scholarly journals Role of innate immunity-triggered pathways in the pathogenesis of Sickle Cell Disease: a meta-analysis of gene expression studies

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Bidossessi Wilfried Hounkpe ◽  
Maiara Marx Luz Fiusa ◽  
Marina Pereira Colella ◽  
Loredana Nilkenes Gomes da Costa ◽  
Rafaela de Oliveira Benatti ◽  
...  
Keyword(s):  
Gene Expression ◽  
Innate Immunity ◽  
Sickle Cell Disease ◽  
Sickle Cell ◽  
Meta Analysis ◽  
Cell Disease ◽  
Expression Studies ◽  
Gene Expression Studies

A Meta-Analysis of Gene Expression Studies Highlights the Role of Innate Immunity in the Pathogenesis of Sickle Cell Disease and Reveals Novel Potential Regulators at the Transcriptomic Level

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 4578-4578
Author(s):  
Bidossessi Wilfried Hounkpe ◽  
Maiara Marx Luz Fiusa ◽  
Marina Pereira Colella ◽  
Loredana Nilkenes Gomes da Costa ◽  
Rafaela Oliveira Benatti ◽  
...  
Keyword(s):  
Gene Expression ◽  
Innate Immunity ◽  
Sickle Cell Disease ◽  
Sickle Cell ◽  
Meta Analysis ◽  
Cell Disease ◽  
Bioinformatics Tools ◽  
Expression Studies ◽  
Gene Expression Studies ◽  
Transcriptomic Level

Abstract Sickle cell disease (SCD) is characterized by chronic inflammation and multisystem tissue damage. Despite the detailed characterization of the inflammatory changes observed in these patients, the precise identity of their critical triggers, as well as the hierarchical relationship between the elements involved in the pathogenesis of this complex disease are yet to be described. Meta-analysis of gene expression studies from public repositories represents a novel strategy, capable to identify key pathogenic mediators and therapeutic targets in complex diseases such as diabetes. The recent development of comprehensive bioinformatics tools further facilitated the identification of relevant genes, pathways and regulatory elements from high-throughput transcriptomic data. Here we performed a meta-analysis of recent gene expression studies with SCD patients, available at the Gene Expression Omnibus public repository. Two databases (GSE35007 and GSE53441) including samples from adults and children with SCD respectively fulfilled our inclusion criteria. We also performed additional meta-analysis comparing the gene expression pattern of these clinical samples with that of heme-stimulated endothelial cells (GSE25014). Meta-analysis was performed with the Inmex bioinformatics tool. Raw data was downloaded, annotated, preprocessed, and submitted to quality check. Differentially expressed genes were identified and ranked based on the RankProd package. Gene set analysis using more than 60 libraries was performed using EnrichR. Transcription factor, kinase enrichment, and pathway cluster analysis were performed using appropriate bioinformatics tools. Only pathways that were identified in more than one library were included. Our results demonstrate that the well-characterized association between innate immunity, hemostasis, angiogenesis and heme metabolism with SCD was also consistently observed at the transcriptomic level, across independent gene expression studies. The enrichment of genes and pathways associated with innate immunity and damage repair-associated pathways supports the model of erythroid danger-associated molecular patterns (DAMPs) as key mediators of the pathogenesis of SCD. In addition, our study generated a novel and large database of candidate genes, pathways, transcription factors and kinases not previously associated with the pathogenesis of SCD, that could be used in future and independent studies in SCD. Disclosures No relevant conflicts of interest to declare.

Differentially Expressed Genes and Pathways in Endothelial Cells Exposed to Hemin or Plasma from Patients with Sickle Cell Disease: A Meta-Analysis of Gene Expression Studies

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 4018-4018
Author(s):  
Maiara M L Fiusa ◽  
Marina Pereira Colella ◽  
Joyce M Annichino-Bizzacchi ◽  
Loredana Nilkenes ◽  
Bidossessi W Hounpke ◽  
...  
Keyword(s):  
Gene Expression ◽  
Endothelial Cells ◽  
Steady State ◽  
Sickle Cell Disease ◽  
Sickle Cell ◽  
Meta Analysis ◽  
P Value ◽  
Cell Disease ◽  
Expression Studies ◽  
Gene Expression Studies

Abstract Introduction: Vaso-occlusion and chronic hemolysis are recognized as the most important pathogenic mechanisms of sickle cell disease (SCD), feeding a vicious circle that leads to acute and chronic complications. Although phenotypic aspects of this pro-inflammatory state have been described in detail, much less is known about the upstream pathways that activate and perpetuate inflammation in SCD. It has been known for more than 50 years that patients with SCD present higher plasma concentrations of heme. More recently, the role of heme as a mediator of inflammation in SCD has been confirmed in relevant models, suggesting that free heme can be a trigger for both microvascular occlusion and acute chest syndrome (ACS). In the past, microarray-based gene expression experiments have been used to study the effects of heme on endothelial cells (EC), as well as gene expression signatures of SCD. These studies can be analyzed in combination, since original raw data are now collected in public archives. In fact, it has been shown that by analyzing data from multiple experiments by meta-analysis, biases and artifacts between datasets can be cancelled out, potentially allowing true relationships to stand out. In order to gain insights into the cellular and molecular pathways activated by heme in endothelial cells (EC), as well as about their potential relevance in SCD, we performed a meta-analysis of microarray-based gene expression studies involving heme, EC and SCD. Material and methods: Microarray data were identified by searching two public databases (GEO and Array-Express) using the following search criteria: (“sickle cell disease” and “homo sapiens”). Eleven studies were identified, of which two were selected for our meta-analysis (GSE1849; GSE25014). One study evaluated the effect of heme 5µM in human primary pulmonary artery (PAECs) and microvascular EC (PMVECs) (12 samples), while the other study evaluated the effect of plasma from SCD patients (9 patients in steady state and 12 patients during ACS) in PAECs. To perform the meta-analysis we used INMEX, an integrative web-based tool for meta-analysis of expression data. For the meta-analysis, we applied a combining rank orders method based in the RankProd package. Genes with expression fold-changes (FC) in the same direction (either up or down) of 1.4 in at least one study were selected as candidates for differentially expressed (cDE) genes. Selected genes were ranked based on p value, and a p value ≤0.05 was considered statistically significant. To further understand functions of the subset of genes that were cDE in both studies, we performed gene ontology enrichment analysis. The functional analysis was undertaken using INMEX, and confirmed in other three gene set analysis tools (Pathway Commons, WikiPathways and KEGG). Only pathways that were identified in more than one tool were considered in the analysis. Results: Two different meta-analysis were performed. Gene expression data from heme-stimulated EC was compared to: (i) data from EC stimulated by plasma from SCD patients at steady-state; or (ii) data from EC stimulated by plasma obtained during ACS. In the first (heme x steady-state) and second (heme x ACS) analysis, 799 and 786 genes were consistently up- or down-regulated in both studies. The up- and down-regulated genes with the lowest p values were C2CD4A (C2 calcium-dependent domain containing 4A), and KLHL23 (kelch-like family member 23), respectively. In addition, genes associated with depletion of reactive oxygen species and coagulation activation were also identified. The most significant pathways identified in the gene set analysis were “IL5-mediated signaling events” (heme x steady-state; p= 0.0012) and “MAPK signaling pathway” (heme x ACS; p= 0.0073512) respectively. Results and conclusion: Genes and pathways that are DE both in EC stimulated by heme or by plasma from SCD patients could be relevant elements in the pathogenesis of inflammation in SCD. Heme has been shown to increase the generation of ROS and to induce the expression of inflammatory and pro-coagulant proteins by EC. The results of our meta-analysis are consistent with these effects. Therefore, the comprehensive list of genes and pathways identified in our study could help the generation new hypothesis about the mechanisms involved in heme-induced activation and perpetuation of inflammation in SCD. Disclosures No relevant conflicts of interest to declare.

scholarly journals Antiphospholipid Antibodies in Sickle Cell Disease: A Systematic Review and Exploratory Meta-Analysis

2021 ◽  
Vol 27 ◽  
pp. 107602962110029
Author(s):  
Mira Merashli ◽  
Alessia Arcaro ◽  
Maria Graf ◽  
Matilde Caruso ◽  
Paul R. J. Ames ◽  
...  
Keyword(s):  
Sickle Cell Disease ◽  
Sickle Cell ◽  
Antiphospholipid Antibodies ◽  
Meta Analysis ◽  
Age Groups ◽  
Anticardiolipin Antibodies ◽  
Cell Disease ◽  
Pooled Prevalence ◽  
The Relationship

The relationship between antiphospholipid antibodies (aPL) and sickle cell disease (SCD) has never been systematically addressed. Our aim was to evaluate potential links between SCD and aPL in all age groups. EMBASE/PubMed was screened from inception to May 2020 and Peto odds ratios for rare events were calculated. The pooled prevalence (PP) of IgG anticardiolipin antibodies (aCL) was higher in individuals with SCD than in controls (27.9% vs 8.7%, P < 0.0001), that of IgM aCL was similar in the two groups (2.9% vs 2.7%); only individuals with SCD were positive for lupus anticoagulant (LA) (7.7% vs 0%, P < 0.0001). The PP of leg ulcers was similar between aPL positive and negative individuals (44% vs 53%) and between patients in acute crisis and stable patients (5.6% vs 7.3%). Reporting of aPL as a binary outcome and not as a titer precluded further interpretation. The results indicate that a prospective case-control study with serial measurements of a panel of aPL in SCD patients might be warranted, in order to understand further the possible pathogenic role of aPL in SCD.

scholarly journals Identifying Potential Drug Targets for Sickle Cell Disease through Gene Expression and Pathway Analysis of GEO Data

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 15-16
Author(s):  
Sharjeel Syed ◽  
Jihad Aljabban ◽  
Jonathan Trujillo ◽  
Saad Syed ◽  
Robert Cameron ◽  
...  
Keyword(s):  
Gene Expression ◽  
Amino Acid ◽  
Sickle Cell Disease ◽  
Sickle Cell ◽  
Drug Targets ◽  
Meta Analysis ◽  
Cell Disease ◽  
Blood Samples ◽  
Disease Modifying Therapies ◽  
Disease Modifying

Background: The pathogenesis of sickle cell disease (SCD) and its complications have been well characterized down to the molecular level. However, there remains a relative dearth of disease modifying therapies that reduce the frequency and number of vas-occlusive crises, hospitalizations, and deaths. Recent advancements in utilizing hydroxyurea and L-glutamine, which both impact unique disease pathways, should pave way for the identification of other molecular pathways as ideal drug targets. In this regard, our meta-analysis serves to identify key genes and associated pathways that are differentially expressed in SC patients. Methods: We employed our STARGEO platform to tag samples from the NCBI Gene Expression Omnibus and performed meta-analysis to compare SC and healthy control transcriptomes. For the meta-analysis, we tagged 285 peripheral blood samples from SC patients and 86 samples from healthy subjects as a control. We then analyzed the signature in Ingenuity Pathway Analysis to elucidate top disease functions from our analysis. Results: From our meta-analysis, we identified iron homeostasis signaling, NRF2-mediated oxidative stress response, cell senescence, and pyrimidine interconversion/biosynthesis as top canonical pathways that were upregulated in the peripheral blood samples from SC patients. Top upstream regulators included membrane associated protein and transporter ABCB6, non-coding RNY3, and erythroid maturation transcription factors GATA1, KLF1, and HIPK2 (with predicted activation). The most upregulated genes included inflammatory modulators RNF182 and IFI27, the latter of which has been shown to inhibit vascular endothelial growth and repair. Several membrane-associated protein coding genes such as GYPA, RAP1GAP, and PAQR9 were also upregulated in the SC samples. RAP1GAP is known to modulate neutrophil cell adhesion and homing while PAQR9 has roles in regulating protein quality control: a role also seen in similarly upregulated YOD1, a deubiquitinating enzyme involved in trafficking of misfolded proteins. Expectedly, also upregulated were HBBP1 and SOX6, which regulate globin genes and have been shown to silence γ-globin expression. Lastly, SLC6A19, the neutral amino acid transporter mutated in Hartnup disease, was also upregulated. Of the downregulated genes, WASF3, a member of the Wiskott-Aldrich syndrome protein family, has been linked to poor survival in many malignancies, including AML and CMML, but has not previously been linked to SCD pathogenesis. ENKUR was also downregulated and has been annotated as a tethering protein to cation channels as well as linked to pathways involving vascular leakage. SIGLEC10, which binds to vascular adhesion proteins, is a key suppressor of inflammatory responses to damage; it's downregulation along with ELAPOR1, a transmembrane protein involved in cellular response to stress, was also observed. Finally, based off the focus genes in our analysis we identified several networks with most being involved in amino acid metabolism, cellular assembly, function, and maintenance, hematological disease, and organismal injury. The top pathway is illustrated in Figure 1. Conclusions: Our study illustrates differentially expressed gene activity in SCD consistent with known pathophysiology such as immune response, endothelial damage and adherence, heme metabolism, and globin regulation. We also showed evidence of genes not previously studied in SCD, which may have novel roles such as those part of the ubiquitin-proteasome system like YOD1 and RNF182. Additionally, while some genes in our analysis like EKLF and GAT1 have been shown to enhance δ-globin expression, paving way for possible drug therapies for B-hemoglobinopathies, others like IFI27, PAQR9, RAP1GAP, ENKUR, SIGLEC10, WASF3, and SOX9 have yet to be studied as mediators of disease pathogenesis in SCD. A target to SOX9, a known suppressor of γ-globin, or ABCB6, a known modulator of erythroid cell shape and hydration, have particularly promising potential as disease modifying therapies. Finally, HIPK2, HBBP1, and SLC6A19 have previously been shown to have intriguing effects on hydroxyurea dosing and responsivity in SC patients and may also be candidate target molecules to enhance existing therapies. These data identify potential candidate pathways for mechanistic studies seeking to confirm a causative role in the pathogenesis of sickle cell disease. Disclosures No relevant conflicts of interest to declare.

scholarly journals Micro RNA Profiling to Identify Regulator of Fetal Hemoglobin Expression in Sickle Cell Disease

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 49-49 ◽  
Author(s):  
Biaoru Li ◽  
Christina M. Torres ◽  
Mayuko Takezaki ◽  
Cindy Neunert ◽  
Abdullah Kutlar ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sickle Cell Disease ◽  
Sickle Cell ◽  
Fetal Hemoglobin ◽  
Mrna Levels ◽  
Cell Disease ◽  
Erythroid Progenitors ◽  
Globin Mrna ◽  
Mirna Genes

Abstract Elevated fetal hemoglobin (HbF) expression ameliorates the clinical severity of sickle cell disease (SCD) by inhibiting hemoglobin S polymerization. Differences in HbF levels are attributed to inherited DNA genetic variations that regulate γ-globin transcription; however the role of microRNA (miRNA) genes in HbF regulation has not been investigated using clinical samples. miRNAs are small non-protein-coding RNA molecules that negatively regulate gene expression through inhibition of mRNA translation. Our goal is to identify miRNA genes with altered expression in sickle cell patients with elevated HbF levels, to elucidate mechanisms of γ-globin gene regulation. After IRB approval, peripheral blood was collected from SCD patients (not on hydroxyurea therapy), followed in the pediatric and adult Sickle Cell Clinics at Georgia Regents University. HbF levels measured by high performance liquid chromatography and complete blood and reticulocyte counts were obtained. Twelve blood samples, six each from SCD subjects with high HbF (19.9±2.1%) or low HbF (4.4±0.9%) levels were analyzed. We observed more severe anemia and higher reticulocyte counts in the low HbF group. After Histopaque separation, red blood cells were processed on a MACS column with anti-CD71 antibody to isolate reticulocytes, followed by total RNA extraction using Trizol. RNA (750ng) was hybridized to a genome-wide miRCURY LNA microRNA Array (Exiqon) containing 1,921 human probes. The microarray raw data were collected on an Agilent G2565BA Microarray Scanner System and normalized by Model-Based Background Correction and Principle Component Analysis. Characterization of miRNA profiles for low HbF compared to high HbF groups identified 327 differentially expressed genes including multiple miR-144 isoforms. We subsequently explored the function of miR-144 because it targets Nrf2 which mediates drug-induced HbF expression and Nrf2 has an antioxidant protective effect in SCD. Therefore, we conducted supervised learning of the normalized microarray data based on miR-144 expression. Interestingly, in the low HbF group we observed two subphenotypes: 1) associated with 8-fold increased miR-144 expression (3 subjects) and 2) associated with no change in miR-144 level (3 subjects) when compared to the high HbF group suggesting a role of miR-144 in HbF regulation. In the supervised learning analysis, there were 62 up-regulated and 33 down-regulated miRNAs (&gt;2-fold; p&lt;0.05) in the first subphenotype. We hypothesized that miRNAs up-regulated in the low HbF group might silence known γ-globin trans-activators. By TargetScan and Miranda analysis 7 miRNAs were predicted to target γ-globin including miR-96 a known negative regulator. There were 4 miRNAs predicted to target Nrf2 and 12 miRNAs that target other transcription factors such as KLF1, KLF4, BCL11A, and GATA2. To define a functional role of miR-144 we conducted studies in adult CD34+ stem cells grown in a two-phase culture system containing Stem Cell Factor (50ng/mL), Interleukin-3 (10ng/mL) and Erythropoietin (4IU/mL). At day 8 in culture, miR-144 mimic, miR-144 antagomir (inhibitor) or scrambled control (100nM, 200nM, and 300nM) were transfected using a Nucleofector System. After 72 hr incubation, RT-qPCR was conducted to measure γ-globin and Nrf2 mRNA levels. miR-144 mimic or antagomir at 100-300nM concentrations had no significant effect on γ-globin mRNA levels. By contrast, flow cytometry analysis using a FITC-anti-γ-globin antibody in erythroid cells treated with miR-144 mimic, produced a 30-70% decrease in HbF positive cells (p&lt;0.05). On the contrary, we observed a 1.8-fold increase in HbF positive cells mediated by 300nM miR-144 antagomir. Evidence that miR-144 targets Nrf2 was established when antagomir treatment increased Nrf2 expression 1.4-fold (p&lt;0.05). Final studies using day 8 erythroid progenitors treated with Nrf2 siRNA demonstrated a 40% decrease in γ-globin mRNA supporting a role of Nrf2 on γ-gene expression. In summary, the miRNA profiles associated with HbF expression in SCD patients combined with functional studies in human primary erythroid progenitors, support a role for miR-144 in γ-globin regulation. These findings will be expanded to a pre-clinical SCD mouse model to develop miR-144 as a potential therapeutic option. Disclosures No relevant conflicts of interest to declare.

Role of coagulation system in pathophysiology of sickle cell disease

1974 ◽  
Vol 133 (4) ◽  
pp. 635-641 ◽  
Author(s):  
F. R. Rickles
Keyword(s):  
Sickle Cell Disease ◽  
Sickle Cell ◽  
Coagulation System ◽  
Cell Disease

scholarly journals Sickle Cell Disease: Role of Oxidative Stress and Antioxidant Therapy

Antioxidants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 296
Author(s):  
Rosa Vona ◽  
Nadia Maria Sposi ◽  
Lorenza Mattia ◽  
Lucrezia Gambardella ◽  
Elisabetta Straface ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Sickle Cell Disease ◽  
Sickle Cell ◽  
Globin Gene ◽  
Organ Damage ◽  
Cell Disease ◽  
Vessel Occlusion ◽  
Antioxidant Agents ◽  
Oxidant Status

Sickle cell disease (SCD) is the most common hereditary disorder of hemoglobin (Hb), which affects approximately a million people worldwide. It is characterized by a single nucleotide substitution in the β-globin gene, leading to the production of abnormal sickle hemoglobin (HbS) with multi-system consequences. HbS polymerization is the primary event in SCD. Repeated polymerization and depolymerization of Hb causes oxidative stress that plays a key role in the pathophysiology of hemolysis, vessel occlusion and the following organ damage in sickle cell patients. For this reason, reactive oxidizing species and the (end)-products of their oxidative reactions have been proposed as markers of both tissue pro-oxidant status and disease severity. Although more studies are needed to clarify their role, antioxidant agents have been shown to be effective in reducing pathological consequences of the disease by preventing oxidative damage in SCD, i.e., by decreasing the oxidant formation or repairing the induced damage. An improved understanding of oxidative stress will lead to targeted antioxidant therapies that should prevent or delay the development of organ complications in this patient population.

Role of Adhesion Molecules and Vascular Endothelium in the Pathogenesis of Sickle Cell Disease

Hematology ◽  
2007 ◽  
Vol 2007 (1) ◽  
pp. 84-90 ◽  
Author(s):  
Marilyn J. Telen
Keyword(s):  
Sickle Cell Disease ◽  
Red Blood Cells ◽  
Adhesion Molecules ◽  
Sickle Cell ◽  
Vascular Endothelium ◽  
Blood Cells ◽  
Cell Disease ◽  
Adhesive Interactions ◽  
Lines Of Evidence

AbstractA number of lines of evidence now support the hypothesis that vaso-occlusion and several of the sequelae of sickle cell disease (SCD) arise, at least in part, from adhesive interactions of sickle red blood cells, leukocytes, and the endothelium. Both experimental and genetic evidence provide support for the importance of these interactions. It is likely that future therapies for SCD might target one or more of these interactions.

Oxidative stress, malaria, sickle cell disease, and innate immunity

2021 ◽  
Author(s):  
Huan Cao ◽  
Mark A. Vickers
Keyword(s):  
Oxidative Stress ◽  
Innate Immunity ◽  
Sickle Cell Disease ◽  
Sickle Cell ◽  
Cell Disease
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