Abstract TP327: Major Inflammatory Pathways in Peripheral Blood Associate With Intracerebral Hemorrhage Volume in Human

Stroke ◽  
2020 ◽  
Vol 51 (Suppl_1) ◽  
Author(s):  
Marc Durocher ◽  
Bradley Ander ◽  
Alan Yee ◽  
Glen Jickling ◽  
Kwan Ng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Intracerebral Hemorrhage ◽  
Peripheral Blood ◽  
Critical Role ◽  
Therapeutic Targets ◽  
Fc Receptor ◽  
Whole Genome ◽  
Blood Draw ◽  
Inflammatory Pathways ◽  
Pathway Activation

Objectives: Intracerebral hemorrhage (ICH) volume is a major determinant of functional outcome. The peripheral immune system plays a critical role in post-ICH damage and repair. Identifying potential modulators of ICH volume may guide the search for therapeutic targets. We performed a whole genome expression study in peripheral blood to examine the immune response following ICH with respect to ICH volume. Methods: Whole-genome RNA expression from 18 ICH subjects (14M/4F) was assessed on Affymetrix HTA 2.0 microarrays. Volumetric measurements were conducted on CT images using AnalyzePro. Multiple Regression including ICH volume while accounting for time from ICH onset to blood draw and interval between scan time and blood draw, was performed. A partial correlation between gene expression and ICH volume was calculated, with FDR p<0.3 (nominal p<0.005) and Pearson Correlation coefficient r>|0.6| considered significant. Pathway analysis and activation/suppression prediction of over-represented pathways was performed (Benjamini-Hochberg p<0.05, pathway activation/suppression Z-score >|2|). Results: Gene expression levels of 281 genes, including coding (mRNA) and non-coding RNA (i.e. several miRNAs) were associated with ICH volume. Major pathways, such as Neuroinflammation Signaling, were predicted to be activated in subjects with larger ICH volumes. So were Inflammasome Pathway, Toll-like Receptor, Leukocyte Extravasation, NF-kB signaling and FC? Receptor-Mediated Phagocytosis – some of which have been associated with poor clinical outcomes. Scavenger mechanisms, such as FC? Receptor-Mediated Phagocytosis, have been implicated in hematoma resolution. Thrombin Signaling, involved in coagulation, was also activated in subjects with larger ICH volumes. Peroxisome Proliferator-Activated Receptor (PPAR) Signaling was predicted to be suppressed in subjects with larger ICH volumes. PPAR pathway activation may have a neuroprotective effect following experimental ICH. Conclusions: We provide human data on genes and pathways associated with ICH volume. The results reveal major inflammatory pathways associated with ICH volume, which may be therapeutic targets for human ICH.

scholarly journals Investigation of low-dose ritonavir on human peripheral blood mononuclear cells using gene expression whole genome microarrays

Genomics ◽  
2010 ◽  
Vol 96 (1) ◽  
pp. 57-65 ◽  
Author(s):  
Saliha Yilmaz ◽  
Marta Boffito ◽  
Sophie Collot-Teixeira ◽  
Ferruccio De Lorenzo ◽  
Laura Waters ◽  
...  
Keyword(s):  
Gene Expression ◽  
Peripheral Blood Mononuclear Cells ◽  
Peripheral Blood ◽  
Low Dose ◽  
Mononuclear Cells ◽  
Human Peripheral Blood ◽  
Whole Genome ◽  
Peripheral Blood Mononuclear ◽  
Blood Mononuclear Cells

Global Epigenomic Profiling Demonstrates That Myelodysplasia Is Characterized by a Distinct Epigenetic Signature with Aberrant DNA Methylation Changes Involving Various Malignant and Hematopoietic Pathways.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2436-2436
Author(s):  
L. Zhou ◽  
J. Opalinska ◽  
D. Sohal ◽  
R. Thompson ◽  
Y. Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Expression Analysis ◽  
Peripheral Blood ◽  
Gene Expression Analysis ◽  
Whole Genome ◽  
Gene Promoters ◽  
Global Methylation ◽  
Peripheral Blood Leucocyte ◽  
Peripheral Blood Leucocytes

Abstract Myelodysplasia (MDS) is a clonal hematopoietic disorder that leads to ineffective hematopoiesis and peripheral cytopenias. DNMT inhibitors such as azacytidine have led to clinical responses in patients, though the genes affected by epigenetic alterations are not well known. Whole genome DNA methylation was analyzed by a recently described novel method, The HELP assay (HpaII tiny fragment Enrichment by Ligation-mediated PCR; Khulan et al, Genome Res. 2006 Aug;16(8)) that uses differential methylation specific restriction digestion by HpaII and MspI followed by amplification, two color labeling and cohybridization to quantitatively determine individual promoter island methylation. A whole genome human promoter array (Nimblegen) was used to determine the level of methylation of 25626 gene promoters by calculating HpaII/MspI cut fragment intensity ratio. Peripheral blood leucocytes from 13 patients with MDS were compared to 9 age matched normal and anemic controls. Gene expression analysis was performed using 37K oligo maskless arrays on cDNA obtained from the same samples. Analysis showed that whole genome methylation profiling has greater discriminatory power in separating clusters of MDS samples from normal and anemic controls when compared to gene expression analysis. Unsupervised clustering based on epigenetic profiling demonstrated that only two cases of early MDS clustered with normals as compared to absolutely no separation between MDS and normals with clustering based on gene expression patterns. A high correlation (r=0.88–0.96) was observed between global methylation profiles of matched sets of bone marrow and peripheral blood leucocyte samples from selected patients demonstrating that peripheral blood leucocytes can be a valid surrogate for epigenomic analysis. Further analysis showed that genes consistently aberrantly methylated in MDS included Syk kinase, HOXB3, several histone acetyltranferases and others. Functional analysis by Ingenuity showed that cancer and cell signaling pathways were the most affected by epigenetic silencing. Most interestingly, a large proportion of gene promoters were also aberrantly hypomethylated. These included genes from Ras oncogene family, the CDC42 GTPase, various methyl binding proteins and other proteins mainly encoding for cancer and hematopoiesis functional pathways, thus biologically validating our analysis. Therefore, our data demonstrates that MDS is characterized by distinct epigenetic aberrations that are preserved in peripheral blood leucocytes. These can be the basis of future studies on pathogenesis and diagnosis for this disease and can potentially uncover a new set of therapeutic gene targets.

Integrative Genomic Analysis Reveals Aberrant Epigenetic Marks in MDS That Can Be Seen in Peripheral Blood Leucocytes

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 595-595 ◽  
Author(s):  
Li Zhou ◽  
Joanna B. Opalinska ◽  
Davendra P. Sohal ◽  
Yongkai Mo ◽  
Suman Kambhampati ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bone Marrow ◽  
Peripheral Blood ◽  
Copy Number ◽  
Gene Expression Analysis ◽  
Whole Genome ◽  
Related Protein ◽  
Epigenetic Marks ◽  
Genome Methylation ◽  
Peripheral Blood Leucocytes

Abstract Myelodysplasia (MDS) is a clonal hematopoietic disorder that leads to ineffective hematopoiesis and peripheral cytopenias. DNMT inhibitors such as azacytidine have led to clinical responses in patients, though global epigenetic alterations in MDS have not been well described. The transmission of these epigenetic marks during hematopoietic differentiation and their role in disease pathophysiology is also unknown. We first compared global methylation profiles of 8 bone marrow samples with peripheral leucocytes by using a recently described novel method, the HELP assay (HpaII tiny fragment Enrichment by Ligation-mediated PCR; Khulan et al, Genome Res. 2006 Aug;16(8)) that uses differential methylation-specific digestion by HpaII and MspI followed by amplification, two color labeling and hybridization to quantitatively determine individual promoter CpG island methylation. A whole genome human promoter array (Nimblegen) was used to determine the level of methylation of 25626 gene promoters by calculating HpaII/MspI cut fragment intensity ratio. We observed a high correlation (r=0.89–0.96) of epigenetic marks between bone marrow and peripheral blood samples suggesting that a majority of epigenetic marks can be also be seen in differentiated cells. We subsequently compared peripheral blood leucocytes from 20 patients with MDS with 10 age-matched normal and anemic controls. Parallel gene expression analysis was performed using 37K oligo maskless arrays on cDNA from the same samples. Analysis showed that whole genome methylation profiling has greater discriminatory power in separating clusters of MDS samples from normal and anemic controls when compared to gene expression analysis. Epigenetic profiling demonstrated two clusters of MDS based on similarity of aberrant epigenetic changes. Overall, there was a trend towards hypermethylation in MDS, albeit not statistically significant given the large number of relatively unchanged genes. Detailed analysis revealed several novel differentially methylated genes that had corresponding changes in gene expression, when MDS samples were compared to the controls with a low false discovery rate of analysis. Interesting genes getting hypomethylated and overexpressed included TNF superfamily member 9, granulocyte pep A, microsomal glutathione S-transferase, homeo box B4, mitochondrial RPL11, and others. Similarly, the set of genes that were getting hypermethylated with associated decrease in gene expression included Evi-1, DAPK, HOXB3, Protein Phosphatase 1, CEBPB, mutated in colorectal cancer (MCC), myeloid-lymphoid or mixed-lineage leukemia 5 (MLL5), plasminogen-related protein B, ovarian cancer related protein 1 (ORP1), and others. In addition, we did array-based comparative genome hybridization (aCGH) to look at exact genome copy number changes in these samples. We found changes that were not detectable by conventional karyotyping in all samples. Commonly seen alterations were del(14q11), del(20q11), del(5q13), del(8p23), amp(1q42), amp(5q11), amp(17q12), amp(19q13) and amp(7q22). Integrative analysis revealed sets of genes that were either silenced by methylation or deletion in different patients. Thus, our data demonstrates that promoter DNA methylation changes are an important phenomenon in MDS evolution, and are associated with changes in expression of genes playing important roles in cancer development and/or progression. We also show that previously unrecognizable changes in copy number exist in most patients with MDS. In addition, our work shows that whole genome methylation assays, even when done on peripheral blood leukocytes, can be used for potential biomarker studies in the diagnosis of MDS.

scholarly journals Prevalence of Inflammatory Pathways Over Immuno-Tolerance in Peripheral Blood Mononuclear Cells of Recent-Onset Type 1 Diabetes

2022 ◽  
Vol 12 ◽  
Author(s):  
Aritania Sousa Santos ◽  
Edécio Cunha-Neto ◽  
Nelson Vinicius Gonfinetti ◽  
Fernanda Bernardi Bertonha ◽  
Pauline Brochet ◽  
...  
Keyword(s):  
Gene Expression ◽  
Peripheral Blood Mononuclear Cells ◽  
Immune Tolerance ◽  
Peripheral Blood ◽  
Mononuclear Cells ◽  
Peripheral Blood Mononuclear ◽  
Regulatory Pathways ◽  
Recent Onset ◽  
Inflammatory Pathways ◽  
Blood Mononuclear Cells

BackgroundChanges in innate and adaptive immunity occurring in/around pancreatic islets had been observed in peripheral blood mononuclear cells (PBMC) of Caucasian T1D patients by some, but not all researchers. The aim of our study was to investigate whether gene expression patterns of PBMC of the highly admixed Brazilian population could add knowledge about T1D pathogenic mechanisms.MethodsWe assessed global gene expression in PBMC from two groups matched for age, sex and BMI: 20 patients with recent-onset T1D (≤ 6 months from diagnosis, in a time when the autoimmune process is still highly active), testing positive for one or more islet autoantibodies and 20 islet autoantibody-negative healthy controls.ResultsWe identified 474 differentially expressed genes between groups. The most expressed genes in T1D group favored host defense, inflammatory and anti-bacterial/antiviral effects (LFT, DEFA4, DEFA1, CTSG, KCNMA1) and cell cycle progression. Several of the downregulated genes in T1D target cellular repair, control of inflammation and immune tolerance. They were related to T helper 2 pathway, induction of FOXP3 expression (AREG) and immune tolerance (SMAD6). SMAD6 expression correlated negatively with islet ZnT8 antibody. The expression of PDE12, that offers resistance to viral pathogens was decreased and negatively related to ZnT8A and GADA levels. The increased expression of long non coding RNAs MALAT1 and NEAT1, related to inflammatory mediators, autoimmune diseases and innate immune response against viral infections reinforced these dataConclusionsOur analysis suggested the activation of cell development, anti-infectious and inflammatory pathways, indicating immune activation, whereas immune-regulatory pathways were downregulated in PBMC from recent-onset T1D patients with a differential genetic profile.

Abstract TP232: A Biomarker Algorithm that Represents Time from Stroke Symptom Onset

Stroke ◽  
2013 ◽  
Vol 44 (suppl_1) ◽  
Author(s):  
Danielle N Doll ◽  
Steven D Brooks ◽  
Stephanie L Rellick ◽  
Reyna L VanGilder ◽  
Alan Cantor ◽  
...  
Keyword(s):  
Gene Expression ◽  
Symptom Onset ◽  
Peripheral Blood ◽  
Stroke Onset ◽  
Stroke Severity ◽  
Blood Draw ◽  
Clinical Covariates ◽  
The Mean ◽  
Mean Time

Background and Purpose: Time of onset is critical when treating ischemic stroke (IS). The purpose of this project was to investigate the use of our 9 gene profile to develop a biomarker algorithm that represents time from stroke onset for use in the clinical setting to improve utilization of tissue plasminogen activator (tPA) and streamline appropriate secondary prevention. Methods: Peripheral blood samples were collected from n=34 IS patients’ ≥18 years of age within 24 hours from symptom onset and 24-48 hours later. Total RNA was extracted from whole blood in Paxgene RNA tubes, amplified, and hybridized to Illumina HumanRef-8v2 bead chips. Gene expression was compared in a univariate manner between patients at both time points using t -test in GeneSpring. Inflation of type one error was corrected by Bonferroni. A linear regression was used to model the change in gene expression as a linear function of time when controlling for age. Results: The mean age of the sample was 71.9± (14.6 sd ) years. Mean time from symptom onset to acute blood draw was 9:29± (6:2 sd ) hours (range 2:35-23:02); to follow up blood draw was 29:24± (7.1 sd ) hours (range 18:45-43:30); and time between acute and follow up blood draw was 19:55± (3.3 sd ) hours (range 13:30-27:32). CA4 and ARG1 expression significantly decreased >1.5 fold, and LY96 expression by >2-fold between baseline and follow up. This decrease in expression was associated with an increase from time of stroke onset and remained significant for only LY96 expression when controlling for age. ARG1 and CA4 expression were significantly lower in older patients. Conclusions: Our profile provides evidence that the expression of LY96 , CA4 , and ARG1 in the peripheral blood may serve as a surrogate for determining the time of stroke onset. In clinical practice, an algorithm based on this biomarker profile and other clinical covariates could be used when time of onset is unknown. To increase the accuracy of our biomarker algorithm, it will be important to determine the effects of age, stroke severity, and other clinical covariates on the expression of these genes over time.

scholarly journals Mitochondrial proline catabolism activates Ras1/cAMP/PKA-induced filamentation inCandida albicans

2018 ◽  
Author(s):  
Fitz Gerald S. Silao ◽  
Meliza Ward ◽  
Kicki Ryman ◽  
Axel Wallström ◽  
Björn Brindefalk ◽  
...  
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Amino Acid ◽  
Critical Role ◽  
Amino Acid Permease ◽  
Atp Production ◽  
Pathway Activation ◽  
Opportunistic Fungal Pathogen ◽  
Pka Pathway

AbstractAmino acids are among the earliest identified inducers of yeast-to-hyphal transitions inCandida albicans, an opportunistic fungal pathogen of humans. Here, we show that the morphogenic amino acids arginine, ornithine and proline are internalized and metabolized in mitochondria via aPUT1- andPUT2-dependent pathway that results in enhanced ATP production. Elevated ATP levels correlate with Ras1/cAMP/PKA pathway activation and Efg1-induced gene expression. The magnitude of amino acid-induced filamentation is linked to glucose availability; high levels of glucose repress mitochondrial function thereby dampening filamentation. Furthermore, arginine-induced morphogenesis occurs more rapidly and independently of Dur1,2-catalyzed urea degradation, indicating that mitochondrial-generated ATP, not CO2, is the primary morphogenic signal derived from arginine metabolism. The important role of the SPS-sensor of extracellular amino acids in morphogenesis is the consequence of induced amino acid permease gene expression, i.e., SPS-sensor activation enhances the capacity of cells to take up morphogenic amino acids, a requisite for their catabolism.C. albicanscells engulfed by murine macrophages filament, resulting in macrophage lysis. Phagocytosedput1-/-andput2-/- cells do not filament and do not lyse macrophages, consistent with a critical role of mitochondrial proline metabolism in virulence.

scholarly journals Identification of Candidate Blood mRNA Biomarkers in Intracerebral Hemorrhage Using Integrated Microarray and Weighted Gene Co-expression Network Analysis

2021 ◽  
Vol 12 ◽  
Author(s):  
Feng Jin ◽  
Lei Li ◽  
Yuehan Hao ◽  
Ling Tang ◽  
Yuye Wang ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Network Analysis ◽  
Intracerebral Hemorrhage ◽  
Signaling Pathway ◽  
Peripheral Blood ◽  
Cell Apoptosis ◽  
Expression Profiles ◽  
Control Group ◽  
High Morbidity ◽  
Blood Draw

PurposeIntracerebral hemorrhage (ICH) is a serious public health hazard due to its high morbidity, disability, and mortality. Currently, the exact molecular mechanisms of ICH are unknown. We tried to identify the ICH-related candidate blood messenger RNA (mRNA) biomarkers by microarray analysis and weighted gene co-expression network analysis (WGCNA).Materials and MethodsWe collected the blood samples from patients with ICH (n = 4) and from vascular risk factor (VRF) controls (n = 4) and analyzed the mRNA expression profiles by competitive endogenous RNA (ceRNA) microarray. Differentially expressed genes (DEGs) were identified and then a weighted gene co-expression network was constructed. Modules with clinical significance were distinguished. Then, we downloaded two Gene Expression Omnibus (GEO) datasets (GSE24265 and GSE125512). Candidate mRNAs were identified by taking the intersection of the DEGs in our microarray, the interesting genes in the key module, and the DEGs in GSE24265. Functional analysis involving Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) and construction of a protein–protein interaction (PPI) network were conducted.ResultsA total of 340 DEGs in our microarray were identified between the ICH group and the control group. Among the eight gene modules established by WGCNA, the yellow module containing 191 genes was the most strongly associated with ICH. Four candidate mRNAs (C3AR1, PAWR, ARNTL2, and LDLRAD4) were identified. In the early stage of ICH (within 24 h), C3AR1, PAWR, and ARNTL2 were highly expressed in the perihematomal tissue, but with low expressions in peripheral blood; in the late stage (72 h after the first blood draw), an obvious upward trend of C3AR1 and PAWR in peripheral blood was seen. Functional analysis showed that candidate mRNAs were concerned with multiple pathways, such as the Wnt signaling pathway and calcium signaling pathway. They might affect the process of ICH through neuroinflammation, cell apoptosis, and pyroptosis.ConclusionWe identified four candidate blood mRNAs (C3AR1, PAWR, ARNTL2, and LDLRAD4) related to ICH. They showed different expression patterns in peripheral blood and perihematomal tissues and changed with time. They might play important roles in ICH through neuroinflammation, cell apoptosis, and pyroptosis and might shed new light to novel biomarkers or therapeutic targets in ICH.

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