Benign Ethnic Neutropenia in Individuals of African Descent: Incidence, Granulocyte Mobilization, and Gene Expression Profiling.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 3069-3069 ◽  
Author(s):  
Matthew Hsieh ◽  
Kay Chin ◽  
Beth Link ◽  
David Stroncek ◽  
Ena Wang ◽  
...  

Abstract Introduction: Benign ethnic neutropenia (BEN) is a condition observed in individuals of African descent, and is characterized by a reduced absolute neutrophil count (ANC) less than 1500/uL in the absence of secondary causes. In contrast to other causes of neutropenia, BEN does not increase risk of oral or systemic infections. BEN has been described in up to 40% of certain ethnic groups, but its incidence in African Americans is unknown. Additionally, the pathogenesis is currently unknown. Through this study, we wish to determine the incidence of BEN, compare the neutrophil increment after dexamethasone (Dex) and granulocyte-colony stimulating factor (G-CSF), and compare peripheral blood (PB) granulocyte gene expression profiles by microarray and PB protein array to controls in order to better understand BEN. Methods: Complete blood count (CBC) data were obtained from the National Health and Nutrition Examination Survey (NHANES) III. White blood cell and absolute neutrophil counts were compared in non-Hispanic whites, non-Hispanic blacks, Mexican-Americans, and others. Normal volunteers of African descent were recruited through an IRB approved study at NIH. Each volunteer underwent three PB leukaphereses: baseline, one day after 8mg of Dex, and one day after 5ug/kg G-CSF. CBCs were measured before and after each drug treatment. Granulocytes were enriched by gravity sedimentation with 6% hetastarch, hypotonic saline lysis of erythrocytes, and density gradient centrifugation using Ficoll-Pague. Granulocyte mRNA were applied to Affymetrix U133 plus 2.0 chips following extraction using a phenol-chloroform based method (RNA Stat 60, Tel-Test) and DNA removal. The gene expression pattern of BEN was compared to that of normals (ANC >4000/uL). Results: The NHANES III sample size included 25,925 individuals. Mean ANC for the each ethnic groups were 4.55 (white), 3.67 (black), 4.80 (Mex-Am), and 4.52 (others) k/uL. The incidence of neutropenia (<1500/uL) was 0.25% (white), 4.05% (black), 0.35% (Mex-Am), and 0.98% (others). Our local incidence of BEN was 5.7% (4 of 70 volunteers screened). The mean WBC in our BEN were 4.13 +/− 0.72 (baseline), 8.57 +/− 0.59 (Dex), and 16.9 +/− 2.3 (G-CSF) k/uL, compared to those of normals, 7.56 +/− 0.95 (baseline), 12.17 +/− 2.13 (Dex), and 29.22 +/− 4.8 (G-CSF) k/uL. The absolute neutrophil increment of BEN volunteers was 4.95 k/uL (94.7% of neutrophil increment in normal volunteers) after Dex, and 12.7 k/uL (60.2% of normal) after G-CSF. Gene expression profile comparisons showed that at baseline, several genes were upregulated more than 10 fold in BEN, including apoptotic factors, metalloproteases 8 and 13, TREML 3&4, TGF-beta, and endothelial factors (endothelin 1, endothelin receptor B, and fibroblast growth factors). These differences were less pronounced after Dex or G-CSF. Additionally, gene expression pattern is markedly different after Dex vs. G-CSF, regardless of the neutrophil count. Conclusions: Our results establish the incidence of BEN in the US at approximately 4%, significantly lower than that suggested by prior small reports. Additionally, the neutrophil increment is much lower in BEN following stimulation with G-CSF, suggesting the mechanism of granulocyte mobilization differs between Dex and G-CSF. Neutrophil mRNA in BEN showed increased expression of apoptotic, endothelial, and some leukocyte specific transcripts. Real-time PCR of candidate genes, accrual of more BEN subjects, and analyses of protein array are ongoing.

2014 ◽  
Vol 26 (1) ◽  
pp. 155
Author(s):  
M. J. Sudano ◽  
D. M. Paschoal ◽  
E. S. Caixeta ◽  
R. R. Maziero ◽  
M. D. Guastali ◽  
...  

Even though FCS provides energy substrates, amino acids, vitamins, growth factors, and heavy-metal chelators, its supplementation has been associated with several embryo abnormalities such as mitochondrial degeneration, metabolic deviations, excessive lipid accumulation, and decreased embryo survival after cryopreservation. The aim of the present study was to evaluate the effect of high FCS concentration in the gene expression pattern of in vitro-produced bovine embryos. Slaughterhouse ovaries were used to obtain oocytes (N = 360), which were matured and fertilized in vitro (Day 0). Presumptive zygotes were divided in 2 culture media: with low (SOFaa with 0.5% BSA and 2.5% FCS) or high (SOFaa with 0.5% BSA and 10% FCS) FCS concentration. Cleavage was evaluated on Day 3. Embryo development was evaluated after 7 days under standard culture conditions (at 38.5°C in atmosphere of 5% O2, 5% CO2, and 90% N2). The produced blastocysts were placed in PBS solution and washed five times. A single blastocyst was frozen in a minimal volume of PBS and stored at –80°C until RNA extraction. Total RNA extraction was performed using the PicoPure RNA isolation Kit (Applied Biosystems®, Foster City, CA, USA). Extracted RNA was evaluated through 2100-Bioanalyzer (Agilent Technologies®, Palo Alto, CA, USA) and DNAse treated (Qiagen®, Valencia, CA, USA). RiboAmp RNA Amplification Kit (Applied Biosystems®) was used to amplify the RNA (T7 RNA polymerase-catalysed amplification reaction). The aRNA output was evaluated through NanoDrop ND-1000 (NanoDrop Technologies®, Wilmington, DE, USA). A biotin-labelled cRNA and fragmented cRNA were obtained through 3′IVT Express Kit (Affymetrix®, Santa Clara, CA, USA) to perform the hybridization (N = 3 per group) using GeneChip Bovine Genome Array (Affymetrix®). Following hybridization, probe arrays were washed, stained, and scanned. Microarray data analysis was performed in the software FlexArray 1.6.1.1. Genes with a fold change of at least 1.5 and a probability of P < 0.05 were considered differentially expressed. The data from in vitro embryo production were analysed through the PROC GLM (SAS Institute Inc., Cary, NC, USA). Cleavage rate (81.4 ± 1.5 and 85.5 ± 1.4) and blastocyst production (41.8 ± 2.4 and 47.2 ± 2.8) were not different (P > 0.05) between low and high FCS concentrations, respectively. A total of 40 genes were differentially expressed between low and high FCS concentration. A total of 28 genes were annotated, with 37 genes up-regulated and 3 genes down-regulated by high FCS concentration. The associated network functions of gene expression, RNA damage and repair, and post-transcriptional modification; and cell-to-cell signalling and interaction were generated by Ingenuity Pathway Analysis® (Redwood City, CA, USA). Differentially expressed genes involved in carbohydrate metabolism (GAPVD1, MGAT4A), lipid metabolism (ELOVL5), cellular assembly and organisation (EZR, LRP2), and cell death and survival (DRT8) were identified. In conclusion, high FCS supplementation was associated with different expression profiles of genes regulating carbohydrate and lipid metabolism, cellular assembly and organisation, and cell death and survival. The authors acknowledge support from FAPESP and LNBio-CNPEM.


PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0246106
Author(s):  
Sun Kyung Kim ◽  
Peter C. Goughnour ◽  
Eui Jin Lee ◽  
Myeong Hyun Kim ◽  
Hee Jin Chae ◽  
...  

Aging is a multifactorial process that involves numerous genetic changes, so identifying anti-aging agents is quite challenging. Age-associated genetic factors must be better understood to search appropriately for anti-aging agents. We utilized an aging-related gene expression pattern-trained machine learning system that can implement reversible changes in aging by linking combinatory drugs. In silico gene expression pattern-based drug repositioning strategies, such as connectivity map, have been developed as a method for unique drug discovery. However, these strategies have limitations such as lists that differ for input and drug-inducing genes or constraints to compare experimental cell lines to target diseases. To address this issue and improve the prediction success rate, we modified the original version of expression profiles with a stepwise-filtered method. We utilized a machine learning system called deep-neural network (DNN). Here we report that combinational drug pairs using differential expressed genes (DEG) had a more enhanced anti-aging effect compared with single independent treatments on leukemia cells. This study shows potential drug combinations to retard the effects of aging with higher efficacy using innovative machine learning techniques.


Author(s):  
Kayley Scott ◽  
Hannah L Morgan ◽  
Christian Delles ◽  
Simon Fisher ◽  
Delyth Graham ◽  
...  

During pregnancy the uterine spiral arteries undergo major vascular remodelling to ensure sufficient uteroplacental perfusion to support the fetus. In pregnancies complicated by hypertensive disorders this remodelling is deficient leading to impaired uteroplacental blood flow and poor maternal and fetal outcomes. The underlying genetic mechanisms for failed vascular remodelling are not fully understood. This study aimed to examine the early-pregnancy associated gene changes in the uterine arteries of stroke-prone spontaneously hypertensive rats (SHRSP) compared to their normotensive counterparts, Wistar-Kyoto rats (WKY). Uterine arteries from gestational day 6.5 WKY and SHRSP were processed for RNA-sequencing, along with virgin, age-matched controls for each strain. Gene expression changes were identified and biological pathways were implicated and interpretated using Ingenuity Pathway Analysis (IPA®). This study found that WKY uterine arteries from early-pregnancy exhibit a gene expression pattern that is suggestive of a pregnancy-dependent reduction in Ca2+ handling and RAAS components and an increase in ATP production. In contrast, the expression pattern of pregnant SHRSP uterine arteries was dominated by an elevated immune response and increased production of ROS and downstream effectors of the RAAS. These results suggest that in a rat model, hypertension during pregnancy impacts uterine artery gene expression patterns as early as the first week of pregnancy. The pathway changes involved may underlie or contribute to the adverse vascular remodelling and resultant placental ischaemia and systemic vascular dysfunction observed in SHRSP in late gestation.


2021 ◽  
Author(s):  
Tenggang Ma ◽  
Hongyu Zhang ◽  
Ziwen Feng ◽  
Renzhong Wang

Abstract Ulcerative colitis (UC) is a chronic inflammatory disease that is prone to recurrent attacks. It has complex pathogenesis, which is closely related to genetics, constitution, dietary habits, and environmental factors. From the comprehensive Gene Expression Omnibus database (GEO), we retrieved gene expression profiles and classified 197 cases of UC into three subgroups for the purpose of predicting the basic molecular characteristics for different types of ulcerative colitis. As expected, each group showed its own clinical peculiarity and way of presentation. In this article, consensus clustering was used to divide the sample into three. The WGCNA analysis was applied to evaluate specific modules and reveal transcriptional differences among the subgroups. Subsequently, pathway and function enrichment analysis was conducted based on WGCNA. In subgroup Ⅰ, fructose and mannose metabolism pathway and cell cycle 11/36 pathway are up-regulated, which could be an indicator of exacerbation. Furthermore, the hematopoietic cell lineage pathway, which was significantly up-regulated in subgroup Ⅱ, might be indicating a disease correlation. In subgroup Ⅲ, the gene expression pattern of the peroxisome pathway is similar to the normal group, which may indicate an early stage of UC. Although no significant prognostic difference existing among the groups, there were significant differences in their underlying biological characteristics. This suggests that transcriptome classifications also represent risk factors for different disease states and ages. In summary, the bioinformatics techniques used in this study contribute to identifying molecular subtypes for diagnosing human ulcerative colitis. The transcriptome classification of UC cases suggests that each subgroup may have its own gene expression pattern and pathway, providing further personalized treatment guidance for patients with ulcerative colitis.


Author(s):  
Aravind P ◽  
Sarojini R. Bulbule ◽  
Hemalatha N ◽  
Anushree G ◽  
Babu R.L ◽  
...  

Abstract Background Free radicals generated in the biological system bring about modifications in biological molecules causing damage to their structure and function. Identifying the damage caused by ROS and RNS is important to predict the pathway of apoptosis due to stress in PC12 cells. The first defense mechanisms against them are antioxidants which act in various pathways through important cellular organelles like the mitochondria and endoplasmic reticulum. Specific biomarkers like Gadd153 which is a marker for endoplasmic reticulum stress, Nrf2 which responds to the redox changes and translocates the antioxidant response elements, and Btg2 which is an antioxidant regulator have not been addressed in different stress conditions previously in PC12 cells. Therefore, the study was conducted to analyze the gene expression pattern (SOD, Catalase, Btg2, Gadd153, and Nrf2) and the protein expression pattern (iNOS and MnSOD) of the antioxidant stress markers in differential stress-induced PC12 cells. Peroxynitrite (1 μM), rotenone (1 μM), H2O2(100 mM), and high glucose (33 mM) were used to induce oxidative and nitrosative stress in PC12 cells. Results The results obtained suggested that rotenone-induced PC12 cells showed a significant increase in the expression of catalase, Btg2, and Gadd153 compared to the control. Peroxynitrite-induced PC12 cells showed higher expression of Btg2 compared to the control. H2O2 and high glucose showed lesser expression compared to the control in all stress marker genes. In contrast, the Nrf2 gene expression is downregulated in all the stress-induced PC12 cells compared to the control. Further, MnSOD and iNOS protein expression studies suggest that PC12 cells exhibit a selective downregulation. Lower protein expression of MnSOD and iNOS may be resulted due to the mitochondrial dysfunction in peroxynitrite-, high glucose-, and H2O2-treated cells, whereas rotenone-induced cells showed lower expression, which could be the result of a dysfunction of the endoplasmic reticulum. Conclusion Different stress inducers like rotenone, peroxynitrite, H2O2, and high glucose increase the NO and ROS. Btg2 and Gadd153 genes were upregulated in the stress-induced cells, whereas the Nrf2 was significantly downregulated in differential stress-induced PC12 cells. Further, antioxidant marker genes were differentially expressed with different stress inducers.


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