Allergy-specific Phenome-Wide Association Study for Immunogenes in Turkish Children

To dissect the role of immunogenetics in allergy and asthma, we performed a phenome-wide association study in 974 Turkish children selected from a cross-sectional study conducted using ISAAC (International Study of Asthma and Allergies in Children) Phase II tools. We investigated 9 loci involved in different immune functions (ADAM33, ADRB2, CD14, IL13, IL4, IL4R, MS4A2, SERPINE1, and TNF) with respect to 116 traits assessed through blood tests, hypertonic saline challenge tests, questionnaires, and skin prick tests. Multiple associations were observed for ADAM33: rs2280090 was associated with reduced MEF240% (i.e., the ratio of Mean Expiratory Flow after 240s of hypertonic saline inhalation with respect to the age- and ancestry-matched reference value) and with an increased risk of allergic bronchitis (p = 1.77*10⁻⁴ and p = 7.94*10⁻⁴, respectively); rs3918396 was associated with wheezing and eczema comorbidity (p = 3.41*10⁻⁴). IL4 rs2243250 was associated with increased FEV240 (Forced Expiratory Flow Volume after 240s of hypertonic saline inhalation; p = 4.81*10⁻⁴) and CD14 rs2569190 was associated with asthma diagnosis (p = 1.36*10⁻³). ADAM33 and IL4 appeared to play a role in the processes linked to allergic airway inflammation and lung function. Due to its association with wheezing and eczema comorbidity, ADAM33 may also be involved in the atopic march.

Aliskiren - a promising strategy for ovarian ischemia/reperfusion injury protection in rats via RAAS

The aim of this study was to evaluate the effects of aliskiren, direct renin inhibitor, as an antioxidant and tissue protective agent and evaluate the molecular, biochemical, and histopathological changes in experimental ischemia and ischemia/reperfusion injury in rat ovaries. Forty-eight female rats were randomly divided into eight groups: in Group 1, only sham operation was performed. Group 2 received 100 mg/kg aliskiren and sham operated. In Group 3, 3 h-period of bilateral ovarian ischemia was applied. Group 4 received a 3-h period of ischemia followed by 3 h of reperfusion. Groups 5 and 6 received 50 and 100 mg/kg, respectively, of aliskiren and bilateral ovarian ischemia was applied (after a 3-h period of ischemia, both ovaries were surgically removed). To Groups 7 and 8, 50 and 100 mg/kg of aliskiren were administered, respectively, and the induction of ischemia was performed. At the end of a 3-h period of ischemia, bilateral vascular clips were removed, and 3 h of reperfusion continued. After the experiments, IL-1β, IL-6, TNF-α, and iNOS mRNA expressions and SOD, GSH, MDA, renin, and angiotensin-II levels were determined and histopathological changes were examined in rat ovaries. Aliskiren treatment normalized excessive changes in cytokine and oxidative stress markers in both ischemia and ischemia/reperfusion injury. Histopathologically, treatment with aliskiren ameliorated the development of ischemia and/or ischemia/reperfusion tissue injury. This study concluded that aliskiren treatment is effective in reversing ischemia and/or ischemia/reperfusion induced ovary damage via the improvement of oxidative stress, reduction of inflammation, and suppression of the renin-angiotensin aldosterone system.

Abstract 3998: Sequencing the B-cell and T-cell repertoire

Immune sequencing allows for the study of complex immunological diseases by sequencing millions of V(D)J combinations from B-cell antibody and T-cell receptors. The popularity of this technique has increased due to recent throughput and read length improvements in next-generation sequencing technologies. However, structural and sequence complexities of antibody genes have made reliable targeting approaches challenging.

We have developed and optimized a method for accurate sequencing of full-length immune gene repertoires of B-cells and T-cells. The method uses a unique barcoding scheme specifically designed to tag every mRNA molecule with a unique identifier (UID) so that all PCR copies of each mRNA fragment can be collapsed into a single consensus sequence. This makes the assay extremely accurate, by resolving PCR bias and sequencing errors as well as allowing quantitative digital molecule counting.

Immune sequencing libraries were generated from total RNA extracted from Peripheral Blood Mononuclear Cells in duplicate from a single patient. The use of UIDs enabled absolute quantification of starting RNA molecules present in the original sample and therefore accurate ranking of the antibody clone abundance, by avoiding the bias incorporated by PCR or sequencing when total reads only were measured. Using the same sequencing method, tumor samples were analyzed for abundance of expanded clones via grouping clones by V gene, J gene and CDR3 similarity and ranking by mRNA abundance. Additionally, the use of isotype-specific primers (IgM, IgD, IgG, IgA and IgE) enabled measurement of the heavy chain isotype proportions within the samples. Further, alignment of full-length heavy chain antibody sequences generated using this method to germline genes from reference databases enabled quantitation of the mutation level of each antibody sequence, thereby providing information on the overall maturity and mutational profile of the sample repertoire.

Citation Format: Fiona J. Stewart, Mehmet Karaca, Kris Adams, Chris Clouser, Bonny Patel, Sonia Timberlake, William Donahue, Lynne Apone, Salvatore Russello, Eileen T. Dimalanta, Theodore B. Davis, Francois Vigneault. Sequencing the B-cell and T-cell repertoire. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3998.

Five new species of Zercon C. L. Koch, 1836 (Acari: Zerconidae) from northwestern Turkey

Mites belonging to the genus Zercon collected from the Thrace region in Turkey are investigated. Five new species, Z. filiformis sp. nov., Z. geliboluensis sp. nov., Z. sklarsimilis sp. nov., Z. tekirdagensis sp. nov. and Z. thracicus sp. nov., are described and illustrated. Zercon similifoveolatus Ivan & Călugăr is newly recorded for the Turkish fauna. Female specimens of Z. sklari Balan are reported and descibed for the first time in Turkey. Some known zerconid mites are recorded from new localities. A key to species of the genus Zercon known from Turkey is included.

Haplotype analysis of non-HLA immunogenetic loci in Turkish and worldwide populations

Immunogenes (i.e., genes related to the immune system and its functions) are involved in the predisposition to numerous traits and their variation contributes to the phenotypic variability observed among human groups. Turkish population presents particular genetic features since its genetic pool is an admixture of European, Middle-Eastern, and Central Asian ancestries. Here, we analyzed the haplotype structure of four immunogenetic loci (i.e., ADAM33; IL13-IL4; IL4R; MS4A2) in 482 subjects from five different regions of Turkey. Genotyping was performed using KASP technology. Turkish data were compared with the haplotype information available from the 1000 Genomes Project Phase 3 (26 human populations from 5 ancestry groups). We did not observe significant differences among Turkish groups. Comparing other ancestries, we identified haplotype similarity of Turkish subjects with European populations in IL13-IL4, IL4R, and ADAM33 loci; and with central Asians in MS4A2 region. Considering loci displaying Turkish-European haplotype similarity (i.e., IL13-IL4, IL4R, and ADAM33), we observed differences between Turkish subjects and northern/western Europeans. Conversely, no significant difference was determined in MS4A2 between Turkish and central Asian populations. Finally, we assessed the haplotypes responsible for the differences between Turkish and European samples and the potential functional effects on the immunogenetic loci investigated.

Neurologic outcome in patients with cardiac arrest complicating ST elevation myocardial infarction treated by mild therapeutic hypothermia: The experience of a tertiary institution

OBJECTIVE

Therapeutic hypothermia improves neurologic prognosis after cardiac arrest. The aim of this study was to report clinical experience with intravascular method of cooling in patients with cardiac arrest resulting from ST-segment elevation myocardial infarction (STEMI).

METHODS

Thirteen patients (11 male, 2 famele; mean age was 39.6±9.4 years) who had undergone mild therapeutic hypothermia (MTH) by intravascular cooling after cardiac arrest due to STEMI were included. Clinical, demographic, and procedural data were analyzed. Neurologic outcome was assessed by Cerebral Performance Category (CPC) score.

RESULTS

Anterior STEMI was observed in 9 patients. One patient died of cardiogenic shock complicating STEMI. Mean cardiopulmonary resuscitation (CPR) duration and door-to-invasive cooling were 32.9±20.1 and 286.1±182.3 minutes, respectively. Precooling Glasgow Coma Scale score was 3 in 9 subjects. Twelve patients were discharged, 11 with CPC scores of 1 at 1-year follow-up. No major complication related to procedure was observed.

CONCLUSION

In comatose survivors of STEMI, therapeutic hypothermia by intravascular method is a feasible and safe treatment modality.

Prediction of early postoperative atrial fibrillation after cardiac surgery: is it possible?

Background

Postoperative atrial fibrillation is common after cardiac surgery. In this study, we aimed to investigate the value of interatrial conduction time for the prediction of early postoperative atrial fibrillation, using intra-operative transoesophageal echocardiography.

Methods

A total of 65 patients undergoing cardiac surgery in our hospital between January and March 2007 were prospectively evaluated, and 59 patients with sinus rhythm were included in the study. We performed transoesophageal echocardiography on all patients, and intra-operatively measured the interatrial conduction time, as recently described. The patients with episodes of atrial fibrillation during the post-surgery hospitalisation period were defined as group 1 and those without episodes were defined as group 2.

Results

Mean interatrial conduction time was 74 ± 15.9 ms in group 1 and 54 ± 7.9 ms in group 2. The difference in interatrial conduction time between the two groups was statistically significant (p < 0.05). In this study we found a statistically significant interatrial conduction delay between the groups. Postoperative atrial fibrillation was more frequent in patients with a longer interatrial conduction time.

Conclusion

Increased interatrial conduction time may cause postoperative atrial fibrillation and it can be measured intraoperatively by transoesophageal echocardiography.

Detection of seasonal asymptomatic dermatophytes in Van cats

The Van cat is a domestic landrace found in the Van province of eastern Turkey. In this study, we aimed to determine the seasonal carriage of dermatophytes in Van cats without clinical lesions. A total of 264 hair specimens were collected from clinically healthy cats in and around the Van Province. Of these samples, 30.3% were obtained in spring, 30.6% in summer, 16.6% in autumn, and 22.3% in winter; 45.1% of samples were from male cats and the rest from female ones. Of the studied cats, 118 were younger than 1 year, 78 were 1-3 years old, and 68 were older than 3 years. The specimens were subjected to direct microscopic examination with 15% potassium hydroxide and cultured on Sabouraud dextrose agar and dermatophyte test medium supplemented with cycloheximide and chloramphenicol. Dermatophyte identification was carried out based on macroscopic and microscopic colony morphology, urease activities, in vitro hair perforation test, growth at 37°C, and pigmentation on corn meal agar. Dermatophytes were isolated from 19 (7.1%) of the 264 specimens examined. The most frequently isolated fungi were Trichophyton terrestre (4.1%), followed by Microsporum gypseum (1.1%), M. nanum (1.1%), and T. mentagrophytes (0.7%), and these fungi may represent a health risk for humans in contact with clinically healthy Van cats. M. canis was not isolated from any of the specimens. Our results show no significant (p>0.05) association between carriage of dermatophytes and the gender of cats. The carriage rate of dermatophytes was high in spring and winter, and the only possible risk factor for infection was age of the animal.

Long term outcomes of surgical revascularization for isolated left main coronary artery stenosis: a single-center surveillance study

OBJECTIVE

The objective of this study was to retrospectively analyze the clinical course and postoperative long-term survival of patients diagnosed with isolated left main coronary artery (LMCA) stenosis after surgical revascularization.

METHODS

A total of 38 patients (27 males, 11 females) who were diagnosed with isolated LMCA stenosis and underwent surgical revascularization were enrolled in the study. Isolated LMCA stenosis was classified into 2 groups: ostial stenosis and nonostial stenosis. Coronary events were defined as death of cardiac origin, the need for a new myocardial revascularization procedure, or the occurrence of myocardial infarction in the course of follow-up. The postoperative assessment period included short- and long-term follow-up. The study endpoint was defined as all-cause mortality.

RESULTS

Among the 38 patients who participated in the study, 25 suffered from ostial LMCA stenosis. The early postoperative mortality rate before hospital discharge was 2.6%. Median duration of postoperative long-term follow-up was 73.43 months (range: 0.17-187.23). Median duration of long-term follow-up free from coronary events or percutaneous coronary interventions was 73.43 months. Postoperative 2-year survival rate was 97.4%, and 5-year survival rate was 92.1%. The postoperative survival period and period free of coronary events of patients with isolated ostial LMCA stenosis did not differ significantly from those of patients with nonostial stenosis (p=0.801, p=0.970, respectively).

CONCLUSION

Postoperative short- and long-term prognosis of isolated LMCA stenosis appears good in terms of mortality and coronary event symptoms.

Monocyte to high-density lipoprotein ratio as a new prognostic marker in patients with STEMI undergoing primary percutaneous coronary intervention

BACKGROUND

Monocyte count to high-density lipoprotein ratio (MHR) has recently emerged as an indicator of inflammation and oxidative stress in the literature. We aimed to investigate the prognostic value of MHR in patients with ST-segment elevation myocardial infarction treated with primary percutaneous coronary intervention (PCI).

METHODS

A total of 513 patients who were hospitalized with diagnosis of acute ST-segment elevation myocardial infarction and treated with primary PCI were retrospectively enrolled in the study. Demographic and clinical data, admission laboratory parameters, and MHR values were recorded. Inhospital major adverse cardiac events (MACE) and mortality were reported as the clinical outcomes.

RESULTS

Twenty-six patients (5%) died, and MACE was observed in 86 patients (17%) during hospital follow-up. Patients were categorized in 3 groups according to tertiles of admission MHR. The rates of inhospital mortality and MACE were significantly higher in tertile 3 group compared to tertile 1 group (10% vs 1%, 27% vs 11%; P < .01 and P < .01). In multivariate regression analysis, age, sex, presence of Killip 3 or 4, left ventricular ejection fraction, troponin I, C-reactive protein, and increased MHR levels (odds ratio, 1.03; 95% confidence interval, 1.01-1.05; P < .01) independently predicted inhospital mortality; age, presence of Killip 3 or 4, troponin I, and increased MHR levels (odds ratio, 1.02; 95% confidence interval, 1.01-1.04; P < .01) independently predicted MACE.

CONCLUSION

Admission MHR values were found to be independently correlated with inhospital MACE and mortality after primary PCI.

Detection of biotinidase gene mutations in Turkish patients ascertained by newborn and family screening

The incidence of biotinidase deficiency in Turkey is currently one of the highest in the world. To expand upon the information about the biotinidase gene (BTD) variations in Turkish patients, we conducted a mutation screening in a large series (n = 210) of probands with biotinidase deficiency, using denaturing high-performance liquid chromatography and direct DNA sequencing. The putative effects of novel mutations were predicted by computational program. Twenty-six mutations, including six novels (p.C143F, p.T244I, c.1212-1222del11, c.1320delG, p.V457L, p.G480R) were identified. Nine of the patients were symptomatic at the initial clinical assessment with presentations of seizures, encephalopathy, and lactic acidemia. The most common mutation in this group of symptomatic patients was c.98-104 del7ins3. Among the screened patients, 72 have partial and 134 have profound biotinidase deficiency (BD) of which 106 are homozygous for BTD mutations. The common mutations (p.R157H, p.D444H, c.98-104del7ins3, p.T532M) cumulatively accounted for 72.3% of all the mutant alleles in the Turkish population.

CONCLUSION

The identification of common mutations and hot spot regions of the BTD gene in Turkish patients is important for mutation screening in the Turkish population and helps to ascertain carriers, may have impact on genetic counseling and implementing prevention programs.

International warfarin genotype-guided dosing algorithms in the Turkish population and their preventive effects on major and life-threatening hemorrhagic events

AIM

To determine the accuracy of international warfarin pharmacogenetic algorithms developed on large multiethnic cohorts (comprising more than 1000 subjects) to predict therapeutic warfarin doses in Turkish patients.

MATERIALS & METHODS

We investigated two Turkish warfarin-treated cohorts: patients with no history of hemorrhagic or thromboembolic event and patients with major and life-threatening hemorrhagic events.

RESULTS

International pharmacogenetic algorithms showed good performances in predicting the therapeutic dose of patients with no history of bleedings, but they did not significantly detect the incorrect warfarin dose of patients with major and life-threatening hemorrhagic events.

CONCLUSION

Although genetic information can predict the therapeutic warfarin dose, the accuracy of the international pharmacogenetic algorithms is not sufficient to be used for warfarin screening in Turkish patients.

Mutation of androgen receptor N-terminal phosphorylation site Tyr-267 leads to inhibition of nuclear translocation and DNA binding

Reactivation of androgen receptor (AR) may drive recurrent prostate cancer in castrate patients. Ack1 tyrosine kinase is overexpressed in prostate cancer and promotes castrate resistant xenograft tumor growth and enhances androgen target gene expression and AR recruitment to enhancers. Ack1 phosphorylates AR at Tyr-267 and possibly Tyr-363, both in the N-terminal transactivation domain. In this study, the role of these phosphorylation sites was investigated by characterizing the phosphorylation site mutants in the context of full length and truncated AR lacking the ligand-binding domain. Y267F and Y363F mutants showed decreased transactivation of reporters. Expression of wild type full length and truncated AR in LNCaP cells increased cell proliferation in androgen-depleted conditions and increased colony formation. However, the Y267F mutant of full length and truncated AR was defective in stimulating cell proliferation. The Y363F mutant was less severely affected than the Y267F mutant. The full length AR Y267F mutant was defective in nuclear translocation induced by androgen or Ack1 kinase. The truncated AR was constitutively localized to the nucleus. Chromatin immunoprecipitation analysis showed that it was recruited to the target enhancers without androgen. The truncated Y267F AR mutant did not exhibit constitutive nuclear localization and androgen enhancer binding activity. These results support the concept that phosphorylation of Tyr-267, and to a lesser extent Tyr-363, is required for AR nuclear translocation and recruitment and DNA binding and provide a rationale for development of novel approaches to inhibit AR activity.

Can the T-peak to T-end interval be a predictor of mortality in patients with ST-elevation myocardial infarction?

BACKGROUND

The interval between the peak and the end of the T wave (Tp-e interval) on 12-lead ECG is a measure of transmural dispersion of repolarization and may be related to malignant ventricular arrhythmias. The objective of this study was to investigate whether the Tp-e interval predicts in-hospital and long-term mortality in patients with ST-segment elevation myocardial infarction (STEMI) undergoing a primary percutaneous coronary intervention (pPCI).

METHODS

This study included 488 consecutive patients with STEMI treated with pPCI. Electrocardiograms were obtained after pPCI and the Tp-e interval was measured in leads without ST-segment elevation.

RESULTS

There were 46 (9.4%) deaths in the population, with a mean follow-up time of 21.1±10.2 months. The Tp-e interval was associated with not only in-hospital ventricular tachycardia/fibrillation, target vessel revascularization, and death but also long-term target vessel revascularization and death. Furthermore, the Tp-e interval measured using the tail method was found to be a significant predictor of long-term mortality in multivariable Cox analyses [odds ratio 1.018, 95% confidence interval (1.004-1.033)]. Findings were similar in the Tp-e interval and the heart rate-corrected Tp-e interval (cTp-e).

CONCLUSION

Tp-e and cTp-e measured using the tail method were found to be predictors of both in-hospital and long-term mortality.

Ultrasonography for the prediction of extension of trophoblastic infiltration into the tubal wall in ampullary pregnancy

OBJECTIVE

Predictive factors of damage to the Fallopian tube may guide the treatment for patients with tubal pregnancy. The purpose of this study was to evaluate the predictive value of ultrasonographic findings in patients affected by ampullary pregnancy for the determination of the depth of trophoblastic infiltration into the tubal wall on histological examination.

MATERIAL AND METHODS

38 patients with ampullary pregnancy undergoing salpingectomy were enrolled into the study. The patients were divided into two subgroups depending on their transvaginal sonography (TVS) findings; either an ectopic gestational sac containing an embryo with cardiac activity or those with a tubal ring. The ampullary pregnancies were histologically classified according to the depth of infiltration of trophoblastic tissue into the tubal wall as follows: stage I: limited to mucosa; stage II: extension to the muscularis layer; stage III: complete infiltration of the tubal wall with or without rupture of the serosa. The association between findings on TVS and stage of trophoblastic invasion, serum beta-human chorionic gonodatropin (β-hCG) levels was evaluated.

RESULTS

Although there was no significant difference among two groups in terms of histological stage of trophoblastic infiltration (p = 0.257), patients in whom an embryo with cardiac activity had been identified were found to have higher percentage of stage II (47.8%) or stage III (8.7%) invasion. However, there was a significant difference in serum β-hCG levels on the day of surgery among the two groups (p = 0.028).

CONCLUSIONS

Ultrasonographic aspect of ampullary pregnancy is associated with depth of trophoblastic infiltration into the tubal wall and serum β-hCG levels.

Genetic diversity of disease-associated loci in Turkish population

Many consortia and international projects have investigated the human genetic variation of a large number of ethno-geographic groups. However, populations with peculiar genetic features, such as the Turkish population, are still absent in publically available datasets. To explore the genetic predisposition to health-related traits of the Turkish population, we analyzed 34 genes associated with different health-related traits (for example, lipid metabolism, cardio-vascular diseases, hormone metabolism, cellular detoxification, aging and energy metabolism). We observed relevant differences between the Turkish population and populations with non-European ancestries (that is, Africa and East Asia) in some of the investigated genes (that is, AGT, APOE, CYP1B1, GNB3, IL10, IL6, LIPC and PON1). As most complex traits are highly polygenic, we developed polygenic scores associated with different health-related traits to explore the genetic diversity of the Turkish population with respect to other human groups. This approach showed significant differences between the Turkish population and populations with non-European ancestries, as well as between Turkish and Northern European individuals. This last finding is in agreement with the genetic structure of European and Middle East populations, and may also agree with epidemiological evidences about the health disparities of Turkish communities in Northern European countries.