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1.  Alternative Capture of Noncoding RNAs or Protein-Coding Genes by Herpesviruses to Alter Host T-Cell Function 
Molecular cell  2014;54(1):67-79.
In marmoset T cells transformed by Herpesvirus saimiri (HVS), a viral U-rich noncoding RNA, HSUR 1, specifically mediates degradation of host microRNA-27 (miR-27). High-throughput sequencing of RNA after crosslinking immunoprecipitation (HITS-CLIP) identified mRNAs targeted by miR-27 as enriched in the T-cell receptor (TCR) signaling pathway, including GRB2. Accordingly, transfection of miR-27 into human T cells attenuates TCR-induced activation of mitogen-activated protein kinases (MAPKs) and induction of CD69. MiR-27 also robustly regulates SEMA7A and IFN-γ, key modulators and effectors of T-cell function. Knockdown or ectopic expression of HSUR 1 alters levels of these proteins in virally-transformed cells. Two other T-lymphotropic γ-herpesviruses, AlHV-1 and OvHV-2, do not produce a noncoding RNA to downregulate miR-27, but instead encode homologs of miR-27 target genes. Thus, oncogenic γ-herpesviruses have evolved diverse strategies to converge on common targets in host T cells.
PMCID: PMC4039351  PMID: 24725595
Noncoding RNA; MicroRNA; T-cell activation; Viral evolution; HITS-CLIP
2.  Virus Meets Host MicroRNA: the Destroyer, the Booster, the Hijacker 
Molecular and Cellular Biology  2014;34(20):3780-3787.
Virus-host interactions highlight key regulatory steps in the control of gene expression. MicroRNAs (miRNAs) are small noncoding RNAs that regulate protein production via base pairing with mRNAs. Both DNA and RNA viruses have evolved mechanisms to degrade, boost, or hijack cellular miRNAs to benefit the viral life cycle. This minireview focuses on recent discoveries in virus-host miRNA interactions.
PMCID: PMC4187717  PMID: 25047834
4.  Context Specific Transcription Factor Prediction 
Annals of biomedical engineering  2007;35(6):1053-1067.
One of the goals of systems biology is the identification of regulatory mechanisms that govern an organism’s response to external stimuli. Transcription factors have been hypothesized as a major contributor to an organism’s response to various outside stimuli, and a great deal of work has been done to predict the set of transcription factors which regulate a given gene. Most of the current methods seek to identify possible binding sites from genomic sequence. Initial attempts at predicting transcription factors from genomic sequences suffered from the problem of false positives. Making the problem more difficult, it has also been shown that while predicted binding sites might be false positives, they can be shown to bind to their corresponding sequences in vitro. One method for rectifying this is through the use of phylogenetic analysis in which only regions which show high evolutionary conservation are analyzed. However such an approach may be too stringent because of the level of degeneracy shown in transcription factor binding site position weight matrices. Due to the degeneracy, there may be only a few bases that need to be conserved across species. Therefore, while a sequence may not show a high level of evolutionary conservation, these sequences may still show high affinity for the same transcription factor. In predicting transcription factor binding we explore the notion that “Co-expression implies co-regulation” [Allocco et al. BMC Bioinformatics 5:18, 2004]. With multiple genes requiring similar transcription factors binding sites, there exists a basis for eliminating false positives. This method allows for the selection of transcription factors binding sites that are active under a given experimental paradigm, thereby allowing us to indirectly incorporate the effects of chromosome and recognition site presentation upon transcription factor binding prediction. Rather than having to rationalize that a few transcription factors binding sites are over-represented in a cluster of genes, one can show that a few transcription factors are active in the cluster of genes that have been grouped together. Although the method focuses on predicting experiment-specific transcription factor binding sites, it is possible that if such a methodology were used in an iterative process where different experiments were analyzed, one could obtain a comprehensive set of transcription factors binding sites which regulate the various dynamic responses shown by biological systems under a variety of conditions hence building a more comprehensive model of transcriptional regulation.
PMCID: PMC4184431  PMID: 17377845
Corticosteroids; Gene expression; Transcription factor binding site; Phylogenetics
6.  Application of speckle tracking in the evaluation of carotid artery function in subjects with hypertension and diabetes 
Speckle tracking enables direct tracking of carotid arterial wall motion. Timing intervals determined with carotid speckle tracking and slopes calculated from carotid artery area (CAA) versus cardiac cycle curves may provide further information on arterial function and stiffness. The proposed arterial stiffness parameters were examined in healthy controls (n=20), non-diabetic hypertensives (n=20), and type-II-diabetics (n=21).
Bilateral ECG-gated ultrasonograms of the distal common carotid were acquired with a 12-MHz vascular probe. Four timing intervals were derived from speckle tracked carotid arterial strain (CAS) curves: 1) carotid pre-distension period (PDP), 2) peak CAS time (PCAST), 3) arterial distension period (ADP), and 4) arterial diastolic time. In addition, CAA curves were recorded over the cardiac cycle and sub-divided into 4 segments S1–S4, relating to arterial distention and contraction periods.
Mean far-wall PDP and peak CAS time were more delayed in diabetics and hypertensives than in controls. Global mean ADP was prolonged and arterial diastolic time was shorter in hypertensives and diabetics versus controls. Slopes of segments S2 and S4 were markedly steeper in the hypertensives/diabetics combined group compared with healthy controls (p=0.03, and p=0.02, respectively).
Speckle tracking based measures of arterial stiffness may provide potential additive value in assessing vascular function in patients at risk for cardiovascular disease.
PMCID: PMC3725197  PMID: 23759168
arterial-stiffness; speckle-tracking; carotid-artery
7.  Altered relationship of plasma triglycerides to HDL cholesterol in patients with HIV/HAART-associated dyslipidemia: further evidence for a unique form of Metabolic Syndrome in HIV patients 
Plasma triglycerides (TG) and HDL-C are inversely related in Metabolic Syndrome (MetS), due to exchange of VLDL-TG for HDL-cholesteryl esters catalyzed by cholesteryl ester transfer protein (CETP). We investigated the relationship of TG to HDL-C in highly-active antiretroviral drug (HAART)-treated HIV patients.
Fasting plasma TG and HDL-C levels were compared in 179 hypertriglyceridemic HIV/HAART patients and 71 HIV-negative persons (31 normotriglyceridemic (NL) and 40 hypertriglyceridemic due to type IV hyperlipidemia (HTG)). CETP mass and activity were compared in 19 NL and 87 HIV/HAART subjects.
Among the three groups, a plot of HDL-C vs. TG gave similar slopes but significantly different y-intercepts (9.24 ± 0.45, 8.16 ± 0.54, 6.70 ± 0.65, sqrt(HDL-C) for NL, HIV and HTG respectively; P<0.001); this difference persisted after adjusting HDL-C for TG, age, BMI, gender, glucose, CD4 count, viral load and HAART strata (7.18 ± 0.20, 6.20 ± 0.05 and 4.55 ± 0.15 sqrt(HDL-C) for NL, HIV and HTG, respectively, P <0.001). CETP activity was not different between NL and HIV, but CETP mass was significantly higher in HIV (1.47 ± 0.53 compared to 0.93 ± 0.27 μg/mL, P<0.0001), hence CETP specific activity was lower in HIV (22.67 ± 13.46 compared to 28.46 ± 8.24 nmol/μg/h, P=0.001).
Dyslipidemic HIV/HAART patients have a distinctive HDL-C plasma concentration adjusted for TG. The weak inverse relationship between HDL-C and TG is not explained by altered total CETP activity; it could result from a non-CETP-dependent mechanism or a decrease in CETP function due to inhibitors of CETP activity in HIV patients’ plasma.
PMCID: PMC3691339  PMID: 23522788
HIV/AIDS; dyslipidemia; insulin resistance; lipodystrophy; cholesteryl ester transfer protein
8.  The ADAS-Cog revisited: Novel composite scales based on ADAS-Cog to improve efficiency in MCI and early AD trials 
The Alzheimer’s Disease Assessment Scale-Cognitive (ADAS-Cog) has been used widely as a cognitive end point in Alzheimer’s Disease (AD) clinical trials. Efforts to treat AD pathology at earlier stages have also used ADAS-Cog, but failure in these trials can be difficult to interpret because the scale has well-known ceiling effects that limit its use in mild cognitive impairment (MCI) and early AD. A wealth of data exists in ADAS-Cog from both historical trials and contemporary longitudinal natural history studies that can provide insights about parts of the scale that may be better suited for MCI and early AD trials.
Using Alzheimer’s Disease Neuroimaging Initiative study data, we identified the most informative cognitive measures from the ADAS-Cog and other available scales. We used cross-sectional analyses to characterize trajectories of ADAS-Cog and its individual subscales, as well as other cognitive, functional, or global measures across disease stages. Informative measures were identified based on standardized mean of 2-year change from baseline and were combined into novel composite endpoints. We assessed performance of the novel endpoints based on sample size requirements for a 2-year clinical trial. A bootstrap validation procedure was also undertaken to assess the reproducibility of the standardized mean changes of the selected measures and the corresponding composites.
All proposed novel endpoints have improved standardized mean changes and thus improved statistical power compared with the ADAS-Cog 11. Further improvements were achieved by using cognitive–functional composites. Combining the novel composites with an enrichment strategy based on cerebral spinal fluid beta-amyloid (Aβ1-42) in a 2-year trial yielded gains in power of 20% to 40% over ADAS-Cog 11, regardless of the novel measure considered.
An empirical, data-driven approach with e xisting instruments was used to derive novel composite scales based on ADAS-Cog 11 with improved performance characteristics for MCI and early AD clinical trials. Together with patient enrichment based on Aβ1-42 pathology, these modified endpoints may allow more efficient clinical trials in these populations and can be assessed without modifying current test administration procedures in ongoing trials.
PMCID: PMC3732822  PMID: 23127469
Alzheimer’s disease; MCI; Mild cognitive impairment; ADAS-Cog; Composite endpoints; Novel endpoints; Clinical trials; Power; Sample size; Ceiling effects
9.  B=Basal Cell Carcinoma: Stressful Life Events and the Tumor Environment 
Archives of general psychiatry  2012;69(6):618-626.
Child emotional maltreatment can result in lasting immune dysregulation that may be heightened in the context of more recent life stress. Basal cell carcinoma (BCC) is the most common skin cancer, and the immune system plays a prominent role in tumor appearance and progression.
To address relationships among recent severe life events, childhood parental emotional maltreatment, depression, and messenger RNA (mRNA) coding for immune markers associated with BCC tumor progression/regression.
University medical center
We collected information about early parent-child experiences, severe life events in the last year as assessed by the Life Events and Difficulties Schedule (LEDS), depression, and mRNA for immune markers associated with BCC tumor progression/regression from BCC tumor patients.
91 BCC patients (ages 23–92) who had all had a previous BCC tumor.
Main Outcome Measures
The expression of four BCC tumor mRNA markers (CD25, CD3ε, ICAM-1, and CD68) that have been linked to BCC tumor progression/regression were assessed in BCC tumor biopsies.
Both maternal and paternal emotional maltreatment interacted with the occurrence of severe life events to predict the local immune response to the tumor (adjusted p=0.009, p=0.03, respectively). Among BCC patients who had experienced a severe life event within the past year, those who were emotionally maltreated by their mothers (p=0.007) or fathers (p=0.02) as children had a poorer immune response to the BCC tumor. Emotional maltreatment was unrelated to BCC immune responses among those who did not experience a severe life event. Depressive symptoms were not associated with the local tumor immune response.
Troubled early parent-child relationships, in combination with a severe life event in the past year, predicted immune responses to a BCC tumor. The immunoreactivity observed in BCCs and the surrounding stroma reflects an anti-tumor-specific immune response that can be altered by stress.
PMCID: PMC3890083  PMID: 22664550
10.  Disease progression model in subjects with mild cognitive impairment from the Alzheimer's disease neuroimaging initiative: CSF biomarkers predict population subtypes 
The objective is to develop a semi-mechanistic disease progression model for mild cognitive impairment (MCI) subjects. The model aims to describe the longitudinal progression of ADAS-cog scores from the Alzheimer's disease neuroimaging initiative trial that had data from 198 MCI subjects with cerebrospinal fluid (CSF) information who were followed for 3 years.
Various covariates were tested on disease progression parameters and these variables fell into six categories: imaging volumetrics, biochemical, genetic, demographic, cognitive tests and CSF biomarkers.
CSF biomarkers were associated with both baseline disease score and disease progression rate in subjects with MCI. Baseline disease score was also correlated with atrophy measured using hippocampal volume. Progression rate was also predicted by executive functioning as measured by the Trail B-test.
CSF biomarkers have the ability to discriminate MCI subjects into sub-populations that exhibit markedly different rates of disease progression on the ADAS-cog scale. These biomarkers can therefore be utilized for designing clinical trials enriched with subjects that carry the underlying disease pathology.
PMCID: PMC3555054  PMID: 22534009
ADAS-cog; CSF biomarkers; disease progression; MCI; nonmem®
11.  Serine/Threonine Kinase 17A Is a Novel Candidate for Therapeutic Targeting in Glioblastoma 
PLoS ONE  2013;8(11):e81803.
STK17A is a relatively uncharacterized member of the death-associated protein family of serine/threonine kinases which have previously been associated with cell death and apoptosis. Our prior work established that STK17A is a novel p53 target gene that is induced by a variety of DNA damaging agents in a p53-dependent manner. In this study we have uncovered an additional, unanticipated role for STK17A as a candidate promoter of cell proliferation and survival in glioblastoma (GBM). Unexpectedly, it was found that STK17A is highly overexpressed in a grade-dependent manner in gliomas compared to normal brain and other cancer cell types with the highest level of expression in GBM. Knockdown of STK17A in GBM cells results in a dramatic alteration in cell shape that is associated with decreased proliferation, clonogenicity, migration, invasion and anchorage independent colony formation. STK17A knockdown also sensitizes GBM cells to genotoxic stress. STK17A overexpression is associated with a significant survival disadvantage among patients with glioma which is independent of age, molecular phenotype, IDH1 mutation, PTEN loss, and alterations in the p53 pathway and partially independent of grade. In summary, we demonstrate that STK17A provides a proliferative and survival advantage to GBM cells and is a potential target to be exploited therapeutically in patients with glioma.
PMCID: PMC3842963  PMID: 24312360
12.  Preoperative Cardiac Variables of Diastolic Dysfunction and Clinical Outcomes in Lung Transplant Recipients 
Journal of Transplantation  2013;2013:391620.
Background. Orthotopic lung transplantation is now widely performed in patients with advanced lung disease. Patients with moderate or severe ventricular systolic dysfunction are typically excluded from lung transplantation; however, there is a paucity of data regarding the prognostic significance of abnormal left ventricular diastolic function and elevated pretransplant pulmonary pressures. Methods. We reviewed the characteristics of 111 patients who underwent bilateral and unilateral lung transplants from 200 to 2009 in order to evaluate the prognostic significance of preoperative markers of diastolic function, including invasively measured pulmonary capillary wedge pressure (PCWP) and echocardiographic variables of diastolic dysfunction including mitral A > E and A′ > E′. Results. Out of 111 patients, 62 were male (56%) and average age was 54.0 ± 10.5 years. Traditional echocardiographic Doppler variables of abnormal diastolic function, including A′ > E′ and A > E, did not predict adverse events (P = 0.49). Mildly elevated pretransplant PCWP (16–20 mmHg) and moderately/severely elevated PCWP (>20 mmHg) were not associated with adverse clinical events after transplant (P = 0.30). Additionally, all clinical endpoints did not show any statistical significance between the two groups. Conclusions. Pre-lung transplant invasive and echocardiographic findings of elevated pulmonary pressures and abnormal left ventricular diastolic function are not predictive of adverse posttransplant clinical events.
PMCID: PMC3791796  PMID: 24163757
13.  β-Blockers and Survival among Danish Patients with Malignant Melanoma: A Population-Based Cohort Study 
To study whether use of β-blockers increases survival in patients with malignant melanoma because experimental data suggest that catecholamine hormones may be involved in stimulating the aggressiveness of malignant melanoma.
A total of 4,179 patients diagnosed with malignant melanoma in Denmark with a median follow-up of 4.9 years and identified in the Danish Cancer Registry participated. Data on β-blocker use, comorbidity, and survival were obtained from medical and administrative databases. Cox proportional hazards models were used to estimate HRs for all-cause mortality with 95% CIs with adjustment for prognostic factors.
A total of 372 (8.9%) patients with malignant melanoma were treated with β-blockers within 90 days of melanoma diagnosis. The median β-blocker duration for exposure within 90 days of melanoma diagnosis, more than 90 days, and no prior exposure was 7.6, 1.4, and 0 years, respectively. The patients receiving β-blockers were older, had more comorbidities, and more cardiovascular and psychotropic drug user than the patients receiving no β-blockers prior to melanoma diagnosis. After adjustment for age and comorbidity index, the HR for melanoma death was 0.87 (95% CI: 0.64–1.20) and for all-cause mortality was 0.81 (95% CI: 0.67–0.97).
Increased survival time of patients with melanoma receiving β-blockers suggests that this class of drugs may hold promise in treatment strategy for these patients.
The observations described here suggest that catecholamines may retard melanoma progression and that β-blockers may have unrecognized potential as a therapeutic intervention for melanoma.
PMCID: PMC3652234  PMID: 21933972
14.  Use of ß-blockers and mortality following ovarian cancer diagnosis: a population-based cohort study 
BMC Cancer  2013;13:85.
Experimental data suggest that catecholamine hormones are involved in stimulating the aggressiveness of ovarian cancer, but few population-based studies have examined this association. We therefore conducted a population-based cohort study to examine whether ß-blockers affect mortality following ovarian cancer diagnosis.
We used the Danish Cancer Registry to identify all patients diagnosed with ovarian cancer in northern Denmark between 1999 and 2010 (n=6,626). Data on medication use, comorbidity, and survival were obtained from medical databases. According to the last redeemed prescription before diagnosis, ß-blocker use was categorized as current (within ≤90 days), previous (>90 days) or never. We used Cox proportional hazards regression to calculate hazard ratios (HRs) for all-cause mortality with 95% confidence intervals (CIs) adjusting for confounding factors.
Among the ovarian cancer patients, 373 (5.6%) were current, 87 (1.3%) previous, and 6,166 (93.1%) were nonusers of ß-blockers. Median duration of use was 19.0 months among current users and 43.0 months among previous users. Median follow-up was 2.55 years (IQR: 0.81-9.23). Nonusers and current users of ß-blockers had similar comorbidity burden whereas previous users had moderate comorbidity more frequently. Compared with nonusers, the adjusted HR was 1.17 (95% CI: 1.02–1.34) for current users and 1.18 (95% CI: 0.90–1.55) for previous users. Secondary analyses stratifying by cancer stage and duration of ß-blocker use supported the overall results.
We found no evidence that ß-blocker use was associated with decreased mortality following ovarian cancer diagnosis.
PMCID: PMC3598679  PMID: 23433478
15.  Carotid arterial wall characteristics are associated with incident ischemic stroke but not coronary heart disease in the ARIC Study 
Background and Purpose
Ultrasound measurements of arterial stiffness are associated with atherosclerosis risk factors, but limited data exist on their association with incident cardiovascular events. We evaluated the association of carotid ultrasound derived arterial stiffness measures with incident coronary heart disease (CHD) and ischemic stroke in the ARIC study.
Carotid arterial strain (CAS) and compliance (AC), distensibility (AD) and stiffness indices (SI), pressure-strain (Ep) and Young’s elastic moduli (YEM) were measured in 10,407 individuals using ultrasound. Hazard ratios for incident CHD (myocardial infarction [MI], fatal CHD, coronary revascularization) and stroke in minimally adjusted (age, sex, center, race) and fully adjusted models (minimally adjusted model + diabetes, height, weight, total cholesterol, high-density lipoprotein cholesterol, tobacco use, systolic blood pressure, antihypertensive medication use, and carotid intima-media thickness (CIMT) were calculated.
The mean age was 55.3 years. Over a mean follow up of 13.8 years, 1,267 incident CHD and 383 ischemic stroke events occurred. After full adjustment for risk factors and CIMT, all arterial stiffness parameters [CAS HR (95% confidence interval [CI]) =1.14 (1.02, 1.28); AD HR=1.19 (1.02, 1.39); SI HR=1.14 (1.04, 1.25); Ep HR=1.17 (1.06, 1.28); YEM HR=1.13 (1.03, 1.24)], except arterial compliance HR=1.02 (0.90, 1.16), were significantly associated with incident stroke but not with CHD.
After adjusting for cardiovascular risk factors, ultrasound measures of carotid arterial stiffness are associated with incident ischemic stroke but not incident CHD events, despite that the 2 outcomes sharing similar risk factors.
PMCID: PMC3246524  PMID: 22033999
arterial stiffness; carotid ultrasound; coronary heart disease; stroke; ARIC
16.  Segmental Analysis of Carotid Arterial Strain Using Speckle-Tracking 
Increased arterial stiffness has been shown to be associated with aging and cardiovascular risk factors. Speckle-tracking algorithms are being used to measure myocardial strain. We evaluated if speckle-tracking could be used to measure carotid arterial wall strain (CAS) reproducibly in healthy volunteers and then examined if CAS was lesser in individuals with diabetes.
Bilateral electrocardiography-gated ultrasound scans of the distal common carotid arteries [D-CCA] (3 cardiac cycles, 14 MHz linear probe, mean 78.7 [Standard deviation (SD) 8.9]) frames per second were performed twice (2–4 days apart) on 10 healthy volunteers to test repeatability. Differences in CAS between healthy (n=20) and diabetic subjects (n=21) were examined. Peak CAS was measured in each of 6 equal segments and averages of all segments (i.e., global average), of the 3 nearest the probe, and of the 3 farthest from the probe (i.e., far wall average) were obtained.
Global CAS (intraclass correlation coefficient [ICC]=0.40) and far wall average (ICC=0.63) had the greatest test-retest reliability. The global and far wall averaged CAS were lower in diabetics (4.29% [Standard Error (SE) 0.27%]; 4.30% [SE 0.44%], respectively) than in controls (5.48% [SE 0.29%], p=0.001; 5.58% [SE 0.44%], p=0.003, respectively). This difference persisted after adjustment for age, gender, race, and hemodynamic parameters.
Speckle-tracking for measuring carotid arterial wall strain is feasible and modestly reliable. Diabetic subjects had a lower carotid arterial wall strain obtained with speckle-tracking when compared with healthy controls.
PMCID: PMC3200442  PMID: 21907541
17.  Real-time co-registration using novel ultrasound technology: ex vivo validation and in vivo applications 
To evaluate whether a novel GPS-like position-sensing technology will enable accurate co-registration of images between imaging modalities.
Co-registration of images obtained by different imaging modalities will allow for comparison and fusion between imaging modalities, and therefore has significant clinical and research implications. We compared US and MR images of carotid endarterectomy (CEA) specimens using a novel position-sensing technology that uses an electromagnetic (EM) transmitter and sensors mounted on a US transducer. We then evaluated in vivo US-US and US-MRI co-registration.
Thirteen CEA specimens underwent 3.0 Tesla MRI, after which images were uploaded to a LOGIQ E9 3D (GE Healthcare) US system and registered by identifying 2–3 common points. A similar method was used to evaluate US-MRI co-registration in patients with carotid atherosclerosis. For carotid intima-media thickness (C-IMT) measurements, ten volunteers underwent bilateral carotid US scans co-registered to 3D US maps created on the initial visit, with a repeat scan 2 days later.
For the CEA specimens, there was a mean 20 (standard error [SE] 2.0) frames per MRI slice. The mean frame difference, over 33 registration markers, between MR and US images for Readers 1 and 2 was −2.82 ± 19.32 (mean ± 95% confidence interval [CI]) frames and 2.09 ± 14.68 (mean ± 95% CI) frames, respectively. The US-MRI intraclass correlation coefficients (ICC) for the first and second readers were 0.995 and 0.997, respectively. For patients with carotid atherosclerosis, the mean US frames per MRI slice (9 [SE 2.3]) was within range of that observed with CEA specimens. Inter-visit, intra-reader, and inter-reader reproducibility of C-IMT measurements were consistently high (side-averaged ICC >0.9).
Accurate co-registration between US and other modalities is feasible with a GPS-like technology, which has significant clinical and research applicability.
PMCID: PMC3123396  PMID: 21439782
18.  Sparse learning and stability selection for predicting MCI to AD conversion using baseline ADNI data 
BMC Neurology  2012;12:46.
Patients with Mild Cognitive Impairment (MCI) are at high risk of progression to Alzheimer’s dementia. Identifying MCI individuals with high likelihood of conversion to dementia and the associated biosignatures has recently received increasing attention in AD research. Different biosignatures for AD (neuroimaging, demographic, genetic and cognitive measures) may contain complementary information for diagnosis and prognosis of AD.
We have conducted a comprehensive study using a large number of samples from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) to test the power of integrating various baseline data for predicting the conversion from MCI to probable AD and identifying a small subset of biosignatures for the prediction and assess the relative importance of different modalities in predicting MCI to AD conversion. We have employed sparse logistic regression with stability selection for the integration and selection of potential predictors. Our study differs from many of the other ones in three important respects: (1) we use a large cohort of MCI samples that are unbiased with respect to age or education status between case and controls (2) we integrate and test various types of baseline data available in ADNI including MRI, demographic, genetic and cognitive measures and (3) we apply sparse logistic regression with stability selection to ADNI data for robust feature selection.
We have used 319 MCI subjects from ADNI that had MRI measurements at the baseline and passed quality control, including 177 MCI Non-converters and 142 MCI Converters. Conversion was considered over the course of a 4-year follow-up period. A combination of 15 features (predictors) including those from MRI scans, APOE genotyping, and cognitive measures achieves the best prediction with an AUC score of 0.8587.
Our results demonstrate the power of integrating various baseline data for prediction of the conversion from MCI to probable AD. Our results also demonstrate the effectiveness of stability selection for feature selection in the context of sparse logistic regression.
PMCID: PMC3477025  PMID: 22731740
19.  Coronary and Intracerebral Arterial Aneurysms in a Young Adult with Acute Coronary Syndrome 
Texas Heart Institute Journal  2012;39(3):380-383.
A 21-year-old man with no known medical history presented with substernal chest pain. Serial 12-lead electrocardiography showed dynamic ST-segment elevations in the anterolateral leads. Emergent coronary angiography revealed diffuse coronary aneurysmal disease and thrombotic occlusion of the left anterior descending coronary artery. The patient underwent urgent coronary artery bypass grafting. Subsequent imaging showed intracerebral aneurysms that involved his right and left middle cerebral arteries. The incidence, multiple causes, and proposed mechanisms of coronary artery aneurysmal formation are discussed, as is the rare association of these lesions with extracardiac arterial aneurysms.
This association between coronary and extracardiac aneurysms is a phenomenon that warrants further study to determine its prevalence and possible causes. Findings could influence recommendations for further screening of patients diagnosed with coronary aneurysmal disease.
PMCID: PMC3368465  PMID: 22719148
Acute coronary syndrome; cerebrovas-cular aneurysms; congenital heart disease; coronary aneurysm/etiology; coronary vessel anomalies; dilatation, pathologic/etiology; intra-cranial aneurysm; Kawasaki disease
20.  Transcription factor network reconstruction using the living cell array 
Journal of theoretical biology  2008;256(3):393-407.
The objective of identifying transcriptional regulatory networks is to provide insights as to what governs an organism’s long term response to external stimuli. We explore the coupling of the living cell array (LCA), a novel microfluidics device which utilizes fluorescence levels as a surrogate for transcription factor activity with reverse Euler deconvolution (RED) a computational technique proposed in this work to decipher the dynamics of the interactions. It is hypothesized that these two methods will allow us to first assess the underlying network architecture associated with the transcription factor network as well as specific mechanistic consequences of transcription factor activation such as receptor dimerization or tolerance.
The overall approach identifies evidence of time-lagged response which may be indicative of mechanisms such as receptor dimerization, tolerance mechanisms which are evidence of various receptor mediated dynamics, and feedback loops which regulate the response of an organism to changing environmental conditions. Furthermore, through the exploration of multiple network architectures, we were able to obtain insights as to the role each transcription factor plays in the overall response and their overall redundancy in the organism’s response to external perturbations. Thus, the LCA along with the proposed analysis technique is a valuable tool for identifying the possible architectures and mechanisms underlying the transcriptional response.
PMCID: PMC3208267  PMID: 18996398
Systems biology; Network reconstruction
21.  Glucocorticoids activate Epstein Barr Virus lytic replication through the upregulation of immediate early BZLF1 gene expression 
Brain, behavior, and immunity  2010;24(7):1089-1096.
Psychological stress-associated immune dysregulation has been shown to disrupt the steady state expression and reactivate latent herpes viruses. One such virus is the Epstein Barr virus (EBV), which is associated with several human malignancies. EBV infects >90% of people living in North America and persists for life in latently infected cells. Although several studies have shown that glucocorticoids (GCs) can directly induce reactivation of the latent virus, the mechanism of stress hormone involvement in the control of EBV gene expression is not well understood. In this study, we tested the hypothesis that GCs can induce the latent EBV genome to lytically replicate through the induction of the EBV immediate early gene BZLF1 which encodes the lytic transactivator protein ZEBRA. We show a dose-dependent upregulation of BZLF1 mRNA expression by hydrocortisone (HC) and dexamethasone (Dex) in Daudi cells, an EBV genome positive Burkitt’s lymphoma cell line, and Dex-induction of the early gene products BLLF3 (encoding for the EBV dUTPase) and BALF5 (encoding for the EBV DNA polymerase). We show that Daudi cells express glucocorticoid receptors (GR) that mediate Dex-dependent upregulation of BZLF1 mRNA levels. This effect was inhibited by both the glucocorticoid receptor antagonist RU486 and by cycloheximide. The results suggest that GCs, in addition to inducing stress-related immune dysregulation, can mediate latent EBV reactivation through the induction of the BZLF1 gene.
PMCID: PMC2939213  PMID: 20466055
Epstein Barr virus; glucocorticoids; glucocorticoid receptor; herpesvirus reactivation; psychological stress
22.  Tumor Site Immune Markers Associated with Risk for Subsequent Basal Cell Carcinomas 
PLoS ONE  2011;6(9):e25160.
Basal cell carcinoma (BCC) tumors are the most common skin cancer and are highly immunogenic.
The goal of this study was to assess how immune-cell related gene expression in an initial BCC tumor biopsy was related to the appearance of subsequent BCC tumors.
Materials and Methods
Levels of mRNA for CD3ε (a T-cell receptor marker), CD25 (the alpha chain of the interleukin (IL)-2 receptor expressed on activated T-cells and B-cells), CD68 (a marker for monocytes/macrophages), the cell surface glycoprotein intercellular adhesion molecule-1 (ICAM-1), the cytokine interferon-γ (IFN-γ) and the anti-inflammatory cytokine IL-10 were measured in BCC tumor biopsies from 138 patients using real-time PCR.
The median follow-up was 26.6 months, and 61% of subjects were free of new BCCs two years post-initial biopsy. Patients with low CD3ε CD25, CD68, and ICAM-1 mRNA levels had significantly shorter times before new tumors were detected (p = 0.03, p = 0.02, p = 0.003, and p = 0.08, respectively). Furthermore, older age diminished the association of mRNA levels with the appearance of subsequent tumors.
Our results show that levels of CD3ε, CD25, CD68, and ICAM-1 mRNA in BCC biopsies may predict risk for new BCC tumors.
PMCID: PMC3182995  PMID: 21980389
23.  Role for catecholamines in tumor progression 
Cancer Biology & Therapy  2010;10(1):30-32.
PMCID: PMC3040831  PMID: 20505322
catecholamines; adrenergic receptors; β-blockers; tumor progression; angiogenesis; invasion/metastasis
24.  Inhibition of p-STAT3 Enhances IFN-α Efficacy Against Metastatic Melanoma in a Murine Model 
Melanoma is a common and deadly tumor that upon metastasis to the central nervous system (CNS) has a median survival duration of less than 6 months. Activation of the signal transducer and activator of transcription 3 (STAT3) has been identified as a key mediator that drives the fundamental components of melanoma malignancy, including immune suppression in melanoma patients. We hypothesized that WP1193, a novel inhibitor of STAT3 signaling, would enhance the anti-tumor activity of IFN-α against metastatic melanoma.
Experimental Design
Combinational therapy of STAT3 blockade agents with IFN-α was investigated in a metastatic and an established syngeneic intracerebral murine tumor model of melanoma. The immunological in vivo mechanisms of efficacy were investigated by T cell and NK cell cytotoxic assays.
IFN-α immunotherapy was synergistic with WP1193 demonstrating marked in vivo efficacy against metastatic and established intracerebral melanoma. At autopsy, it was noted that there was a decreased trend in mice with melanoma developing leptomeningeal disease (LMD) treated with combinational therapy. The combinational approach enhanced both NK and T cell-mediated anti-tumor cytotoxicity.
The immune modulatory effects of STAT3 blockade can enhance the therapeutic efficacy of IFN-α immunotherapy by enhancing both innate and adaptive cytotoxic T cell activities. This combination therapy has the potential in the treatment of metastatic melanoma that is typically refractory to this type of immune therapeutic approach.
PMCID: PMC2936966  PMID: 20388845
Melanoma; IFN-α; STAT3; leptomeningeal disease; CD8+ T cell
25.  Coronary microcirculatory vasodilator function in relation to risk factors among patients without obstructive coronary disease and low to intermediate Framingham score 
European Heart Journal  2009;31(8):936-942.
The study aim was to evaluate the relation between the Framingham risk score (FRS) and the presence of coronary risk factors to coronary microcirculatory vasodilator function in patients with early coronary atherosclerosis.
Methods and results
We evaluated 1063 patients (age: 50 ± 12 years, 676 (64%) females) without significant narrowing (<30%) on coronary angiography who underwent invasive assessment of coronary endothelial function. Coronary blood flow (CBF) in response to the endothelium-dependent vasodilator acetylcholine was evaluated as well as the microvascular (endothelium-independent) coronary flow reserve (CFR) in response to intracoronary adenosine. Coronary blood flow and CFR were analysed in relation to the FRS and the presence of traditional and novel risk factors. The estimated 10 years risk in this group was 5.4 ± 5.2%. Higher FRS was associated with lower CBF in men (P = 0.008), and was a univariate predictor of lower CFR (P = 0.012) in all patients. Multivariable analysis identified a higher FRS (P < 0.001), female sex (P < 0.001) and a positive family history of coronary disease (P = 0.043) as independent predictors of reduced CFR.
In patients without obstructive coronary disease, a higher FRS was an independent predictor of reduced CFR. The current study provides insight into the relation between cardiac risk profile and coronary microcirculatory function, and suggests that impaired microcirculatory vasodilator function may be present even in patients with a low to intermediate Framingham score.
PMCID: PMC2854505  PMID: 19897496
Coronary atherosclerosis; Female; Framingham risk score; Endothelial function; Microcirculation

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