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1.  Ribonucleotide Reductase Subunit M2 Predicts Survival in Subgroups of Patients with Non-Small Cell Lung Carcinoma: Effects of Gender and Smoking Status 
PLoS ONE  2015;10(5):e0127600.
Ribonucleotide reductase catalyzes the conversion of ribonucleotide diphosphates to deoxyribonucleotide diphosphates. The functional enzyme consists of two subunits - one large (RRM1) and one small (RRM2 or RRM2b) subunit. Expression levels of each subunit have been implicated in prognostic outcomes in several different types of cancers.
Experimental Design
Immunohistochemistry for RRM1 and RRM2 was performed on a lung cancer tissue microarray (TMA) and analyzed. 326 patients from the microarray were included in this study.
In non-small cell lung cancer (NSCLC), RRM2 expression was strongly predictive of disease-specific survival in women, non-smokers and former smokers who had quit at least 10 years prior to being diagnosed with lung cancer. Higher expression was associated with worse survival. This was not the case for men, current smokers and those who had stopped smoking for shorter periods of time. RRM1 was not predictive of survival outcomes in any subset of the patient group.
RRM2, but not RRM1, is a useful predictor of survival outcome in certain subsets of NSCLC patients.
PMCID: PMC4441434  PMID: 26001082
2.  Assessment of Nutritional and Depression Status in Free-Living El­derly in Tabriz, Northwest Iran 
Health Promotion Perspectives  2013;3(2):288-293.
Background: Malnutrition and depression are the common health problems in elderly population. Poor nutrition might have a strong effect on the incidence of depression. The aims of this study were to assess the nutritional and depression status and the possibly relationship between these variables in the urban free-liv­ing elderly in Tabriz, northwestern Iran.
Methods: This cross-sectional study was carried out on 184 elderly people (male=97; female=87) with age 60 years or elder in 2012. All subjects entered to the study voluntarily from those attending to daily care centers for elderly peo­ple. Mini Nutritional Assessment (MNA) tool and Geriatric Depression Score (GDS) were used to evaluate nutritional status and depression scores, respec­tively. Con­tinuous variables were expressed as mean ± standard deviation (SD) and qualita­tive data were presented as frequency (percent). Spearman’s correla­tion was em­ployed to determine the relationship between variables.
Results:Up to 50% of subjects had poor nutrition status. About 14% of elderly people had serve depression and 28.3% had mild depression. There was a posi­tive significant correlation between MNA and GDS tests in both gender (r=0.416; P<0.001).
Conclusion: There was no acceptable level of nutritional status and mental health in the elderly people. Further studies are needed to evaluate the other factors that can effect on the quality of life in this population.
PMCID: PMC3963672  PMID: 24688979
Depression; Elderly; Geriatric Depression Score; Mini Nutritional Assessment; Iran
3.  Pseudomonas aeruginosa induces pigment production and enhances virulence in a white phenotypic variant of Staphylococcus aureus 
Staphyloxanthin is a virulence factor which protects Staphylococcus aureus in stress conditions. We isolated two pigment variants of S. aureus and one strain of Pseudomonas aeruginosa from a single wound infection. S. aureus variants displayed white and yellow colony phenotypes. The sequence of the operons for staphyloxanthin synthesis indicated that coding and promoter regions were identical between the two pigment variants. Quorum sensing controls pigment synthesis in some bacteria. It is also shown that P. aeruginosa quorum-sensing molecules affect S. aureus transcription. We explored whether the co-infecting P. aeruginosa can affect pigment production in the white S. aureus variant. In co-culture experiments between the white variants and a selected number of Gram-positive and Gram-negative bacteria, only P. aeruginosa induced pigment production in the white variant. Gene expression analysis of the white variant did not indicate upregulation of the crtM and other genes known to be involved in pigment production (sigB, sarA, farnesyl pyrophosphate synthase gene [FPP-synthase], hfq). In contrast, transcription of the catalase gene was significantly upregulated after co-culture. P. aeruginosa-induced pigment synthesis and catalase upregulation correlated with increased resistance to polymyxin B, hydrogen peroxide, and the intracellular environment of macrophages. Our data indicate the presence of silent but functional staphyloxanthin synthesis machinery in a white phenotypic variant of S. aureus which is activated by a co-infecting P. aeruginosa via inter-species communication. Another S. aureus virulence factor, catalase is also induced by this co-infecting bacterium. The resulting phenotypic changes are directly correlated with resistance of the white variant to stressful conditions.
PMCID: PMC3825675  PMID: 24232573
Staphylococcus aureus; Pseudomonas aeruginosa; staphyloxanthin; catalase; interspecies interaction
4.  Expression Levels of Estrogen Receptor Beta in Conjunction with Aromatase Predict Survival in Non-Small Cell Lung Cancer 
Estrogen signaling pathways may play a significant role in the pathogenesis of non-small cell lung cancers (NSCLC) as evidenced by the expression of aromatase and estrogen receptors (ERα and ERβ) in many of these tumors. Here we examine whether ERα and ERβ levels in conjunction with aromatase define patient groups with respect to survival outcomes and possible treatment regimens. Immunohistochemistry was performed on a high-density tissue microarray with resulting data and clinical information available for 377 patients. Patients were subdivided by gender, age and tumor histology, and survival data was determined using the Cox proportional hazards model and Kaplan-Meier curves. Neither ERα nor ERβ alone were predictors of survival in NSCLC. However, when coupled with aromatase expression, higher ERβ levels predicted worse survival in patients whose tumors expressed higher levels of aromatase. Although this finding was present in patients of both genders, it was especially pronounced in women ≥ 65 years old, where higher expression of both ERβ and aromatase indicated a markedly worse survival rate than that determined by aromatase alone. Conclusion: Expression of ERβ together with aromatase has predictive value for survival in different gender and age subgroups of NSCLC patients. This predictive value is stronger than each individual marker alone. Our results suggest treatment with aromatase inhibitors alone or combined with estrogen receptor modulators may be of benefit in some subpopulations of these patients.
PMCID: PMC3175023  PMID: 21511357
NSCLC; tissue microarray; aromatase; estrogen receptor; immunohistochemistry; prognosis
5.  Progesterone and estrogen receptor expression and activity in human non-small cell lung cancer 
Steroids  2011;76(9):910-920.
Lung cancer is the most common cause of cancer mortality in male and female patients in the US. Although it is clear that tobacco smoking is a major cause of lung cancer, about half of all women with lung cancer worldwide are never-smokers. Despite a declining smoking population, the incidence of non-small cell lung cancer (NSCLC), the predominant form of lung cancer, has reached epidemic proportions particularly in women. Emerging data suggest that factors other than tobacco, namely endogenous and exogenous female sex hormones, have a role in stimulating NSCLC progression. Aromatase, a key enzyme for estrogen biosynthesis, is expressed in NSCLC. Clinical data show that women with high levels of tumor aromatase (and high intratumoral estrogen) have worse survival than those with low aromatase. The present and previous studies also reveal significant expression and activity of estrogen receptors (ERα, ERβ) in both extranuclear and nuclear sites in most NSCLC. We now report further on the expression of progesterone receptor (PR) transcripts and protein in NSCLC. PR transcripts were significantly lower in cancerous as compared to non-malignant tissue. Using immunohistochemistry, expression of PR was observed in the nucleus and/or extranuclear compartments in the majority of human tumor specimens examined. Combinations of estrogen and progestins administered in vitro cooperate in promoting tumor secretion of vascular endothelial growth factor and, consequently, support tumor-associated angiogenesis. Further, dual treatment with estradiol and progestin increased the numbers of putative tumor stem/progenitor cells. Thus, ER- and/or PR-targeted therapies may offer new approaches to manage NSCLC.
PMCID: PMC3129425  PMID: 21600232
Progesterone; Estrogen; Steroid hormone receptor; Non-small cell lung cancer; VEGF; Progenitor cells; Cancer stem cells; Angiogenesis
6.  An Enterobacter plasmid as a new genetic background for the transposon Tn1331 
Genus Enterobacter includes important opportunistic nosocomial pathogens that could infect complex wounds. The presence of antibiotic resistance genes in these microorganisms represents a challenging clinical problem in the treatment of these wounds. In the authors’ screening of antibiotic-resistant bacteria from complex wounds, an Enterobacter species was isolated that harbors antibiotic-resistant plasmids conferring resistance to Escherichia coli. The aim of this study was to identify the resistance genes carried by one of these plasmids.
The plasmids from the Enterobacter isolate were propagated in E. coli and one of the plasmids, designated as pR23, was sequenced by the Sanger method using fluorescent dyeterminator chemistry on a genetic analyzer. The assembled sequence was annotated by search of the GenBank database.
Plasmid pR23 is composed of the transposon Tn1331 and a backbone plasmid that is identical to the plasmid pPIGDM1 from Enterobacter agglomerans. The multidrug-resistance transposon Tn1331, which confers resistance to aminoglycoside and beta lactam antibiotics, has been previously isolated only from Klebsiella. The Enterobacter plasmid pPIGDM1, which carries a ColE1-like origin of replication and has no apparent selective marker, appears to provide a backbone for propagation of Tn1331 in Enterobacter. The recognition sequence of Tn1331 transposase for insertion into pPIGDM1 is the pentanucleotide TATTA, which occurs only once throughout the length of this plasmid.
Transposition of Tn1331 into the Enterobacter plasmid pPIGDM1 enables this transposon to propagate in this Enterobacter. Since Tn1331 was previously isolated only from Klebsiella, this report suggests horizontal transfer of this transposon between the two bacterial genera.
PMCID: PMC3259689  PMID: 22259249
transposon Tn1331; Enterobacter; wound infection
7.  Presence of a putative tumor-initiating progenitor cell population predicts poor prognosis in smokers with non-small cell lung cancer 
Cancer research  2010;70(16):6639-6648.
Smoking is the most important known risk factor for the development of lung cancer. Tobacco exposure results in chronic inflammation, tissue injury and repair. A recent hypothesis argues for a stem/progenitor cell involved in airway epithelial repair that may be a tumor-initiating cell in lung cancer, and which may be associated with recurrence and metastasis. We used immunostaining, quantitative real-time PCR, Western blots and lung cancer tissue microarrays to identify subpopulations of airway epithelial stem/progenitor cells under steady state conditions, normal repair, aberrant repair with premalignant lesions and lung cancer and their correlation with injury and prognosis. We identified a population of keratin 14 (K14)-expressing progenitor epithelial cells that was involved in repair after injury. Dysregulated repair resulted in persistence of K14+ cells in the airway epithelium in premalignant lesions. The presence of K14+ cells in non-small cell lung cancer (NSCLC) samples predicted poorer outcomes. This was especially true in smokers where the presence of K14+ cells in NSCLC was predictive of metastasis. The presence of K14+ progenitor airway epithelial cells in NSCLC predicted a poor prognosis and this predictive value was strongest in smokers, where it also correlated with metastasis. This suggests that reparative K14+ progenitor cells may be tumor-initiating cells in this subgroup of smokers with NSCLC.
PMCID: PMC2924777  PMID: 20710044
Lung carcinogenesis; dysregulated repair; injury
8.  Epithelial Membrane Protein-2 is a Novel Therapeutic Target in Ovarian Cancer 
The tetraspan protein epithelial membrane protein-2 (EMP2) has been shown to regulate the surface display and signaling from select integrin pairs, and it was recently identified as a prognostic biomarker in human endometrial cancer. In this study, we assessed the role of EMP2 in human ovarian cancer.
Experimental Design
We examined the expression of EMP2 within a population of women with ovarian cancer using tissue microarray assay technology. We evaluated the efficacy of EMP2-directed antibody therapy using a fully human recombinant bivalent antibody fragment (diabody) in vitro and ovarian cancer xenograft models in vivo.
EMP2 was found to be highly expressed in over 70% of serous and endometrioid ovarian tumors compared to non-malignant ovarian epithelium using a human ovarian cancer tissue microarray. Using anti-EMP2 diabody, we evaluated the in vitro response of 9 human ovarian cancer cell lines with detectable EMP2 expression. Treatment of human ovarian cancer cell lines with anti-EMP2 diabodies induced cell death and retarded cell growth, and these response rates correlated with cellular EMP2 expression. We next assessed the effects of anti-EMP2 diabodies in mice bearing xenografts from the ovarian endometrioid carcinoma cell line OVCAR5. Anti-EMP2 diabodies significantly suppressed tumor growth and induced cell death in OVCAR5 xenografts.
These findings indicate that EMP2 is expressed in the majority of ovarian tumors and it may be a feasible target in vivo.
PMCID: PMC2913478  PMID: 20670949
Epithelial membrane protein-2; ovarian cancer; antibody therapy; diabody; xenograft
9.  Protein expression based multimarker analysis of breast cancer samples 
BMC Cancer  2011;11:230.
Tissue microarray (TMA) data are commonly used to validate the prognostic accuracy of tumor markers. For example, breast cancer TMA data have led to the identification of several promising prognostic markers of survival time. Several studies have shown that TMA data can also be used to cluster patients into clinically distinct groups. Here we use breast cancer TMA data to cluster patients into distinct prognostic groups.
We apply weighted correlation network analysis (WGCNA) to TMA data consisting of 26 putative tumor biomarkers measured on 82 breast cancer patients. Based on this analysis we identify three groups of patients with low (5.4%), moderate (22%) and high (50%) mortality rates, respectively. We then develop a simple threshold rule using a subset of three markers (p53, Na-KATPase-β1, and TGF β receptor II) that can approximately define these mortality groups. We compare the results of this correlation network analysis with results from a standard Cox regression analysis.
We find that the rule-based grouping variable (referred to as WGCNA*) is an independent predictor of survival time. While WGCNA* is based on protein measurements (TMA data), it validated in two independent Affymetrix microarray gene expression data (which measure mRNA abundance). We find that the WGCNA patient groups differed by 35% from mortality groups defined by a more conventional stepwise Cox regression analysis approach.
We show that correlation network methods, which are primarily used to analyze the relationships between gene products, are also useful for analyzing the relationships between patients and for defining distinct patient groups based on TMA data. We identify a rule based on three tumor markers for predicting breast cancer survival outcomes.
PMCID: PMC3142534  PMID: 21651811
Tissue microarray; breast cancer; tumor marker; prognostic marker; WGCNA
10.  Shear Stress Influences Spatial Variations in Vascular Mn-SOD Expression 
Fluid shear stress modulates vascular production of endothelial superoxide anion (O2˙) and nitric oxide (˙NO). Whether the characteristics of shear stress influence the spatial variations in mitochondrial manganese superoxide dismutase (Mn-SOD) expression in vasculatures is not well-defined. We constructed a 3-D Computational Fluid Dynamics model simulating spatial variations in shear stress at the arterial bifurcation. In parallel, explants of arterial bifurcations were sectioned from the human left main coronary bifurcation and right coronary arteries for immunohisto-localization of Mn-SOD expression. We demonstrated that Mn-SOD staining was prominent in the athero-protective regions, but was nearly absent in the lateral wall of arterial bifurcation. Pulsatile shear stress (PSS: mean shear stress τave= 23 dyn·cm−2) up-regulated Mn-SOD mRNA expression at a higher level than did oscillatory shear stress (OSS: τave= 0.02 dyn·cm−2 ± 3.0 dyn·cm−2·s−1 at 1 Hz) in cultured bovine aortic endothelial cells (PSS by 11.3±0.4-fold versus OSS by 5.0±0.5-fold. p < 0.05, n=4). Furthermore, PSS decreased the extent of Low Density Lipoprotein (LDL) nitration, whereas OSS increased by Liquid chromatography and tandem mass spectrometry (P < 0.05, n=4). Treatment with Mn-SOD siRNA significantly increased intracellular nitrotyrosine level in presence of LDL (n=4, p < 0.5). Our findings indicate that shear stress in the athero-prone versus athero-protective regions regulates spatial variations in mitochondrial Mn-SOD expression. Shear stress modulated LDL protein nitration via Mn-SOD expression.
PMCID: PMC3008554  PMID: 18434620
Shear stress; Mn-SOD; superoxide anion; nitric oxide; nitrotyrosine
11.  Differential expression of anterior gradient gene AGR2 in prostate cancer 
BMC Cancer  2010;10:680.
The protein AGR2 is a putative member of the protein disulfide isomerase family and was first identified as a homolog of the Xenopus laevis gene XAG-2. AGR2 has been implicated in a number of human cancers. In particular, AGR2 has previously been found to be one of several genes that encode secreted proteins showing increased expression in prostate cancer cells compared to normal prostatic epithelium.
Gene expression levels of AGR2 were examined in prostate cancer cells by microarray analysis. We further examined the relationship of AGR2 protein expression to histopathology and prostate cancer outcome on a population basis using tissue microarray technology.
At the RNA and protein level, there was an increase in AGR2 expression in adenocarcinoma of the prostate compared to morphologically normal prostatic glandular epithelium. Using a tissue microarray, this enhanced AGR2 expression was seen as early as premalignant PIN lesions. Interestingly, within adenocarcinoma samples, there was a slight trend toward lower levels of AGR2 with increasing Gleason score. Consistent with this, relatively lower levels of AGR2 were highly predictive of disease recurrence in patients who had originally presented with high-stage primary prostate cancer (P = 0.009).
We have shown for the first time that despite an increase in AGR2 expression in prostate cancer compared to non-malignant cells, relatively lower levels of AGR2 are highly predictive of disease recurrence following radical prostatectomy.
PMCID: PMC3009682  PMID: 21144054
12.  Hemodynamics Influences Vascular Peroxynitrite Formation: Implication for LDL Apo B-100 Nitration 
Free radical biology & medicine  2006;42(4):519-529.
Hemodynamics, specifically, fluid shear stress, modulates the focal nature of atherogenesis. Superoxide anion (O2−.) reacts with nitric oxide (.NO) at a rapid diffusion-limited rate to form peroxynitrite (O2−. +.NO → ONOO−). Immunohistostaining of human coronary arterial bifurcations or curvatures, where oscillatory shear stress (OSS) develops, revealed presence of nitrotyrosine staining, a fingerprint of peroxynitrite; whereas in straight segments, where pulsatile shear stress (PSS) occurs, nitrotyrosine was absent. We examined vascular nitrative stress in models of OSS and PSS. Bovine aortic endothelial cells (BAEC) were exposed to fluid shear stress that simulates arterial blood flow: (1) PSS at a mean shear stress (τave) of 23 dyn·cm−2 and a temporal gradient (∂τ/∂t) at 71 dyn·cm−2sec−1, and (2) OSS at τave= 0.02 dyn·cm−2 and ∂τ/∂t = ± 3.0 dyn·cm−2·s−1 at a frequency of 1 Hz. OSS significantly up-regulated NADPH oxidase (Nox4) expression accompanied with an increase in O2−. production. In contrast, PSS up-regulated eNOS expression accompanied with.NO production (total NO2− and NO3−). To demonstrate that O2−. and.NO implicate in ONOO− formation, we added low density lipoprotein cholesterol (LDL) to the medium in which BAEC were exposed to the above flow conditions. The medium was analyzed for LDL apo B-100 nitrotyrosine by liquid chromatography, electro ionization spray, and tandem mass spectrometry (LC/ESI/MS/MS). OSS induced higher levels of 3-nitrotyrosine, di-tyrosine, and o-hydroxy-phenylalanine compared with PSS. In the presence of ONOO−, specific apo B-100 tyrosine residues underwent nitration in the α and β helices: α-1 (Tyr144), α-2 (Tyr2524), β-2 (Tyr3295), α-3 (Tyr4116), and β-2 (Tyr4211). Hence, the characteristics of shear stress in the arterial bifurcations influenced the relative production of O2−. and.NO with an implication for ONOO− formation as evidenced by LDL protein nitration.
PMCID: PMC2561143  PMID: 17275684
shear stress; superoxide anion; nitric oxide; nitrotyrosine; LDL
13.  Evidence that Mycobacterial PE_PGRS Proteins Are Cell Surface Constituents That Influence Interactions with Other Cells 
Infection and Immunity  2001;69(12):7326-7333.
The elucidation of the genomic sequence of Mycobacterium tuberculosis revealed the presence of a novel multigene family designated PE/PE_PGRS that encodes numerous, highly related proteins of unknown function. In this study, we demonstrate that a transposon insertion in a PE_PGRS gene (1818PE_PGRS) found in Mycobacterium bovis BCG Pasteur, which is the BCG homologue of the M. tuberculosis H37Rv gene Rv1818c, introduces new phenotypic properties to this BCG strain. These properties include dispersed growth in liquid medium and reduced infection of macrophages. Complementation of the 1818PE_PGRS::Tn5367 mutant with the wild-type gene restores both aggregative growth (clumping) in liquid medium and reestablishes infectivity of macrophages to levels equivalent to those for the parent BCG strain. Western blot analysis using antisera raised against the 1818PE_PGRS protein shows that PE_PGRS proteins are found in cell lysates of BCG and M. tuberculosis H37Ra and in the cell wall fraction of M. tuberculosis H37Rv. Moreover, immunofluorescent labeling of mycobacteria indicates that certain PE_PGRS proteins are localized at the cell surface of BCG and M. tuberculosis. Together these results suggest that certain PE_PGRS proteins may be found at the surface of mycobacteria and influence both cell surface interactions among mycobacteria as well as the interactions of mycobacteria with macrophages.
PMCID: PMC98818  PMID: 11705904

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