Gene Expression of PSORI-CM01 and Yinxieling in the Treatment of Psoriasis Vulgaris

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Yue Lu ◽  
Yao Qi ◽  
Li Li ◽  
Yuhong Yan ◽  
Danni Yao ◽  
...  

Background. This study aimed to explore the mechanisms of action of the PSORI-CM01 and Yinxieling formulas in the treatment of patients with psoriasis vulgaris by analyzing gene expression in peripheral blood mononuclear cells (PBMCs). Methods. PBMC samples were collected from 21 patients before and after treatment. The study included nine patients in the PSORI-CM01 treatment group, 12 patients in the Yinxieling treatment group, and nine patients in the healthy control group. Gene expression levels in PBMCs were determined using the Affymetrix gene chip technology. Results. In the PSORI-CM01 group before and after treatment, a total of 668 differentially expressed genes were found, of which 445 were upregulated and 223 were downregulated. Before and after Yinxieling treatment, 657 differentially expressed genes were found, of which 168 were upregulated and 489 were downregulated. Venn analysis showed that 78 genes were not differentially expressed in the PSORI-CM01 group and 74 were not differentially expressed in the Yinxieling group compared with those in the controls. Among these genes, 72 genes were common to both groups, which were the genes on which the two drugs acted jointly. The results of KEGG analysis and Venn analysis on the signalling pathways of drug action in treatment groups showed that haemostasis and pathways involving Rho GTPases were common signalling pathways of drug action in the two groups. Conclusions. By a comparative analysis of the treatment groups, we found that both drugs have a positive effect on patients with psoriasis vulgaris, primarily by regulating the pathways related to platelet activation, aggregation, and blood coagulation. Trial registration: ChiCTR, ChiCTR-TRC-14005185, Registered 8 August 2014, http://www.chictr.org.cn/showproj.aspx?proj=4390

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 1255-1255
Author(s):  
Reena Das ◽  
Aggarwal Anu ◽  
Manu Jamwal ◽  
Prashant Sharma ◽  
Man Updesh Singh Sachdeva ◽  
...  

Abstract Introduction Global transcriptome analysis of circulating reticulocytes using microarrays is challenging due to the high abundance of globin transcripts. In order to accurately measure the transcriptome in reticulocytes, we planned to study the reticulocytes transcriptome profile before and after globin depletion. Patients with Hereditary Spherocytosis (HS) were recruited because of high reticulocytosis and also there was no global trancriptome profile available for the disease to the best of our knowledge. Methods Reticulocytes were purified by passing EDTA anticoagulated red cell suspensions through a column of microcrystalline cellulose and α-cellulose mixture. The extraction of total RNA was done fresh prior to microarray analysis using TRIzol reagent (Invitrogen) and RNeasy columns as per manufacturer's instruction. The globin transcripts were depleted with starting quantity of 3 µg of total RNA.using GLOBINclearTMHuman kit (Ambion, Austin, TX). RNA quality were assessed before and after depletion using Agilent Technologies 2100 Bioanalyzer in each sample used for the study. The Agilent Low Input Quick Amp Labelling kit was used to generate cRNA with a sample input of 200 ng total RNA in single-color microarray analysis (SurePrint G3 Human Gene Expression v3 8x60K Microarray, G4858A- 072363). cRNA was hybridized for 17 hours at 65˚C. After thorough washing, the results were extracted with Feature Extraction Project software and analysed using GeneSpring v13.0. For this study, differentially expressed genes were identified according to the criteria: t-test unpaired p (Corr) cut-off = 0.05 and fold-change cut-off of 2.0. These differentially expressed genes were imported in PANTHER (Protein Analysis Through Evolutionary Relationships) classification system to classify the genes. Results Transcriptome profiling of reticulocyte RNA from HS patients revealed 5318 annotated transcripts and 2744 lnc-RNA/uncharacterized transcripts to be differentially regulated before globin depletion. After globin depletion increase (8196 annotated transcripts and 4292 lnc-RNA) in the number of differentially regulated genes were observed. An increase of 54% and 56% was seen in annotated transcripts and noncoding transcripts respectively after globin depletion. This increased coverage may be attributed to the removal of the globin transcript. Gene Ontology analysis for molecular function, biological process, cellular component and protein class did not reveal any difference in the percentage of the category, though the number of transcripts was more after depletion. There were approximately 7% more pathways in the globin transcript depleted samples. Namely, 2-arachidonoylglycerol biosynthesis, biotin biosynthesis, carnitine metabolism, cobalamin biosynthesis, coenzyme a linked carnitine metabolism, cysteine biosynthesis, flavin biosynthesis, phenylalanine biosynthesis, sulfate assimilation, tyrosine biosynthesis pathways, etc. were elucidated only after globin depletion. Conclusions The globin transcript reduction followed by microarray analysis represents a robust methodology for studying pathophysiology of hematologic diseases which are not related to globin chain disorders. Furthermore we describe the global transcriptome profile of HS for the first time. Globin transcript depletion elucidates the better number of the transcripts and eventually the pathways which may have been earlier masked under the abundance of globin mRNAs. Pathway analysis and validation experiments are required to explain the role of these differentially expressed genes in the pathophysiology of HS. Disclosures No relevant conflicts of interest to declare.


2021 ◽  
Author(s):  
Urja A Parekh ◽  
Mohit Mazumder ◽  
Harpreet Kaur ◽  
Elia Brodsky

Glioblastoma multiforme (GBM) is a heterogeneous, invasive primary brain tumor that develops chemoresistance post therapy. Theories regarding the aetiology of GBM focus on transformation of normal neural stem cells (NSCs) to a cancerous phenotype or tumorigenesis driven via glioma stem cells (GSCs). Comparative RNA-Seq analysis of GSCs and NSCs can provide a better understanding of the origin of GBM. Thus, in the current study, we performed various bioinformatics analyses on transcriptional profiles of a total 40 RNA-seq samples including 20 NSC and 20 GSC, that were obtained from the NCBI-SRA (SRP200400). First, differential gene expression (DGE) analysis using DESeq2 revealed 358 significantly differentially expressed genes between GSCs and NSCs (padj. value <0.05, log2fold change ±3) with 192 upregulated and 156 downregulated genes in GSCs in comparison to NSCs. Subsequently, exploratory data analysis using the principal component analysis (PCA) based on key significant genes depicted the clear separation between both the groups. Further, the Hierarchical clustering confirmed the distinct clusters of GSC and NSC samples. Eventually, the biological enrichment analysis of the significant genes showed their enrichment in tumorigenesis pathways such as Wnt-signalling, VEGF-signalling and TGF-β-signalling pathways. Conclusively, our study depicted significant differences in the gene expression patterns between NSCs and GSCs. Besides, we also identified novel genes and genes previously unassociated with gliomagenesis that may prove to be valuable in establishing diagnostic, prognostic biomarkers and therapeutic targets for GBM.


2016 ◽  
Vol 8 (1) ◽  
pp. 17-32
Author(s):  
Marjorie Maharaj ◽  

You are here: Home › Differential Gene Expression after Emotional Freedom Techniques (EFT) Treatment: A Novel Pilot Protocol for Salivary mRNA Assessment doi 10.9769/EPJ.2016.8.1.MM Marjorie E. Maharaj, Department of Applied Psychology, Akamai University, Hilo, HI Abstract: Biopsychology is a rapidly expanding field of study since the completion of the Human Genome Project in 2003. There is little data measuring the effect of psychotherapeutic interventions on gene expression, due to the technical, logistical, and financial requirements of analysis. Being able to measure easily the effects of therapeutic experiences can validate the benefits of intervention. In order to test the feasibility of gene expression testing in a private practice setting, this study compared messenger ribonucleic acid (mRNA) and gene expression before and after psychotherapy and a control condition. With four non-clinical adult participants, it piloted a novel methodology using saliva stored at room temperature. A preliminary test of the interleukin- 8 (IL8) gene in both blood and saliva was performed in order to determine equivalency in the two biofluids; convergent validity was found. Following saliva test validation, a broad, genome-wide analysis was performed to detect differential gene expression in samples collected before and after treatment with Emotional Freedom Techniques (EFT), an evidence-based practice combining acupressure and cognitive exposure. The control treatment was non-therapeutic social interaction. To establish a baseline, participants received the control first, followed a week later by EFT. Analysis of samples was performed at three time points: immediately before treatment, immediately after, and 24 hours later. Differential expression between EFT and control was found in numerous genes implicated in overall health (p < 0.05). Further, the differentially expressed genes in this study were shown to be linked to immunity, pro or anti-inflammatory, as well as neuronal processes in the brain. Ten of the 72 differentially expressed genes are identified as promising targets for downstream research. The data show promise for the future use of salivary samples to determine the effects of therapy; this pilot protocol also illustrated the challenges and limitations of novel technologies employed in biopsychology. Keywords: epigenetics, DNA, mRNA, gene expression, protein synthesis, brain plasticity, neurogenesis, biopsychology


2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Alassane Thiam ◽  
Michel Sanka ◽  
Rokhaya Ndiaye Diallo ◽  
Magali Torres ◽  
Babacar Mbengue ◽  
...  

Abstract Background Plasmodium falciparum malaria remains a major health problem in Africa. The mechanisms of pathogenesis are not fully understood. Transcriptomic studies may provide new insights into molecular pathways involved in the severe form of the disease. Methods Blood transcriptional levels were assessed in patients with cerebral malaria, non-cerebral malaria, or mild malaria by using microarray technology to look for gene expression profiles associated with clinical status. Multi-way ANOVA was used to extract differentially expressed genes. Network and pathways analyses were used to detect enrichment for biological pathways. Results We identified a set of 443 genes that were differentially expressed in the three patient groups after applying a false discovery rate of 10%. Since the cerebral patients displayed a particular transcriptional pattern, we focused our analysis on the differences between cerebral malaria patients and mild malaria patients. We further found 842 differentially expressed genes after applying a false discovery rate of 10%. Unsupervised hierarchical clustering of cerebral malaria-informative genes led to clustering of the cerebral malaria patients. The support vector machine method allowed us to correctly classify five out of six cerebral malaria patients and six of six mild malaria patients. Furthermore, the products of the differentially expressed genes were mapped onto a human protein-protein network. This led to the identification of the proteins with the highest number of interactions, including GSK3B, RELA, and APP. The enrichment analysis of the gene functional annotation indicates that genes involved in immune signalling pathways play a role in the occurrence of cerebral malaria. These include BCR-, TCR-, TLR-, cytokine-, FcεRI-, and FCGR- signalling pathways and natural killer cell cytotoxicity pathways, which are involved in the activation of immune cells. In addition, our results revealed an enrichment of genes involved in Alzheimer’s disease. Conclusions In the present study, we examine a set of genes whose expression differed in cerebral malaria patients and mild malaria patients. Moreover, our results provide new insights into the potential effect of the dysregulation of gene expression in immune pathways. Host genetic variation may partly explain such alteration of gene expression. Further studies are required to investigate this in African populations.


2016 ◽  
Vol 24 (3) ◽  
pp. 223
Author(s):  
L. Liu ◽  
B. Li ◽  
Y.L. Zhu ◽  
C.Y. Wang ◽  
F.C. Li

<p>This study investigated the mechanisms controlling hair follicle development in the Rex rabbit. The Agilent rabbit gene expression microarray was used to determine differentially expressed genes in Rex rabbit foetuses with different wool densities. The expression patterns of selected differentially-expressed genes were further investigated by quantitative real-time PCR. Compared to low wool density rabbits, 1342 differentially expressed probes were identified in high wool density rabbits, including 950 upregulated probes and 392 downregulated probes. Gene ontology analysis revealed that the most upregulated differentially expressed probes belonged to receptors and the most downregulated differentially expressed probes belonged to DNA binding molecules. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the differentially expressed probes were mainly involved in the sonic hedgehog (Shh) and Eph signalling pathways. The results also suggest that transforming growth factor-beta 1, growth hormone receptor, and the keratin-associated protein 6.1 genes, as well as the Shh and Eph signalling pathways, may be involved in the regulation of hair follicle developmental in Rex rabbits.</p>


2009 ◽  
Vol 19 (4) ◽  
pp. 352-359 ◽  
Author(s):  
Peter P. Mueller ◽  
Andreas Drynda ◽  
Diane Goltz ◽  
René Hoehn ◽  
Hansjörg Hauser ◽  
...  

AbstractThe detailed molecular processes associated with postnatal remodelling of blood vessels are presently not understood. To characterize the response of the patients undergoing stenting of the patent arterial duct, we harvested samples of vascular tissue during surgical repair. Histological analysis of explanted ducts confirmed the patency of the ducts immediately after birth. As expected, a previously unstented duct that was examined 7 months after birth had become closed and ligamentous. Whole genome expression profiling of these samples showed that a large fraction, over 10%, of the gene sequences examined were expressed differentially between the samples taken from patients with open as opposed to the ligamentous duct. Interestingly, in 2 patients in whom closure was prevented by insertion of stents, one showed an expression profile that was similar to that of the patient initially having an unstented open duct, whereas the other was more closely related to the profile of the patient with a duct that had become ligamentous. Moreover, in 2 specimens obtained from patients with stented pulmonary arteries, a large fraction of the genes that were differentially expressed were identical to the pattern seen in the samples from the patients with open ducts. The gene regulation appeared to be independent of the nature of the respective malformations, and the site of implantation of the stents. These findings suggest that a set of differentially expressed genes are indicative for a transcriptional programme in neonatal remodelling of the arterial duct, which may also take place in patients in whom ductal closure is prevented by stents, or in those with stented pulmonary arteries. The differentially expressed genes included a significant number of extracellular matrix synthetic genes, and could therefore be predictive for vascular remodelling and neointimal formation.


2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Rasmita Rani Das ◽  
Seema Pradhan ◽  
Ajay Parida

AbstractScreening the transcriptome of drought tolerant variety of little millet (Panicum sumatrense), a marginally cultivated, nutritionally rich, susbsistent crop, can identify genes responsible for its hardiness and enable identification of new sources of genetic variation which can be used for crop improvement. RNA-Seq generated ~ 230 million reads from control and treated tissues, which were assembled into 86,614 unigenes. In silico differential gene expression analysis created an overview of patterns of gene expression during exposure to drought and salt stress. Separate gene expression profiles for leaf and root tissue revealed the differences in regulatory mechanisms operating in these tissues during exposure to abiotic stress. Several transcription factors were identified and studied for differential expression. 61 differentially expressed genes were found to be common to both tissues under drought and salinity stress and were further validated using qRT-PCR. Transcriptome of P. sumatrense was also used to mine for genic SSR markers relevant to abiotic stress tolerance. This study is first report on a detailed analysis of molecular mechanisms of drought and salinity stress tolerance in a little millet variety. Resources generated in this study can be used as potential candidates for further characterization and to improve abiotic stress tolerance in food crops.


2013 ◽  
Vol 40 (12) ◽  
pp. 1249 ◽  
Author(s):  
Hai-fen Li ◽  
Xiao-Ping Chen ◽  
Fang-he Zhu ◽  
Hai-Yan Liu ◽  
Yan-Bin Hong ◽  
...  

Peanut (Arachis hypogaea L.) produces flowers aerially, but the fruit develops underground. This process is mediated by the gynophore, which always grows vertically downwards. The genetic basis underlying gravitropic bending of gynophores is not well understood. To identify genes related to gynophore gravitropism, gene expression profiles of gynophores cultured in vitro with tip pointing upward (gravitropic stimulation sample) and downward (control) at both 6 and 12 h were compared through a high-density peanut microarray. After gravitropic stimulation, there were 174 differentially expressed genes, including 91 upregulated and 83 downregulated genes at 6 h, and 491 differentially expressed genes including 129 upregulated and 362 downregulated genes at 12 h. The differentially expressed genes identified were assigned to 24 functional categories. Twenty pathways including carbon fixation, aminoacyl-tRNA biosynthesis, pentose phosphate pathway, starch and sucrose metabolism were identified. The quantitative real-time PCR analysis was performed for validation of microarray results. Our study paves the way to better understand the molecular mechanisms underlying the peanut gynophore gravitropism.


2019 ◽  
Vol 80 (04) ◽  
pp. 240-249
Author(s):  
Jiajia Wang ◽  
Jie Ma

Glioblastoma multiforme (GBM), an aggressive brain tumor, is characterized histologically by the presence of a necrotic center surrounded by so-called pseudopalisading cells. Pseudopalisading necrosis has long been used as a prognostic feature. However, the underlying molecular mechanism regulating the progression of GBMs remains unclear. We hypothesized that the gene expression profiles of individual cancers, specifically necrosis-related genes, would provide objective information that would allow for the creation of a prognostic index. Gene expression profiles of necrotic and nonnecrotic areas were obtained from the Ivy Glioblastoma Atlas Project (IVY GAP) database to explore the differentially expressed genes.A robust signature of seven genes was identified as a predictor for glioblastoma and low-grade glioma (GBM/LGG) in patients from The Cancer Genome Atlas (TCGA) cohort. This set of genes was able to stratify GBM/LGG and GBM patients into high-risk and low-risk groups in the training set as well as the validation set. The TCGA, Repository for Molecular Brain Neoplasia Data (Rembrandt), and GSE16011 databases were then used to validate the expression level of these seven genes in GBMs and LGGs. Finally, the differentially expressed genes (DEGs) in the high-risk and low-risk groups were subjected to gene ontology enrichment, Kyoto Encyclopedia of Genes and Genomes pathway, and gene set enrichment analyses, and they revealed that these DEGs were associated with immune and inflammatory responses. In conclusion, our study identified a novel seven-gene signature that may guide the prognostic prediction and development of therapeutic applications.


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