Audrey Papp - Academia.edu (original) (raw)

Papers by Audrey Papp

Clinical Pharmacology & Therapeutics, Sep 30, 2013

The association of nonfunctional variants of the cholesteryl ester transfer protein (CETP) with e... more The association of nonfunctional variants of the cholesteryl ester transfer protein (CETP) with efficacy of statins has been a subject of debate. We evaluated whether three functional CETP variants influence statin efficacy. The effect of CETP genotype on achieved levels of high-density lipoprotein cholesterol (HDLc), low-density lipoprotein cholesterol (LDLc), and total cholesterol during statin treatment was estimated by meta-analysis of the linear regression outcomes of three studies (11,021 individuals). The effect of these single-nucleotide polymorphisms (SNPs) on statin response in protecting against myocardial infarction (MI) was estimated by meta-analysis of statin × SNP interaction terms from logistic regression in five studies (16,570 individuals). The enhancer SNP rs3764261 significantly increased HDLc by 0.02 mmol/l per T allele (P = 6 × 10(-5)) and reduced protection against MI by statins (interaction odds ratio (OR) = 1.19 per T allele; P = 0.04). Focusing on functional CETP variants, we showed that in carriers of the rs3764261 T variant, HDLc increased more during statin treatment, and protection against MI by statins appeared to be reduced as compared with those in noncarriers.

The Journal of Immunology

Human alveolar macrophages (AMs) are the primary target of Mycobacterium tuberculosis (M.tb) in t... more Human alveolar macrophages (AMs) are the primary target of Mycobacterium tuberculosis (M.tb) in the lung, where M.tb establishes intracellular residence and growth. This study characterizes M.tb-AM interactions and processes driving inter-subject variability. AMs were obtained by bronchoalveolar lavage from 28 healthy donors and cultured in the presence and absence of virulent M.tb strain H37Rv engineered to produce bioluminescence. Luminescence intensity (RLU) was measured at 2, 24, 48, and 72h post infection. At 2, 24, and 72h, we also measured 27 secreted proteins and AM RNA transcriptomes using AmpliSeq, targeting 20,804 genes, including 2,228 non-coding RNAs. RLUs reveal large differences in M.tb uptake at 2h, varying rates of intracellular adaptation between 2 and 24h, and a range of growth rates from 48 to 72h, resulting in discrete donor groups for each type of interaction. We identify 5039 significant differentially expressed RNAs (DE genes), revealing immune-related pathwa...

Panel A: Association p values assessing relationship between CETP SNP... more Panel A: Association p values assessing relationship between CETP SNPs and Δ9 splice variant formation in human livers (n = 94). Only rs9930761 and rs5883 in exon 8–10 region can account for increased formation of the Δ9 splice variant. rs289714 (intron 9), rs5882 (I405V), and rs1801706 (G84A) show varying degrees of LD with rs9930761, accounting for the observed association p values. Details for the SNPs in this study are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031930#pone.0031930.s008" target="_blank">Table S3</a>. Panel B: Percent Δ9 splice variant of total CETP mRNA as a function of rs5883T>C and rs9930761C>T. Homozygous minor allele carriers for rs5883/rs9930761 were not observed. All livers were heterozygous for both rs9930761 and rs5883, except for two livers heterozygous only for rs9930761, indicating that rs5883 is necessary for enhanced splicing. Using ANOVA with Dunnett's post-test, p values for both homozygous vs. rs9930761 and vs. rs5883 are P<0.01.</p

Mycobacterium tuberculosis(M.tb) establishes residence and growth in human alveolar macrophages (... more Mycobacterium tuberculosis(M.tb) establishes residence and growth in human alveolar macrophages (AMs). Large inter-individual variation inM.tb-AM interactions is a potential early indicator of TB risk and efficacy of therapies and vaccines. Herein, we systematically analyze interactions of a virulentM.tbstrain with freshly isolated human AMs from 28 healthy adult donors, measuring host RNA expression and secreted candidate proteins associated with TB pathogenesis over 72h. We observe large inter-individual differences in bacterial uptake and growth, with tenfold variation inM.tbload at 72h, reflected by large variation of gene expression programs. Systems analysis of differential and variable RNA and protein expression identifies TB-associated genes and networks (e.g., IL1BandIDO1). RNA time profiles document early stimulation of M1-type macrophage gene expression followed by emergence of an M2-type profile. The fine-scale resolution of this work enables the separation of genes and ...

Average expression of invariable genes in 4 GTEx brains. Shows the variation of 200 invariable ge... more Average expression of invariable genes in 4 GTEx brains. Shows the variation of 200 invariable genes expressed in 4 GTEx brain regions. (PDF 189 kb)

Table S1. Sequencing and mapping statistics. Listed are the sequencing details and mapping statis... more Table S1. Sequencing and mapping statistics. Listed are the sequencing details and mapping statistics for the presented data. Sequencing sets varied in the number of lanes per run, sequencing technology, and inclusion of paired reads. For sets with replicate runs, the number of lanes for each run and the sequencer technology are separated by slashes. Some replicate runs were generated under different sequencing conditions (SOLiD5500 technology vs wildfire technology) and this is indicated when appropriate. Table S2. Normalizing genes identified by mathematical modeling. 2a Top 200 invariable genes. Lists top 20 genes found to be constant across subjects and tissues. 2b Top 200 stable genes. Lists top 20 genes found to be constant across subjects, but different between tissues. Table S3. Differentially expressed genes between brain regions. Lists all significantly (FDR ≤ 0.05) differentially expressed genes between any two brain regions identified by RUVseq after removing unwanted va...

Cancer Research, 2009

Objective: Genetic alterations of BRCA1 and P53, both located on chromosome 17, are common in man... more Objective: Genetic alterations of BRCA1 and P53, both located on chromosome 17, are common in many gynecologic cancers. Mutations in NF1 , also located on chromosome 17, have been implicated in the development of neurologic and hematologic cancers but to date, research has not focused on the role of NF1 in gynecologic cancers. We aimed to determine if the loss or partial loss of NF1 is an initiating event in the development of epithelial ovarian cancer (EOC), in comparison to BRCA1 and P53 . Materials and Methods: Loss of heterozygosity (LOH) for NF1, BRCA1 , and P53 , all located on chromosome 17, was analyzed in tumors from 64 primary EOC tumors with SNaPshot primer extension. LOH was defined by allelic ratios >1.5. mRNA expression of these three genes was also measured with RT-PCR, to determine whether LOH is linked to a drastic downregulation of mRNA expression. Results: Seven SNPs were evaluated as markers for quantitation of LOH. LOH was demonstrated in 45% (21/47) of sampl...

C31. TRANSLATIONAL STUDIES IN SARCOIDOSIS, 2019

International journal of molecular sciences, Jan 9, 2017

Tuberculosis (TB) is a global epidemic caused by the infection of human macrophages with the worl... more Tuberculosis (TB) is a global epidemic caused by the infection of human macrophages with the world's most deadly single bacterial pathogen, Mycobacterium tuberculosis (M.tb). M.tb resides in a phagosomal niche within macrophages, where trace element concentrations impact the immune response, bacterial metal metabolism, and bacterial survival. The manipulation of micronutrients is a critical mechanism of host defense against infection. In particular, the human zinc transporter Zrt-/Irt-like protein 8 (ZIP8), one of 14 ZIP family members, is important in the flux of divalent cations, including zinc, into the cytoplasm of macrophages. It also has been observed to exist on the membrane of cellular organelles, where it can serve as an efflux pump that transports zinc into the cytosol. ZIP8 is highly inducible in response to M.tb infection of macrophages, and we have observed its localization to the M.tb phagosome. The expression, localization, and function of ZIP8 and other divalent ...

American journal of respiratory cell and molecular biology, Oct 9, 2017

Many aspects of pathogenic granuloma formation are poorly understood requiring new relevant labor... more Many aspects of pathogenic granuloma formation are poorly understood requiring new relevant laboratory models that represent the complexity (genetics and diversity) of human disease. To address this need, we developed an in vitro model of granuloma formation using human peripheral blood mononuclear cells (PBMCs) derived from patients with active sarcoidosis, latent tuberculosis (TB) infection (LTBI), or normal healthy controls. PBMCs were incubated for 7 days with uncoated polystyrene beads or beads coated with purified protein derivative (PPD) or human serum albumin (HSA). In response to PPD-coated beads, PBMCs from sarcoidosis and LTBI donors formed robust multicellular aggregates resembling granulomas displaying a typical Th1 type immune response, as assessed by cytokine analyses. In contrast, minimal PBMC aggregation occurred when control PBMCs were incubated with PPD-coated beads, while the response to uncoated beads was negligible in all groups. Sarcoidosis PBMCs responded to ...

BMC Medical Genomics, 2012

Background: Sulfamethoxazole (SMX) is a commonly used antibiotic for prevention of infectious dis... more Background: Sulfamethoxazole (SMX) is a commonly used antibiotic for prevention of infectious diseases associated with HIV/AIDS and immune-compromised states. SMX-induced hypersensitivity is an idiosyncratic cutaneous drug reaction with genetic components. Here, we tested association of candidate genes involved in SMX bioactivation and antioxidant defense with SMX-induced hypersensitivity. Results: Seventy seven single nucleotide polymorphisms (SNPs) from 14 candidate genes were genotyped and assessed for association with SMX-induced hypersensitivity, in a cohort of 171 HIV/AIDS patients. SNP rs761142 T > G, in glutamate cysteine ligase catalytic subunit (GCLC), was significantly associated with SMX-induced hypersensitivity, with an adjusted p value of 0.045. This result was replicated in a second cohort of 249 patients (p = 0.025). In the combined cohort, heterozygous and homozygous carriers of the minor G allele were at increased risk of developing hypersensitivity (GT vs TT, odds ratio = 2.2, 95% CL 1.4-3.7, p = 0.0014; GG vs TT, odds ratio = 3.3, 95% CL 1.6-6.8, p = 0.0010). Each minor allele copy increased risk of developing hypersensitivity 1.9 fold (95% CL 1.4-2.6, p = 0.00012). Moreover, in 91 human livers and 84 B-lymphocytes samples, SNP rs761142 homozygous G allele carriers expressed significantly less GCLC mRNA than homozygous TT carriers (p < 0.05). Conclusions: rs761142 in GCLC was found to be associated with reduced GCLC mRNA expression and with SMX-induced hypersensitivity in HIV/AIDS patients. Catalyzing a critical step in glutathione biosynthesis, GCLC may play a broad role in idiosyncratic drug reactions.

American Journal of Physiology-Lung Cellular and Molecular Physiology, 2008

Zinc is an essential micronutrient and cytoprotectant involved in the host response to inflammato... more Zinc is an essential micronutrient and cytoprotectant involved in the host response to inflammatory stress. We tested whether zinc transporters, the critical regulators that maintain intracellular zinc concentrations, play a role in cell survival, particularly in lung epithelia, during inflammation. Initially, mRNA transcripts were quantitatively measured by RT-PCR for all known human zinc transporters, including 14 importers (SLC39A1–14) and 10 exporters (SLC30A1–10), in primary human lung epithelia obtained from multiple human donors and BEAS-2B cell cultures under baseline and TNF-α-stimulated conditions. While many zinc transporters were constitutively expressed, only SLC39A8 (Zip8) mRNA was strongly induced by TNF-α. Endogenous Zip8 protein was not routinely detected under baseline conditions. In sharp contrast, TNF-α induced the expression of a glycosylated protein that translocated to the plasma membrane and mitochondria. Increased Zip8 expression resulted in an increase in i...

American journal of respiratory cell and molecular biology, Jan 22, 2018

The mechanisms underlying abnormal granuloma formation in patients with sarcoidosis are complex a... more The mechanisms underlying abnormal granuloma formation in patients with sarcoidosis are complex and remain poorly understood. A novel in vitro human granuloma model was used to determine the molecular mechanisms of granuloma-genesis in patients with sarcoidosis in response to putative disease-causing mycobacterial antigens. Peripheral blood mononuclear cells (PBMCs) from patients with active sarcoidosis and from normal, disease-free controls were incubated for 7 days with purified protein derivative (PPD)-coated polystyrene beads. Molecular responses were analyzed, as reflected by differential expression (DE) of genes, extracellular cytokine patterns, and cell surface receptor expression. Unbiased systems biology approaches were used to identify signaling pathways engaged during granuloma formation. Model findings were compared to human lung and mediastinal lymph node gene expression profiles. Compared to identically treated PBMCs of controls (n = 5), PPD-treated sarcoidosis PBMCs (...

European Journal of Pharmaceutical Sciences, May 1, 2017

The blood-brain barrier (BBB) expresses numerous membrane transporters that supply needed nutrien... more The blood-brain barrier (BBB) expresses numerous membrane transporters that supply needed nutrients to the central nervous system (CNS), consisting mostly of solute carriers (SLC transporters), or remove unwanted substrates via extrusion pumps through the action of ATP binding cassette (ABC) transporters. Previous work has identified many BBB transporters using hybridization arrays or qRT-PCR, using targeted probes. Here we have performed next-generation sequencing of the transcriptome (RNAseq) extracted from cerebral cortex tissues and brain microvessel endothelial cells (BMEC) obtained from two donors. The same RNA samples had previously been measured for transporter expression using qRT-PCR (Geier et al., 2013), yielding similar expression levels for overlapping mRNAs (R = 0.66, p b 0.001). RNAseq confirms a number of transporters highly enriched in BMECs (e.g., ABCB1, ABCG2, SLCO2B1, and SLC47A1), but also detects novel BMEC transporters. Multiple splice isoforms detected by RNAseq are either robustly enriched or depleted in BMECs, indicating differential RNA processing in the BBB. The Complete RNAseq data are publically available (GSE94064).

Translational Psychiatry, Jan 22, 2013

Epistatic gene-gene interactions could contribute to the heritability of complex multigenic disor... more Epistatic gene-gene interactions could contribute to the heritability of complex multigenic disorders, but few examples have been reported. Here, we focus on the role of aberrant dopaminergic signaling, involving the dopamine transporter DAT, a cocaine target, and the dopamine D2 receptor, which physically interacts with DAT. Splicing polymorphism rs2283265 of DRD2, encoding D2 receptors, were shown to confer risk of cocaine overdose/death (odds ratio B3) in subjects and controls from the Miami Dade County Brain Bank. 1 Risk of cocaine-related death attributable to the minor allele of rs2283265 was significantly enhanced to OR ¼ 7.5 (P ¼ 0.0008) in homozygous carriers of the main 6-repeat allele of DAT rs3836790, a regulatory VNTR in intron8 lacking significant effect itself. In contrast, carriers of the minor 5-repeat DAT allele showed no significant risk (OR ¼ 1.1, P ¼ 0.84). DAT rs3836790 and DRD2 rs2283265 also interacted by modulating DAT protein activity in the ventral putamen of cocaine abusers. In high-linkage disequilibrium with the VNTR, DAT rs6347 in exon9 yielded similar results. Assessing the impact of DAT alone, a rare DAT haplotype formed by the minor alleles of rs3836790 and rs27072, a regulatory DAT variant in the 3 0-UTR, occurred in nearly one-third of the cocaine abusers but was absent in African American controls, apparently conferring strong risk. These results demonstrate gene-gene-drug interaction affecting risk of fatal cocaine intoxication.

BioTechniques, May 1, 2003

We present a PCR method for identification of single nucleotide polymorphisms (SNPs), using allel... more We present a PCR method for identification of single nucleotide polymorphisms (SNPs), using allele-specific primers designed for selective amplification of each allele. Matching the SNP at the 3′ end of the forward or reverse primer, and additionally incorporating a 3′ mismatch to prevent amplification of the incorrect allele, results in selectivity of the allele-specific primers. DNA melting analysis with fluorescent SYBR ® Green affords detection of the PCR products. By incorporating a GC-rich sequence into one of the two allele-specific primers to increase the melting temperature, both alleles can be measured simultaneously at their respective melting temperatures. Applying the DNA melting analysis to SNPs in ApoE and ABCA1 yielded results identical to those obtained with other genotyping methods. This provides a cost-effective, high-throughput method for amplification and scoring of SNPs.

PloS one, 2018

Human alveolar macrophages (HAM) are primary bacterial niche and immune response cells during Myc... more Human alveolar macrophages (HAM) are primary bacterial niche and immune response cells during Mycobacterium tuberculosis (M.tb) infection, and human blood monocyte-derived macrophages (MDM) are a model for investigating M.tb-macrophage interactions. Here, we use a targeted RNA-Seq method to measure transcriptome-wide changes in RNA expression patterns of freshly obtained HAM (used within 6 h) and 6 day cultured MDM upon M.tb infection over time (2, 24 and 72 h), in both uninfected and infected cells from three donors each. The Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (AmpliSeq) uses primers targeting 18,574 mRNAs and 2,228 non-coding RNAs (ncRNAs) for a total of 20,802 transcripts. AmpliSeqTM yields highly precise and reproducible gene expression profiles (R2 >0.99). Taking advantage of AmpliSeq's reproducibility, we establish well-defined quantitative RNA expression patterns of HAM versus MDM, including significant M.tb-inducible genes, in networks and pathways ...

Biochemical and biophysical research communications, Jan 28, 2016

Dementia with Lewy Bodies (DLB) is the second most common neurodegenerative disorder in the elder... more Dementia with Lewy Bodies (DLB) is the second most common neurodegenerative disorder in the elderly. The development and progression of DLB remain unclear. In this study we used next generation sequencing to assess RNA expression profiles and cellular processes associated with DLB in the anterior cingulate cortex, a brain region affected by DLB pathology. The expression measurements were made in autopsy brain tissues from 8 DLB subjects and 10 age-matched controls using AmpliSeq technology with ion torrent sequencing. The analysis of RNA expression profiles revealed 490 differentially expressed genes, among which 367 genes were down-regulated and 123 were up-regulated. Functional enrichment analysis of genes differentially expressed in DLB indicated downregulation of genes associated with myelination, neurogenesis, and regulation of nervous system development. miRNA binding sites enriched in these mRNAs yielded a list of candidate miRNAs participating in DLB pathophysiology. Our stu...