Yulia Dementieva

Analysis of European mitochondrial haplogroups with Alzheimer disease risk

We examined the association of mtDNA variation with Alzheimer disease (AD) risk in Caucasians (989 cases and 328 controls) testing the effect of individual haplogroups and single nucleotide polymorphisms (SNPs). Logistic regression analyses were used to assess risk of haplogroups and SNPs with AD in both main effects and interaction models. Males classified as haplogroup U showed an increase in risk (OR = 2.30; 95% CI, 1.03-5.11; P = 0.04) of AD relative to the most common haplogroup H, while females demonstrated a significant decrease in risk with haplogroup U (OR = 0.44 ; 95% CI, 0.24-0.80; P = 0.007). Our results were independent of APOE genotype, demonstrating that the effect of mt variation is not confounded by APOE4 carrier status. We suggest that variations within haplogroup U may be involved in AD expression in combination with environmental exposures or nuclear proteins other than APOE.

Eradication of Therapy-resistant Human Prostate Tumors Using an Ultrasound-guided Site-specific Cancer Terminator Virus Delivery Approach

Intratumoral injections of a replication-incompetent adenovirus (Ad) expressing melanoma differentiation-associated gene-7/interleukin-24 (Ad.mda-7), a secreted cytokine displaying cancer-selective, apoptosis-inducing properties, profoundly inhibits prostate cancer (PC) growth in immune-incompetent animals. In contrast, Ad.mda-7 is ineffective in PCs overexpressing antiapoptotic proteins such as Bcl-2 or Bcl-x(L). However, intratumoral injections of a conditionally replication-competent Ad (CRCA) in which expression of the adenoviral E1A gene is driven by the cancer-specific promoter of progression-elevated gene-3 (PEG-3) and which simultaneously expresses mda-7/interleukin (IL)-24 in the E3 region of the Ad (Ad.PEG-E1A-mda-7), a cancer terminator virus (CTV), is highly active in these cells. A major challenge for gene therapy is systemic delivery of nucleic acids directly into an affected tissue. Ultrasound (US) contrast agents (microbubbles-MBs) are viable candidates for gene delivery/therapy. Here, we show that MB/Ad.mda-7 complexes targeted to DU-145 cells using US dramatically reduced tumor burden in xenografted nude mice. Additionally, US-guided MB/CTV delivery completely eradicated not only targeted DU-145/Bcl-x(L)-therapy-resistant tumors, but also nontargeted distant tumors (established in the opposite flank), thereby implementing a cure. These findings highlight potential therapeutic applications of this novel image-guided gene therapy technology for advanced PC patients with metastatic disease.

Helicobacter pylori Infection Rate Decreases in Symptomatic Children : A Retrospective Analysis of 13 Years (1993-2005) From a Gastroenterology Clinic in West Virginia

Background The rate of Helicobacter pylori is decreasing in the developed countries, but few long-term studies are available from the United States. We retrospectively assessed the annual H. pylori infection rate in symptomatic children seen in our clinic over a 13-year study period. Study A retrospective analysis of all children who had histologic diagnosis of H. pylori infection between January 1993 and December 2005 in our pediatric gastroenterology clinic was performed. The annual infection rate and the overall infection rate were calculated. Results A total of 1743 upper endoscopy reports were reviewed, of which 212 (12.1%) were diagnosed with H. pylori infection. A significant decrease in mean annual H. pylori infection rate was noted in the last 6 years of the study period (2000 to 2005), compared with the first 7 years (1993 to 1999) (18.2% vs. 7.3%, respectively; P=0.001). Conclusions The incidence of H. pylori infection in symptomatic children in our clinic is decreasing. A national multicenter study will be needed to assess whether this drop is a local phenomenon or a national trend.

Proteomic and genomic analysis of PITX2 interacting and regulating networks

MINT‐6823902: YB‐1 (uniprotkb:P67809) physically interacts (MI:0218) with PITX2 (uniprotkb: Q99697) by anti bait coimmunoprecipitation (MI:0006)

Seasonal distribution and eosinophilic esophagitis: the experience in children living in rural communities.

To the Editor: Eosinophilic esophagitis (EoE) is a clinicopathologic condition closely associated with food and environmental allergies.1 Previous reports documented a higher prevalence of EoE during the pollen seasons and during the allergic seasons of the year (spring and summer).2–5 However, most of those reports were described in patients living in urban and suburban communities, where a high level of air pollution may explain this phenomenon. To our knowledge, there are no reports on seasonal distribution of EoE in children living in rural areas (defined as r1000 people/square mile; US Census Bureau). In the present study, we investigated the seasonal trend of EoE in children who live in rural communities of West Virginia, Kentucky, and Ohio (tri-state area). The charts of all upper endoscopic procedures performed between 2003 and 2010 were reviewed. Endoscopic data of all newly diagnosed children with EoE were collected and constituted our study group (test group). The control groups included children who were diagnosed with gastroesophageal reflux disease (GERD) by histology (control 1), and children who had normal esophageal biopsies (normal, control 2). Children with the diagnosis of other diseases such as: celiac disease, autoimmune diseases, inflammatory bowel disease, eosinophilic gastroenteritis, and other, were excluded from the study. For final analysis, the charts were separated by the procedure date and the season was defined as followed: winter seasonmonths: December, January, and February; spring season-months: March, April, and May; summer seasonmonths: June, July, and August; and autumn season-months: September, October, and November. The study was approved by the Marshall University, Joan C. Edwards School of Medicine IRB committee. Mucosal biopsies from the small intestine (X2), stomach (X4), and esophagus (X3) were obtained in all upper endoscopy procedures irrespective of the mucosal appearance. Previous data suggested that 3 esophageal biopsies from the distal esophagus with >15 eosinophils/HPF would yield a diagnostic accuracy of 97% for EoE.6 Accordingly, in the present study we used biopsies from the distal esophagus of children from all groups. The histologic diagnosis of EoE, GERD, and normal esophagus was established according to the number of eosinophils counted in at least 1 esophageal biopsy as previously described: EoE, >15 eosinophils/HPF; GERD, <5 eosinophils/HPF; and normal esophagus, 0 eosinophils/HPF.1,7 Children with eosinophils number between >5 and <15/HPF were excluded from the study as the exact clinical diagnosis (EoE vs. GERD) for this eosinophil range has not been yet established.1 Statistical analyses were performed using SAS software release 9.2 (SAS Institute Inc., Cary, NC) and R.8 P-values r0.05 were considered to be statistically significant. The w test of independence was performed using PROC FREQ procedure. A total of 1626 upper endoscopy procedures were performed between 2003 and 2010, of which 95 patients were newly diagnosed with EoE. In the EoE group, male sex was predominant (M:F ratio was 2.1:1.0). All children with EoE had failed anti-acid medication (H2 blockers or proton pump inhibitor) for at least 2 months. The most common clinical symptoms were abdominal pain, vomiting, and refluxassociated symptoms. Chocking and dysphagia was noted in 18 children. Allergy testing was done in all EoE patients showing food allergy in 38 children and environmental allergy in 41 children. All the children diagnosed with EoE were referred from a total of 50 counties (35, West Virginia; 6, southern Ohio; 9, northern Kentucky). All counties fulfilled the rural area criteria. A total of 653 upper endoscopy procedures were performed between 2007 and 2009, of which 229 children were newly diagnosed with GERD (control 1) and 241 children had normal esophagus (control 2). The w analysis of status (EoE, GERD, normal) versus season (winter, spring, summer, autumn) found no significant association (P=0.2035). For the individual disease, the distribution of newly diagnosed children with EoE was similar throughout the year (winter, 30 patients; spring, 29 patients; summer, 20 patients; autumn, 16 patients; P=0.115), whereas children with GERD or children with normal esophagus had a higher distribution in the winter and/or spring seasons (P=0.005 and 0.000, respectively). EoE is clearly associated with environmental and geographic factors, but many confounding factors of this disease are yet to be uncovered. Epidemiological studies have shown that the disease’s prevalence is unevenly distributed among adults and children living across the United States,9 demonstrating higher rate in urban/suburban areas compared with rural areas.7,9 Few investigators reported an increase incidence of EoE during the allergy seasons (low during winter, high during spring and fall),3–5 but those findings were not confirmed by others.10–12 In the present study, we showed that the diagnosis of EoE in children from the rural communities was evenly spread throughout the year without any seasonal preference. We explain these results by the various confounding factors that may modify the phenotypic expression of EoE such as: the geographic location of our patient population (rural area), low air pollution in the area (http://airnow. gov), and possibly the monoethnic composition of our patients (>94% white, 2011 census report, http://quickfacts. census.gov/qfd/states/54000.html). In conclusion, we demonstrated no seasonal preference in the diagnosis of EoE in children living in rural communities in the tri-state area. Further studies that focus on children living in rural communities in the Unites States are needed to further substantiate our findings.

The Molecular Clock of Neutral Evolution Can Be Accelerated or Slowed by Asymmetric Spatial Structure

Over time, a population acquires neutral genetic substitutions as a consequence of random drift. A famous result in population genetics asserts that the rate, K, at which these substitutions accumulate in the population coincides with the mutation rate, u, at which they arise in individuals: K = u. This identity enables genetic sequence data to be used as a “molecular clock” to estimate the timing of evolutionary events. While the molecular clock is known to be perturbed by selection, it is thought that K = u holds very generally for neutral evolution. Here we show that asymmetric spatial population structure can alter the molecular clock rate for neutral mutations, leading to either Ku. Our results apply to a general class of haploid, asexually reproducing, spatially structured populations. Deviations from K = u occur because mutations arise unequally at different sites and have different probabilities of fixation depending on where they arise. If birth rates are uniform across sites, then K ≤ u. In general, K can take any value between 0 and Nu. Our model can be applied to a variety of population structures. In one example, we investigate the accumulation of genetic mutations in the small intestine. In another application, we analyze over 900 Twitter networks to study the effect of network topology on the fixation of neutral innovations in social evolution.

Fatal Methadone Toxicity: Potential Role of CYP3A4 Genetic Polymorphism

Methadone is difficult to administer as a therapeutic agent because of a wide range of interindividual pharmacokinetics, likely due to genetic variability of the CYP450 enzymes responsible for metabolism to its principal metabolite 2-ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine (EDDP). CYP3A4 is one of the primary CYP450 isoforms responsible for the metabolism of methadone to EDDP in humans. The purpose of this study was to evaluate the role of CYP3A4 genetic polymorphisms in accidental methadone fatalities. A study cohort consisting of 136 methadone-only and 92 combined methadone/benzodiazepine fatalities was selected from cases investigated at the West Virginia and Kentucky Offices of the Chief Medical Examiner. Seven single nucleotide polymorphisms (SNPs) were genotyped within the CYP3A4 gene. Observed allelic and genotypic frequencies were compared with expected frequencies obtained from The National Center for Biotechnology Information dbSNP database. SNPs rs2242480 and rs2740574 demonstrated an apparent enrichment within the methadone-only overdose fatalities compared with the control group and the general population. This enrichment was not apparent in the methadone/benzodiazepine cases for these two SNPs. Our findings indicate that there may be two or more SNPs on the CYP3A4 gene that cause or contribute to the methadone poor metabolizer phenotype.

Obesity is not a risk factor in children with reflux esophagitis: a retrospective analysis of 738 children.

Obesity has been associated with various gastrointestinal diseases in children, but the role of obesity in gastroesophageal reflux disease (GERD) has not been clearly established. The aim of the study was to investigate whether obesity and/or being overweight are risk factors for reflux esophagitis in children. A retrospective analysis of endoscopy charts was reviewed. Demographic, weight, height, and histology results were obtained from each patient. The body mass index (BMI) and BMI Z-score were calculated according to known formula. The diagnosis of GERD was established by histology. The charts of 738 children were reviewed; of these, 345 (47%) children were overweight or obese. Histological findings compatible with GERD were found in 254 (65%) children with normal weight, 111 (69%) overweight children, and 126 (68%) obese children (P > 0.05). Among those reviewed, the mean age of children with normal weight was significantly younger than that of overweight or obese children (P = 0.0001). A single variant analysis showed a significant association between GERD and male gender (P = 0.0001). Multivariant analysis (gender, age, and BMI Z-score) showed that GERD was significantly associated with male gender (P < 0.0001), but not with age (P = 0.443) or BMI Z-score (P = 0.098). In symptomatic children with histologically proven GERD, only male gender was an independent risk factor for GERD, not obesity or being overweight. Large, prospective studies in children that capture a larger spectrum of GERD are clearly warranted.

Identification of the Early VIP-Regulated Transcriptome and its Associated Interactome in Resting and Activated Murine CD4 T Cells

More than 40 years after the discovery of vasoactive intestinal peptide (VIP), its transcriptome in the immune system has still not been completely elucidated. In an attempt to understand the biological role of this neuropeptide in immunity, we chose CD4 T cells as a cellular system. Agilent Mouse Whole Genome microarrays were hybridized with fluorescently labeled total RNA isolated from resting CD4 T cells cultured +/-10(-7)M VIP for 5h or PMA/ionomycin activated CD4 T cells cultured +/-10(-7)M VIP for 5h. These VIP-regulated transcriptomes were analyzed by Significance Analysis of Microarrays (SAM) and Ingenuity Pathway Analysis (IPA) software to identify relevant signaling pathways modulated by VIP in the absence and presence of T cell activation. In resting CD4 T cells, VIP-modulated 368 genes, ranging from 3.49 to -4.78-fold. In the PMA/ionomycin activated CD4 T cells, 326 gene expression levels were changed by VIP, ranging from 2.94 to -1.66-fold. IPA analysis revealed that VIP exposure alters cellular function through EGFR signaling in resting CD4 T cells, and modulates immediate early genes, Fos and CREM/ICER, in activated CD4 T cells. These gene expression changes are suggested to explain at a molecular level how VIP can regulate T cell homing to the gut and induce regulatory T cell generation.

A High Omega-3 Fatty Acid Diet has Different Effects on Early and Late Stage Myeloid Progenitors

The effects of the polyunsaturated omega-3 (n-3) and omega-6 (n-6) fatty acids (FA) on hematopoiesis are complex in that both FA forms are processed into leukotrienes, eicosanoids, and prostaglandins, which can have independent effects. These FA have antagonistic effects in that n-6 FA prostaglandins tend to be pro-proliferative and pro-inflammatory, while the effects of n-3 FA prostaglandins are the opposite. We have previously shown that diets high in n-3 FA reduce the size of the middle to later stage myeloid progenitor compartment in FVB X sv129 F1hybrid mice. To assay the effects of high n-3 FA diets on earlier stages of myelopoiesis, we fed C57BL/6J mice diets high in n-3 FA or levels of n-3/n-6 FA similar to western diets and assayed the effects on myelopoiesis with flow cytometry and colony forming cell assays. Results indicate an expansion of the common myeloid progenitor cell compartment in high n-3 FA diets, which does not persist into later stages where the number of progenitor cells is actually lower in high n-3 FA fed animals. Investigations in vitro with the hematopoietic stem cell line EML-clone 1 indicate that cells cultured with eicosapentaenoic acid (n-3 FA) or arachidonic acid (n-6 FA) have no differences in cell viability but that arachidonic acid more rapidly produces progenitors with low levels of the macrophage developmental marker, F4/80.