Significance of O6-methyl guanine methyltransferase promoter methylation in high grade glioma patients: optimal cutoff point, CpG locus, and genetic assay.

PURPOSE: To evaluate O6-methyl guanine methyltransferase (MGMT) promoter methylation status in high grade glioma patients and to identify the best cutoff point as well as the most predictive CpG loci for patients survival. METHOD: Consecutive high grade glioma patients treated with surgical gross total resection followed by concomitant radiochemotherapy and adjuvant chemotherapy were included in this retrospective observational study. Methylation status of MGMT promoter CpG island of resected tumor tissue were evaluated using next generation sequencing assay. The outcomes were grouped as CpG 70-78, CpG 79-83, CpG 84-87, CpG 70-87, and whole promoter. Quantitative analyses were dichotomized as methylated or unmethylated based on the cutoff points set to %10, and methylation was further graded as <%10 unmethylated, %10-30 low-methylated, and %30-100 high-methylated. RESULTS: Total of 95 patients with the mean age of 51.50 ± 12.36 years were included in the study. Overall survival (OS) and progression free survival (PFS) were 14.53 ± 1.92 (95% CI 10.77-18.30) and 10.90 ± 2.05 (95% CI 6.89-14.92) months, respectively. MGMT promoter was methylated in 38.2% of cases and high-methylated in 10.5% of cases. Methylation status of MGMT promoter was recognized as a very powerful predictor of OS and PFS. In particular, high-methylation of CpG 79-83 and CpG 84-87 islands at promoter region were strongly associated with better survival outcomes (p < 0.05). CONCLUSION: Our outcomes support the prognostic value of MGMT promoter methylation in patients with high grade glioma. Sequencing of whole promoter CpG islands demonstrated that methylation of particular CpG sites might predict clinical outcomes more precisely.

Iron Refractory Iron Deficiency Anemia Due to 374 Base Pairs Deletion in the TMPRSS6 Gene.

Iron refractory iron deficiency anemia is an autosomal recessive disorder arising from defects in iron metabolism that cause microcytic anemia to grow resistant to treatment. The patients usually do not respond to orally administered iron treatment and partially respond to intravenous iron administration. Mutations of TMPRSS6 gene which encodes matriptase-2 are the main cause of the disorder. Here, we describe the case of a 6-month-old Syrian boy who had hypochromic-microcytic anemia and normal ferritin levels at presentation. The patient did not respond to 1 month of iron therapy and his hemoglobin levels increased only after red blood cell transfusion. Mutation analysis demonstrated a novel 374 base pairs homozygote deletion spanning exon 15 of TMPRSS6 gene. Our results expand the mutation spectrum of TMPRSS6 gene in iron refractory iron deficiency anemia.

Camptodactyly-Arthropathy-Coxa Vara-Pericarditis Syndrome Resembling Juvenile Idiopathic Arthritis: A Single-Center Experience from Southern Turkey.

Camptodactyly-arthropathy-coxa vara-pericarditis (CACP) syndrome, caused by biallelic pathogenic mutations in the PRG4 gene, is characterized by early-onset camptodactyly, noninflammatory arthropathy, coxa vara deformity, and rarely, pericardial effusion. Herein, we report 3 patients with CACP syndrome from 2 unrelated families. All patients are female, born to consanguineous parents, and had camptodactyly since the first years of their lives. Two patients had a prior diagnosis of juvenile idiopathic arthritis. Hip changes were present in 2 patients, and 2 of 3 patients had undergone surgery for camptodactyly. Routine echocardiographic evaluations were normal during the 2-year follow-up. This paper represents the third study including CACP patients from Turkey. Clinically, all 3 patients resembled juvenile idiopathic arthritis cases and received unnecessary medication. There is also an ongoing need for improving awareness of CACP and an effective treatment focusing on the lubrication of the joint space in CACP patients.

The potential utility of real-time PCR of the 16S-rRNA gene in the diagnosis of neonatal sepsis.

Istanbullu K, Köksal N, Çetinkaya M, Özkan H, Yakut T, Karkucak M, Dogan H. The potential utility of real-time PCR of the 16S-rRNA gene in the diagnosis of neonatal sepsis. Turk J Pediatr 2019; 61: 493-499. The purpose of this study was to evaluate the efficacy of real-time polymerase chain reaction (PCR) of the 16S rRNA gene in diagnosis of neonatal sepsis and compare it with conventional blood culture. A total of 150 infants were enrolled in this prospective study. The infants were classified into two groups: sepsis group (n=100) and control group (n=50). Blood samples for complete blood count, C-reactive protein, procalcitonin, serum-amyloid A, blood culture and PCR were obtained before initiating antibiotic treatment. Eight specific probes were used to perform PCR analysis for detection of 8 different microorganisms. The positivity rates of blood culture and PCR were found as 11% and 3%, respectively. The diagnosis of neonatal sepsis by PCR revealed a 16.6 % sensitivity, 97.8 % specificity, 33.3% positive predictive value and 94.8% negative predictive value compared with the blood culture. This study showed a low sensitivity of PCR of the 16S rRNA gene in the diagnosis of neonatal sepsis. This may be associated with the identification of rare microorganisms in the blood culture that were not included to PCR analysis. Implementation of all suspectible microorganisms into PCR assay may increase the sensitivity of 16S rRNA gene PCR in diagnosis of neonatal sepsis.

MaFOS-GDM trial: Maternal fish oil supplementation in women with gestational diabetes and cord blood DNA methylation at insulin like growth factor-1 (IGF-1) gene.

BACKGROUND: To evaluate the effects of maternal fish oil supplementation in women with gestational diabetes mellitus (GDM) on birthweight and DNA methylation at insulin like growth factor-1 (IGF-1) gene in their offspring. METHODS: Randomized controlled trial. A total of 120 women with GDM were randomized to one of the two groups between 24 and 28 weeks of the pregnancy: Group 1 (n = 52) received fish oil liquid softgel (Ocean plus®) and Group 2 (Placebo) (n = 68) sunflower oil liquid softgel. The birthweight and DNA methylation at IGF-1 gene of the offsprings were assessed. RESULTS: We observed a significant inverse association between fish oil use during pregnancy and birthweight (ß = -0.18, s.e.:125, P = .04), corresponding to a 250 g lower birthweight among infants born to fish oil users. This association didn't persist in multivariate analysis. Cord blood IGF-1 was lower in fish oil group (P = .001). Cord blood DNA methylation percentages at CpG-1044 and CpG-611 sites of IGF-1 gene promoter 1 (P1) region were higher in fish oil group compared to placebo group (P = .02 and P = .001, respectively). However, CpG-1044 and CpG-611 methylations were not associated to birthweight (ß = 0.04, s.e: 25.1, P = .66 and ß = 0.04, s.e: 22.7, P = 0.66, respectively). CONCLUSIONS: Maternal fish oil use has small effects on birthweight and DNA methylation when given to mothers with GDM at late pregnancy. Future studies are needed to show associations between maternal fish oil use and neonatal DNA methylations. CLINICAL TRIAL REGISTRATION: "Fish Oil Supplementation in Women with Gestational Diabetes". IDENTIFIER: NCT02371343.

Effect of Cytokine Signaling 3 Gene Polymorphisms in Childhood Obesity.

OBJECTIVE: Although polymorphisms in suppressor of cytokine signaling 3 (SOCS3) was reported to be related to obesity, Metabolic syndrome (MS), and type 2 diabetes mellitus in various adult studies, there is a lack of data in children. In this study, we examined eight reported polymorphisms of SOCS3 in obese Turkish children and adolescent with and without MS and compared the results with that of controls. METHODS: One hundred and forty eight obese and 63 age- and sex-matched control subjects were enrolled in the study. Obesity classification was carried out according to body mass index. World Health Organization and National Cholesterol Education Program criteria were used for the diagnosis of MS. Genotyping procedure was carried out by polymerase chain reaction and Sanger sequencing protocol. RESULTS: The frequency of rs2280148 polymorphism was significantly higher in obese subjects with MS than in the control group, whereas the frequency of rs8064821 polymorphism was significantly higher in obese subjects with MS than in obese children without MS. CONCLUSION: The significant associations of certain SOCS3 polymorphisms with obesity parameters in both MS and MS -related insulin resistance, hypertension, and fatty liver suggest that polymorphisms in this gene may play a role in the pathogenesis of MS and also that they can be potentially used as a marker for attenuated or aggressive disease.

Maturity onset diabetes of youth (MODY) in Turkish children: sequence analysis of 11 causative genes by next generation sequencing.

BACKGROUND: Maturity-onset diabetes of the youth (MODY), is a genetically and clinically heterogeneous group of diseasesand is often misdiagnosed as type 1 or type 2 diabetes. The aim of this study is to investigate both novel and proven mutations of 11 MODY genes in Turkish children by using targeted next generation sequencing. METHODS: A panel of 11 MODY genes were screened in 43 children with MODY diagnosed by clinical criterias. Studies of index cases was done with MISEQ-ILLUMINA, and family screenings and confirmation studies of mutations was done by Sanger sequencing. RESULTS: We identified 28 (65%) point mutations among 43 patients. Eighteen patients have GCK mutations, four have HNF1A, one has HNF4A, one has HNF1B, two have NEUROD1, one has PDX1 gene variations and one patient has both HNF1A and HNF4A heterozygote mutations. CONCLUSIONS: This is the first study including molecular studies of 11 MODY genes in Turkish children. GCK is the most frequent type of MODY in our study population. Very high frequency of novel mutations (42%) in our study population, supports that in heterogenous disorders like MODY sequence analysis provides rapid, cost effective and accurate genetic diagnosis.