogenesis of multiple sclerosis and the mouse model of MS, experimental autoimmune encephalomyelitis (EAE). To more fully understand the role of microglia in EAE we characterized microglial transcriptomes before the onset of motor symptoms (pre-onset) and during symptomatic EAE. We compared the transcriptome in brain, where behavioral changes are initiated, and spinal cord, where damage is revealed as motor and sensory deficits. We used a RiboTag strategy to characterize ribosome-bound mRNA only in microglia without incurring possible transcriptional changes after cell isolation. Brain and spinal cord samples clustered separately at both stages of EAE, indicating regional heterogeneity. Differences in gene expression were observed in the brain and spinal cord of pre-onset and symptomatic animals with most profound effects in the spinal cord of symptomatic animals. Canonical pathway analysis revealed changes in neuroinflammatory pathways, immune functions and enhanced cell division in both pre-onset and symptomatic brain and spinal cord. We also observed a continuum of many pathways at pre-onset stage that continue into the symptomatic stage of EAE. Our results provide additional evidence of regional and temporal heterogeneity in microglial gene expression patterns that may help in understanding mechanisms underlying various symptomology in MS.

scholarly journals Analysis of Transcriptional Changes in Different Brassica napus Synthetic Allopolyploids

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 82
Author(s):  
Yunxiao Wei ◽  
Guoliang Li ◽  
Shujiang Zhang ◽  
Shifan Zhang ◽  
Hui Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Napus ◽  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Female Parent ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Transcriptional Changes ◽  
Aa Genome ◽  
High Degree

Allopolyploidy is an evolutionary and mechanistically intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the gene expression patterns of eight F2 synthetic Brassica napus using RNA sequencing. We found that B. napus allopolyploid formation was accompanied by extensive changes in gene expression. A comparison between F2 and the parent shows a certain proportion of differentially expressed genes (DEG) and activation\silent gene, and the two genomes (female parent (AA)\male parent (CC) genomes) showed significant differences in response to whole-genome duplication (WGD); non-additively expressed genes represented a small portion, while Gene Ontology (GO) enrichment analysis showed that it played an important role in responding to WGD. Besides, genome-wide expression level dominance (ELD) was biased toward the AA genome, and the parental expression pattern of most genes showed a high degree of conservation. Moreover, gene expression showed differences among eight individuals and was consistent with the results of a cluster analysis of traits. Furthermore, the differential expression of waxy synthetic pathways and flowering pathway genes could explain the performance of traits. Collectively, gene expression of the newly formed allopolyploid changed dramatically, and this was different among the selfing offspring, which could be a prominent cause of the trait separation. Our data provide novel insights into the relationship between the expression of differentially expressed genes and trait segregation and provide clues into the evolution of allopolyploids.

scholarly journals Combined Metabolome and Transcriptome Profiling Reveal Optimal Harvest Strategy Model Based on Different Production Purposes in Olive

Foods ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 360
Author(s):  
Guodong Rao ◽  
Jianguo Zhang ◽  
Xiaoxia Liu ◽  
Xue Li ◽  
Chenhe Wang
Keyword(s):  
Gene Expression ◽  
Olive Oil ◽  
Expression Patterns ◽  
Transcriptome Profiling ◽  
Minor Components ◽  
Harvest Time ◽  
Rna Seq ◽  
Optimal Harvest ◽  
Harvest Strategy ◽  
Different Color

Olive oil has been favored as high-quality edible oil because it contains balanced fatty acids (FAs) and high levels of minor components. The contents of FAs and minor components are variable in olive fruits of different color at harvest time, which render it difficult to determine the optimal harvest strategy for olive oil producing. Here, we combined metabolome, Pacbio Iso-seq, and Illumina RNA-seq transcriptome to investigate the association between metabolites and gene expression of olive fruits at harvest time. A total of 34 FAs, 12 minor components, and 181 other metabolites (including organic acids, polyols, amino acids, and sugars) were identified in this study. Moreover, we proposed optimal olive harvesting strategy models based on different production purposes. In addition, we used the combined Pacbio Iso-seq and Illumina RNA-seq gene expression data to identify genes related to the biosynthetic pathways of hydroxytyrosol and oleuropein. These data lay the foundation for future investigations of olive fruit metabolism and gene expression patterns, and provide a method to obtain olive harvesting strategies for different production purposes.

Sign in / Sign up

Export Citation Format

Share Document