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author:("Xu, huachun")
1.  Distinctive RNA Expression Profiles in Blood Associated with Alzheimer’s Disease after Accounting for White Matter Hyperintensities 
Defining the RNA transcriptome in Alzheimer’s Disease (AD) will help understand disease mechanisms and provide biomarkers. Though the AD blood transcriptome has been studied, effects of white matter hyperintensities (WMH) were not considered. This study investigated the AD blood transcriptome and accounted for WMH.
RNA from whole blood was processed on whole-genome microarrays.
293 probe sets were differentially expressed in AD versus controls, 5 of which were significant for WMH status. The 288 AD-specific probe-sets classified subjects with 87.5% sensitivity and 90.5% specificity. They represented 188 genes of which 29 have been reported in prior AD blood and 89 in AD brain studies. Regulated blood genes included MMP9, MME (Neprilysin), TGFβ1, CA4, OCLN, ATM, TGM3, IGFR2, NOV, RNF213, BMX, LRRN1, CAMK2G, INSR, CTSD, SORCS1, SORL1 and TANC2.
RNA expression is altered in AD blood irrespective of WMH status. Some genes are shared with AD brain.
PMCID: PMC4139468  PMID: 24731980
Alzheimer’s disease; RNA; white matter hyperintensities; blood; brain
2.  Distinctive RNA Expression Profiles in Blood Associated with White Matter Hyperintensities in Brain 
Background and Purpose
White Matter Hyperintensities (WMH) are areas of high signal detected by T2 and FLAIR sequences on brain Magnetic Resonance Imaging (MRI). Although associated with aging, cerebrovascular risk factors and cognitive impairment, the pathogenesis of WMH remains unclear. RNA expression was assessed in the blood of individuals with and without extensive WMH to search for evidence of oxidative stress, inflammation and other abnormalities described in WMH lesions in brain.
Subjects included 20 with extensive WMH (WMH+), 45% of whom had Alzheimer’s disease, and 18 with minimal WMH (WMH-), 44% of whom had Alzheimer’s disease. All subjects were clinically evaluated and had quantitative MRIs. Total RNA from whole blood was processed on human whole genome Affymetrix HU133 Plus 2.0 microarrays. RNA expression was analyzed using an analysis of covariance (ANCOVA).
241 genes were differentially regulated at ±1.2 fold difference (p <0.005) in subjects with WMH+ as compared to WMH-, regardless of cognitive status, and 50 genes were differentially regulated with at least ±1.5 fold difference (p <0.005). Cluster and principal components analyses showed that the expression profiles for these genes distinguished WMH+ from WMH- subjects. Function analyses suggested that WMH-specific genes were associated with oxidative stress, inflammation, detoxification, and hormone signaling, and included genes associated with oligodendrocyte proliferation, axon repair, long term potentiation and neurotransmission.
The unique RNA expression profile in blood associated with WMH is consistent with roles of systemic oxidative stress and inflammation as well as other potential processes in the pathogenesis or consequences of WMH.
PMCID: PMC3694808  PMID: 20966416
White matter; MRI; gene expression profiling; blood; ischemia; inflammation; oxidative stress; Alzheimer’s disease
3.  Y Chromosome gene expression in the blood of male ischemic stroke patients compared to male controls 
Gender medicine  2012;9(2):68-75.e3.
Background and Purpose
Gender is suggested to be an important determinant of ischemic stroke risk factors, etiology and outcome. However, the basis for this remains unclear. The Y chromosome is unique in males. Genes expressed in men on the Y chromosome that are associated with stroke may be important genetic contributors to the unique features of males with ischemic stroke, which would be helpful for explaining sex differences observed between men and women.
Blood samples were obtained from 40 males at ≤ 3, 5 and 24 hours following ischemic stroke and from 41 male controls (July 2003- April 2007). RNA was isolated from blood and processed on Affymetrix Human U133 Plus 2.0 Arrays. Y chromosome genes differentially expressed between male stroke and male control subjects were identified using an analysis of covariance (ANCOVA) adjusted for age and batch. A p<0.05 and fold change (FC) > ∣1.2∣ were considered significant.
Seven genes on the Y chromosome were differentially expressed in males with ischemic strokes compared to controls. Five of these genes (VAMP7, CSF2RA, SPRY3, DHRSX, PLCXD1,) are located on pseudoautosomal regions (PARs) of the human Y chromosome. The other two genes (EIF1AY and DDX3Y) are located on the non-recombining region of the human Y chromosome (NRY). The identified genes were associated with immunology, RNA metabolism, vesicle fusion and angiogenesis.
Specific genes on the Y chromosome are differentially expressed in blood following ischemic stroke. These genes provide insight into potential molecular contributors to sex differences in ischemic stroke.
PMCID: PMC3454519  PMID: 22365286
gene expression; ischemic stroke; gender; blood; Y chromosome
4.  DNA repair/replication transcripts are down regulated in patients with Fragile X Syndrome 
BMC Research Notes  2013;6:90.
Fragile X Syndrome (FXS) and its associated disorders are caused by the expansion of the CGG repeat in the 5’ untranslated region of the fragile X mental retardation 1 (FMR1) gene, with disease classification based on the number of CGG repeats. The mechanisms of repeat expansion are dependent on the presence of cis elements and the absence of trans factors both of which are not mutually exclusive and contribute to repeat instability. Expansions associated with trans factors are due to the haploinsuffient or reduced expression of several DNA repair/metabolizing proteins. The reduction of expression in trans factors has been primarily conducted in animal models without substantial examination of many of these expansion mechanisms and trans factors in humans.
To understand the trans factors and pathways associated with trinucleotide repeat expansion we have analyzed two microarray datasets which characterized the transcript expression in patients with FXS and in controls.
We observed significant down regulation of DNA damage/repair pathway transcripts. This observation was consistent in both datasets, which used different populations. Within these datasets, several transcripts overlapped in the direction of association and fold change. Further characterization of these genes will be critical to understand their role in trinucleotide repeat instability in FXS.
PMCID: PMC3637561  PMID: 23497562
Haploinsufficiency; FMR1; DNA repair/replication proteins
5.  MeCP2 modulates gene expression pathways in astrocytes 
Molecular Autism  2013;4:3.
Mutations in MECP2 encoding methyl-CpG-binding protein 2 (MeCP2) cause the X-linked neurodevelopmental disorder Rett syndrome. Rett syndrome patients exhibit neurological symptoms that include irregular breathing, impaired mobility, stereotypic hand movements, and loss of speech. MeCP2 protein epigenetically modulates gene expression through genome-wide binding to methylated CpG dinucleotides. While neurons have the highest level of MeCP2 expression, astrocytes and other cell types also express detectable levels of MeCP2. Recent studies suggest that astrocytes likely control the progression of Rett syndrome. Thus, the object of these studies was to identify gene targets that are affected by loss of MeCP2 binding in astrocytes.
To identify gene targets of MeCP2 in astrocytes, combined approaches of expression microarray and chromatin immunoprecipitation of MeCP2 followed by sequencing (ChIP-seq) were compared between wild-type and MeCP2-deficient astrocytes. MeCP2 gene targets were compared with genes in the top 10% of MeCP2 binding levels in gene windows either within 2 kb upstream of the transcription start site, or the ‘gene body’ that extended from transcription start to end site, or 2 kb downstream of the transcription end site.
A total of 118 gene transcripts surpassed the highly significant threshold (P < 0.005, fold change > 1.2) in expression microarray analysis from triplicate cultures. The top 10% of genes with the highest levels of MeCP2 binding were identified in two independent ChIP-seq experiments. Together this integrated, genome-wide screen for MeCP2 target genes provided an overlapping list of 19 high-confidence MeCP2-responsive gene transcripts in astrocytes. Validation of candidate target gene transcripts by RT-PCR revealed that expression of Apoc2, Cdon, Csrp and Nrep were consistently responsive to MeCP2 deficiency in astrocytes.
The first MeCP2 ChIP-seq and gene expression microarray analysis in astrocytes reveals a set of potential MeCP2 target genes that may contribute to normal astrocyte signaling, cell division and neuronal support functions, the loss of which may contribute to the Rett syndrome phenotype.
PMCID: PMC3561260  PMID: 23351786
MeCP2; Epigenetics; Astrocytes; Rett syndrome; ChIP-seq; Transcription
6.  Gene expression profiling of blood in brain arteriovenous malformation patients 
Translational stroke research  2011;2(4):575-587.
Brain arteriovenous malformations (BAVMs) are an important cause of intracranial hemorrhage (ICH) in young adults. Gene expression profiling of blood has led to the identification of stroke biomarkers, and may help identify BAVM biomarkers and illuminate BAVM pathogenesis. It is unknown whether blood gene expression profiles differ between 1) BAVM patients and healthy controls, or 2) unruptured and ruptured BAVM patients at presentation. We characterized blood transcriptional profiles in 60 subjects (20 unruptured BAVM, 20 ruptured BAVM, and 20 healthy controls) using Affymetrix whole genome expression arrays. Expression differences between groups were tested by ANOVA, adjusting for potential confounders. Genes with absolute fold change ≥ 1.2 (false discovery rate corrected p ≤ 0.1) were selected as differentially expressed and evaluated for over-representation in KEGG biological pathways (p ≤ 0.05). Twenty-nine genes were differentially expressed between unruptured BAVM patients and controls, including 13 which may be predictive of BAVM. Patients with ruptured BAVM compared to unruptured BAVM differed in expression of 1490 genes, with over-representation of genes in 8 pathways including MAPK, VEGF, Wnt signaling and several inflammatory pathways. These results suggest clues to the pathogenesis of BAVM and/or BAVM rupture and point to potential biomarkers or new treatment targets.
PMCID: PMC3241209  PMID: 22184505
arteriovenous malformation; blood; gene expression; intracranial hemorrhage; microarray analysis
7.  Plasmodium falciparum Gametocyte Development 1 (Pfgdv1) and Gametocytogenesis Early Gene Identification and Commitment to Sexual Development 
PLoS Pathogens  2012;8(10):e1002964.
Malaria transmission requires the production of male and female gametocytes in the human host followed by fertilization and sporogonic development in the mosquito midgut. Although essential for the spread of malaria through the population, little is known about the initiation of gametocytogenesis in vitro or in vivo. Using a gametocyte-defective parasite line and genetic complementation, we show that Plasmodium falciparum gametocyte development 1 gene (Pfgdv1), encoding a peri-nuclear protein, is critical for early sexual differentiation. Transcriptional analysis of Pfgdv1 negative and positive parasite lines identified a set of gametocytogenesis early genes (Pfge) that were significantly down-regulated (>10 fold) in the absence of Pfgdv1 and expression was restored after Pfgdv1 complementation. Progressive accumulation of Pfge transcripts during successive rounds of asexual replication in synchronized cultures suggests that gametocytes are induced continuously during asexual growth. Comparison of Pfge gene transcriptional profiles in patient samples divided the genes into two groups differing in their expression in mature circulating gametocytes and providing candidates to evaluate gametocyte induction and maturation separately in vivo. The expression profile of one of the early gametocyte specific genes, Pfge1, correlated significantly with asexual parasitemia, which is consistent with the ongoing induction of gametocytogenesis during asexual growth observed in vitro and reinforces the need for sustained transmission-blocking strategies to eliminate malaria.
Author Summary
As malaria control efforts move toward eradication it becomes increasingly important to develop interventions that block transmission. Consequently, advances are needed in our understanding of the production of gametocytes, which are required to transmit the disease. This report provides a first view of the initial stages of gametocytogenesis in vitro and in vivo and demonstrates that during each asexual replication cycle a subpopulation of parasites convert to gametocyte development providing a long transmission window. We also identify a gene that is critical for gametocyte production, P. falciparum gametocyte development 1 (Pfgdv1) and a set of genes specifically expressed during early gametocytogenesis in P. falciparum (Pfge genes). The expression profile and peri-nuclear location of Pfgdv1 in a subpopulation of schizonts is consistent with a role in an early step in gametocytogenesis. The RNA levels of Pfgdv1 and the Pfge genes accumulated gradually over several asexual cycles in vitro suggesting ongoing gametocyte formation during asexual growth. The further evaluation of these genes in a cohort of malaria infected patients indicated they are good candidates for markers to distinguish ring stage parasites committed to gametocyte production from circulating mature gametocytes, allowing direct analysis of the initiation of sexual differentiation in vivo.
PMCID: PMC3475683  PMID: 23093935
8.  Profiles of lacunar and non-lacunar stroke 
Annals of neurology  2011;70(3):477-485.
Determining which small deep infarcts (SDI) are of lacunar, arterial or cardioembolic etiology is challenging, but important in order to deliver optimal stroke prevention therapy. We sought to distinguish lacunar from non-lacunar causes of SDI using a gene expression profile.
A total of 184 ischemic strokes were analyzed. Lacunar stroke was defined as a lacunar syndrome with infarction <15mm in a region supplied by penetrating arteries. RNA from blood was processed on whole genome microarrays. Genes differentially expressed between lacunar (n=30) and non-lacunar strokes (n=86) were identified (false discovery rate ≤0.05, fold change>|1.5|) and used to develop a prediction model. The model was evaluated by cross-validation and in a second test cohort (n=36). The etiology of SDI of unclear cause (SDI≥15mm or SDI with potential embolic source) (n=32) was predicted using the derived model.
A 41 gene profile discriminated lacunar from non-lacunar stroke with greater than 90% sensitivity and specificity. Of the 32 SDI of unclear cause, 15 were predicted to be lacunar and 17 were predicted to be non-lacunar. The identified profile represents differences in immune response between lacunar and non-lacunar stroke.
Profiles of differentially expressed genes can distinguish lacunar from non-lacunar stroke. SDIs of unclear cause were frequently predicted to be of non-lacunar etiology, suggesting comprehensive workup of SDI is important to identify potential cardioembolic and arterial causes. Further study is required to evaluate the gene profile in an independent cohort and determine the clinical and treatment implications of SDI of predicted non-lacunar etiology.
PMCID: PMC3201749  PMID: 21796664
Lacunar stroke; small vessel disease; small deep infarct; gene expression
9.  UGT1A1 is a major locus influencing bilirubin levels in African Americans 
Total serum bilirubin is associated with several clinical outcomes, including cardiovascular disease, diabetes and drug metabolism. We conducted a genome-wide association study in 619 healthy unrelated African Americans in an attempt to replicate reported findings in Europeans and Asians and to identify novel loci influencing total serum bilirubin levels. We analyzed a dense panel of over two million genotyped and imputed SNPs in additive genetic models adjusting for age, sex, and the first two significant principal components from the sample covariance matrix of genotypes. Thirty-nine SNPs spanning a 78 kb region within the UGT1A1 displayed P-values <5 × 10−8. The lowest P-value was 1.7 × 10−22 for SNP rs887829. None of SNPs in the UGT1A1 remained statistically significant in conditional association analyses that adjusted for rs887829. In addition, SNP rs10929302 located in phenobarbital response enhancer module was significantly associated with bilirubin level with a P-value of 1.37 × 10−11; this enhancer module is believed to have a critical role in phenobarbital treatment of hyperbilirubinemia. Interestingly, the lead SNP, rs887829, is in strong linkage disequilibrium (LD) (r2≥0.74) with rs10929302. Taking advantage of the lower LD and shorter haplotypes in African-ancestry populations, we identified rs887829 as a more refined proxy for the causative variant influencing bilirubin levels. Also, we replicated the reported association between variants in SEMA3C and bilirubin levels. In summary, UGT1A1 is a major locus influencing bilirubin levels and the results of this study promise to contribute to understanding of the etiology and treatment of hyperbilirubinaemia in African-ancestry populations.
PMCID: PMC3306855  PMID: 22085899
GWAS; replications; bilirubin; African Americans
10.  Signatures of cardioembolic and large vessel ischemic stroke 
Annals of neurology  2010;68(5):681-692.
The cause of stroke remains unknown or cryptogenic in many patients. We sought to determine whether gene expression signatures in blood can distinguish between cardioembolic and large vessel causes of stroke, and whether these profiles can predict stroke etiology in the cryptogenic group.
A total of 194 samples from 76 acute ischemic stroke patients were analyzed. RNA was isolated from blood and run on Affymetrix U133 Plus2.0 microarrays. Genes that distinguish large vessel from cardioembolic stroke were determined at 3, 5, and 24 hours following stroke onset. Predictors were evaluated using cross-validation and a separate set of patients with known stroke subtype. The cause of cryptogenic stroke was predicted based on a model developed from strokes of known cause and identified predictors.
A 40 gene profile differentiated cardioembolic stroke from large vessel stroke with >95% sensitivity and specificity. A separate 37 gene profile differentiated cardioembolic stroke due to atrial fibrillation from non-atrial fibrillation causes with >90% sensitivity and specificity. The identified genes elucidate differences in inflammation between stroke subtypes. When applied to patients with cryptogenic stroke, 17% are predicted to be large vessel and 41% to be cardioembolic stroke. Of the cryptogenic strokes predicted to be cardioembolic, 27% were predicted to have atrial fibrillation.
Gene expression signatures distinguish cardioembolic from large vessel causes of ischemic stroke. These gene profiles may add valuable diagnostic information in the management of patients with stroke of unknown etiology though they need to be validated in future independent, large studies.
PMCID: PMC2967466  PMID: 21031583
Gene expression; ischemic stroke; biomarker
11.  Regional genome transcriptional response of adult mouse brain to hypoxia 
BMC Genomics  2011;12:499.
Since normal brain function depends upon continuous oxygen delivery and short periods of hypoxia can precondition the brain against subsequent ischemia, this study examined the effects of brief hypoxia on the whole genome transcriptional response in adult mouse brain.
Pronounced changes of gene expression occurred after 3 hours of hypoxia (8% O2) and after 1 hour of re-oxygenation in all brain regions. The hypoxia-responsive genes were predominantly up-regulated in hindbrain and predominantly down-regulated in forebrain - possibly to support hindbrain survival functions at the expense of forebrain cognitive functions. The up-regulated genes had a significant role in cell survival and involved both shared and unshared signaling pathways among different brain regions. Up-regulation of transcriptional signaling including hypoxia inducible factor, insulin growth factor (IGF), the vitamin D3 receptor/retinoid X nuclear receptor, and glucocorticoid signaling was common to many brain regions. However, many of the hypoxia-regulated target genes were specific for one or a few brain regions. Cerebellum, for example, had 1241 transcripts regulated by hypoxia only in cerebellum but not in hippocampus; and, 642 (54%) had at least one hepatic nuclear receptor 4A (HNF4A) binding site and 381 had at least two HNF4A binding sites in their promoters. The data point to HNF4A as a major hypoxia-responsive transcription factor in cerebellum in addition to its known role in regulating erythropoietin transcription. The genes unique to hindbrain may play critical roles in survival during hypoxia.
Differences of forebrain and hindbrain hypoxia-responsive genes may relate to suppression of forebrain cognitive functions and activation of hindbrain survival functions, which may coordinately mediate the neuroprotection afforded by hypoxia preconditioning.
PMCID: PMC3218040  PMID: 21988864
12.  Gene Expression Profiling of Blood for the Prediction of Ischemic Stroke 
Background and Purpose
A blood based biomarker of acute ischemic stroke would be of significant value in clinical practice. This study aimed to 1) replicate in a larger cohort our previous study using gene expression profiling to predict ischemic stroke1 and 2) refine prediction of ischemic stroke by including control groups relevant to ischemic stroke.
Ischemic stroke patients (n=70, 199 samples) were compared to controls who were healthy (n=38), had vascular risk factors (n=52), and who had myocardial infarction (n=17). Whole blood was drawn ≤3h, 5h and 24h after stroke onset and from controls. RNA was processed on whole genome microarrays. Genes differentially expressed in ischemic stroke were identified and analyzed for predictive ability to discriminate stroke from controls.
The 29 probe sets previously reported1 predicted a new set of ischemic strokes with 93.5% sensitivity and 89.5% specificity. 60- and 46-probe sets differentiated control groups from 3h and 24h ischemic stroke samples, respectively. A 97-probe set correctly classified 86% of ischemic strokes (3h + 24h), 84% of healthy subjects, 96% of vascular risk factor subjects and 75% with myocardial infarction.
This study replicated our previously reported gene expression profile in a larger cohort and identified additional genes that discriminate ischemic stroke from relevant control groups. This multi-gene approach shows potential for a point-of-care test in acute ischemic stroke.
PMCID: PMC2987675  PMID: 20798371
gene expression profiling; blood; ischemia; stroke; biomarkers
13.  Blood brain barrier breakdown and repair by src after thrombin-induced injury 
Annals of neurology  2010;67(4):526-533.
Thrombin mediates the life-threatening cerebral edema that occurs following intracerebral hemorrhage. Therefore, we examined the mechanisms of thrombin-induced injury to the blood-brain barrier (BBB) and subsequent mechanisms of BBB repair.
Intracerebroventricular (i.c.v.) injection of thrombin (20 U) was used to model intraventricular hemorrhage in adult rats.
Thrombin reduced brain microvascular endothelial cell (BMVEC) and peri-vascular astrocyte immunoreactivity –indicating either cell injury or death; and, functionally disrupted the BBB as measured by increased water content and extravasation of sodium fluorescein and Evans blue dyes 24h later. Administration of non-specific src family kinase inhibitor PP2 immediately following thrombin injections blocked brain edema and BBB disruption. At 7 to 14 days after thrombin injections newborn endothelial cells and astrocytes were observed around cerebral vessels at the time when BBB permeability and cerebral water content resolved. Delayed administration of PP2 on days 2 through 6 following thrombin injections prevented resolution of the edema and abnormal BBB permeability.
Thrombin, via its PAR receptors, is postulated to activate src kinase phosphorylation of molecules that acutely injure the BBB and produce edema. Thus, acute administration of src antagonists blocks edema. In contrast, src blockade for 2-6 days following thrombin injections is postulated to prevent resolution of edema and abnormal BBB permeability in part because src kinase proto-oncogene members stimulate proliferation of newborn BMVECs and peri-vascular astrocytes in the “neurovascular niche” that repair the damaged BBB. Thus, src kinases not only mediate acute BBB injury but also mediate chronic BBB repair after thrombin-induced injury.
PMCID: PMC2919346  PMID: 20437588
14.  Brain and blood microRNA expression profiling of ischemic stroke, intracerebral hemorrhage, and kainate seizures 
MicroRNAs (miRNAs) regulate gene expression and have a critical role in many biologic and pathologic processes. We hypothesized that miRNA expression profiles in injured brain (hippocampus) would show common as well as unique profiles when compared with those of blood. Adult, untouched, control rats were compared with rats with sham surgeries, ischemic strokes, brain hemorrhage (lysed blood, fresh blood, or thrombin), and kainate-induced seizures. Brain and whole-blood miRNA expression profiles were assessed 24 h later using TaqMan rodent miRNA arrays. MicroRNA response profiles were different for each condition. Many miRNAs changed more than 1.5-fold in brain and blood after each experimental manipulation, and several miRNAs were upregulated or downregulated in both brain and blood after a given injury. A few miRNAs (e.g., miR-298, miR-155, and miR-362-3p) were upregulated or downregulated more than twofold in both brain and blood after several different injuries. The results show the possible use of blood miRNAs as biomarkers for brain injury; that selected blood miRNAs may correlate with miRNA changes in the brain; and that many of the mRNAs, previously shown to be regulated in brain and blood after brain injury, are likely accounted for by changes in miRNA expression.
PMCID: PMC2949089  PMID: 19724284
blood; brain; epilepsy; hemorrhage; ischemia; microRNA (miRNA)
15.  Brief focal cerebral ischemia that simulates transient ischemic attacks in humans regulates gene expression in rat peripheral blood 
Blood gene expression profiles of very brief (5 and 10 mins) focal ischemia that simulates transient ischemic attacks in humans were compared with ischemic stroke (120 mins focal ischemia), sham, and naïve controls. The number of significantly regulated genes after 5 and 10 mins of cerebral ischemia was 39 and 160, respectively (fold change ⩾∣1.5∣ and P<0.05). There were 103 genes common to brief focal ischemia and ischemic stroke. Ingenuity pathway analysis showed that genes regulated in the 5 mins group were mainly involved in small molecule biochemistry. Genes regulated in the 10 mins group were involved in cell death, development, growth, and proliferation. Such genes were also regulated in the ischemic stroke group. Genes common to ischemia were involved in the inflammatory response, immune response, and cell death—indicating that these pathways are a feature of focal ischemia, regardless of the duration. These results provide evidence that brief focal ischemia differentially regulates gene expression in the peripheral blood in a manner that could distinguish brief focal ischemia from ischemic stroke and controls in rats. We postulate that this will also occur in humans.
PMCID: PMC2949112  PMID: 19738631
blood; focal cerebral ischemia; gene expression; rat; stroke; transient ischemic attack
16.  Genome response to tissue plasminogen activator in experimental ischemic stroke 
BMC Genomics  2010;11:254.
Tissue plasminogen activator (tPA) is known to have functions beyond fibrinolysis in acute ischemic stroke, such as blood brain barrier disruption. To further delineate tPA functions in the blood, we examined the gene expression profiles induced by tPA in a rat model of ischemic stroke.
tPA differentially expressed 929 genes in the blood of rats (p ≤ 0.05, fold change ≥ |1.2|). Genes identified had functions related to modulation of immune cells. tPA gene expression was found to be dependent on the reperfusion status of cerebral vasculature. The majority of genes regulated by tPA were different from genes regulated by ischemic stroke.
tPA modulates gene expression in the blood of rats involving immune cells in a manner that is dependent on the status of vascular reperfusion. These non-fibrinolytic activities of tPA in the blood serve to better understand tPA-related complications.
PMCID: PMC2875237  PMID: 20406488
17.  Identification and validation of suitable endogenous reference genes for gene expression studies in human peripheral blood 
BMC Medical Genomics  2009;2:49.
Gene expression studies require appropriate normalization methods. One such method uses stably expressed reference genes. Since suitable reference genes appear to be unique for each tissue, we have identified an optimal set of the most stably expressed genes in human blood that can be used for normalization.
Whole-genome Affymetrix Human 2.0 Plus arrays were examined from 526 samples of males and females ages 2 to 78, including control subjects and patients with Tourette syndrome, stroke, migraine, muscular dystrophy, and autism. The top 100 most stably expressed genes with a broad range of expression levels were identified. To validate the best candidate genes, we performed quantitative RT-PCR on a subset of 10 genes (TRAP1, DECR1, FPGS, FARP1, MAPRE2, PEX16, GINS2, CRY2, CSNK1G2 and A4GALT), 4 commonly employed reference genes (GAPDH, ACTB, B2M and HMBS) and PPIB, previously reported to be stably expressed in blood. Expression stability and ranking analysis were performed using GeNorm and NormFinder algorithms.
Reference genes were ranked based on their expression stability and the minimum number of genes needed for nomalization as calculated using GeNorm showed that the fewest, most stably expressed genes needed for acurate normalization in RNA expression studies of human whole blood is a combination of TRAP1, FPGS, DECR1 and PPIB. We confirmed the ranking of the best candidate control genes by using an alternative algorithm (NormFinder).
The reference genes identified in this study are stably expressed in whole blood of humans of both genders with multiple disease conditions and ages 2 to 78. Importantly, they also have different functions within cells and thus should be expressed independently of each other. These genes should be useful as normalization genes for microarray and RT-PCR whole blood studies of human physiology, metabolism and disease.
PMCID: PMC2736983  PMID: 19656400
18.  Src Kinase Inhibition Decreases Thrombin Induced Injury and Cell Cycle Re-Entry in Striatal Neurons 
Neurobiology of disease  2008;30(2):201-211.
Since Src kinase inhibitors decrease brain injury produced by intracerebral hemorrhage (ICH) and thrombin is activated following ICH, this study determined whether Src kinase inhibitors decrease thrombin induced brain injury. Thrombin injections into adult rat striatum produced focal infarction and motor deficits. The Src kinase inhibitor PP2 decreased thrombin-induced Src activation, infarction in striatum and motor deficits in vivo. Thrombin applied to cultured post-mitotic striatal neurons caused: injury to axons and dendrites; many TUNEL positive neuronal nuclei; and re-entry into the cell cycle as manifested by cyclin D1 expression, induction of several other cell cycle genes and cyclin-dependent kinase 4 activation. PP2 dose-dependently attenuated thrombin-induced injury to the cultured neurons; and attenuated thrombin-induced neuronal cell cycle re-entry. These results are consistent with the hypotheses that Src kinase inhibitors decrease injury produced by ICH by decreasing thrombin activation of Src kinases and, at least in part, by decreasing Src induced cell cycle re-entry.
PMCID: PMC2413433  PMID: 18343677
thrombin; mitogenic signaling; cell cycle; neuronal apoptosis; intracerebral hemorrhage; striatum
19.  Novel insights into the relationships between dendritic cell subsets in human and mouse revealed by genome-wide expression profiling 
Genome Biology  2008;9(1):R17.
Genome-wide expression profiling of mouse and human leukocytes reveal conserved transcriptional programs of plasmacytoid or conventional dendritic cell subsets.
Dendritic cells (DCs) are a complex group of cells that play a critical role in vertebrate immunity. Lymph-node resident DCs (LN-DCs) are subdivided into conventional DC (cDC) subsets (CD11b and CD8α in mouse; BDCA1 and BDCA3 in human) and plasmacytoid DCs (pDCs). It is currently unclear if these various DC populations belong to a unique hematopoietic lineage and if the subsets identified in the mouse and human systems are evolutionary homologs. To gain novel insights into these questions, we sought conserved genetic signatures for LN-DCs and in vitro derived granulocyte-macrophage colony stimulating factor (GM-CSF) DCs through the analysis of a compendium of genome-wide expression profiles of mouse or human leukocytes.
We show through clustering analysis that all LN-DC subsets form a distinct branch within the leukocyte family tree, and reveal a transcriptomal signature evolutionarily conserved in all LN-DC subsets. Moreover, we identify a large gene expression program shared between mouse and human pDCs, and smaller conserved profiles shared between mouse and human LN-cDC subsets. Importantly, most of these genes have not been previously associated with DC function and many have unknown functions. Finally, we use compendium analysis to re-evaluate the classification of interferon-producing killer DCs, lin-CD16+HLA-DR+ cells and in vitro derived GM-CSF DCs, and show that these cells are more closely linked to natural killer and myeloid cells, respectively.
Our study provides a unique database resource for future investigation of the evolutionarily conserved molecular pathways governing the ontogeny and functions of leukocyte subsets, especially DCs.
PMCID: PMC2395256  PMID: 18218067

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