Association of 3'UTR variations of EGFR and KRAS oncogenes with clinical parameters in lung cancer tumours.

BACGROUND INFORMATION: Lung cancer is one of the leading types of cancer deaths worldwide, with approximately 2 million people diagnosed with lung cancer each year. In this study, we aimed to determine the exonic and 3'UTR sequences of EGFR, PIK3CA and KRAS genes in 39 sporadic lung cancer tumors and to reveal the changes in the miRNA binding profile of tumors with somatic variation in the 3'UTR region and to examine the relationship of these changes with clinical parameters. RESULTS: A statistically significant correlation was found between the presence of miRNA that could not bind to the 3'UTR region due to variation in at least one of the EGFR or KRAS genes and the presence of metastasis in the tumor. At the same time, Kaplan-Meier analysis between those with and without alterations in the miRNA profile due to somatic variation in the 3'UTR region showed that survival was lower in those with miRNA alterations and this was statistically significant. CONCLUSIONS: In our study, it was shown that variations in the 3'UTR regions of EGFR and KRAS oncogenes may cause increased expression of these oncogenes by preventing the binding of miRNAs, and it was suggested that this may be related to metastasis, survival and drug resistance mechanism. SIGNIFICANCE: In this study, we show that hsa-miR-124-3p, hsa-miR-506-3p, hsa-miR-1290 and hsa-miR-6514-3p are particularly prominent in lung carcinoma in relation to these biological pathways and the roles that variations in the 3'UTR regions of oncogenes may play in the carcinogenesis process.

Variant Analysis of miRNA Regulatory Genes in 35 Sporadic Lung Carcinoma Tumors.

Lung cancer is one of the cancer types with the highest mortality worldwide. The most frequently mutated genes known to be clinically important in lung cancers are EGFR, BRAF, and KRAS genes. Therefore, the therapeutic agents developed are directed against variants that cause over-activation of the EGFR-KRAS-BRAF-BRAF-MEK/ERK signalling pathway. However, different responses of patients to Tyrosine Kinase Inhibitors (TKIs) suggest that new prognostic biomarkers should be defined and epigenetic mechanisms may be related to this situation. METHODS: In this study, sequence analyses of AGO2, DICER, and DROSHA genes involved in miRNA biogenesis and EGFR, KRAS, and BRAF genes were performed in 35 patients with sporadic lung cancer. RESULTS: We found variations in genes involved in miRNA biogenesis that have not been previously reported in the literature. In addition, we found 4 different variants in the EGFR gene that have been described in the literature. In addition, a statistically significant association was found between the presence of mutations in at least one of the genes involved in miRNA biogenesis and metastasis (p:0.02). CONCLUSIONS: In conclusion, genomic dysregulation of key miRNA biogenesis genes may be one of the possible reasons for the differential response of patients to therapeutic agents and the development of metastasis in EGFR wild type tumours.

A novel LTBP2 gene variant in a Turkish family with juvenile-onset open-angle glaucoma.

BACKGROUND: Juvenile-onset open-angle glaucoma (JOAG) is a rare form of primary open-angle glaucoma (POAG) with an early age of onset before 40 years. Latent transforming growth factor-beta binding protein 2 (LTBP-2) is an extracellular matrix protein with a multi-domain structure and homology to fibrillins. LTBP2 gene variants have been associated with JOAG in a small number of patients. Herein, we report a novel missense variant in the LTBP2 gene in a Turkish family with JOAG. MATERIALS AND METHODS: Blood samples were obtained from three siblings (a 20-year-old woman with JOAG, 26-year-old man with JOAG, and 15-year-old girl with posterior embryotoxon) for genetic analysis. Their father had moderate-severe POAG and the 24-year-old brother had JOAG. The mother and 32-year-old sister were healthy. Although the parents reported no consanguinity, they come from the same village. RESULTS: Clinical exome sequencing analysis of the two siblings with JOAG revealed a novel c.607C>T p.(R203C) (rs777450651) homozygous LTBP2 variant, while the variant was heterozygous in their 15-year-old sister. There were no mutations in the MYOC, CYP1B1, or FBN1 genes. CONCLUSION: We documented a novel missense mutation in the LTBP2 gene leading to a severe form of JOAG with refractory IOP and progressive optic nerve damage, which seems to show autosomal recessive inheritance.

Chromosome 1p status in neuroblastoma correlates with higher expression levels of miRNAs targeting neuronal differentiation pathway.

Neuroblastoma (NB) is characterized by acquired segmental and numerical chromosome aberrations. Although deletions of distal 1p and 11q are frequent alterations, no candidate tumor suppressor gene residing in these chromosomal sites could be identified so far. In the present study, we detected the genomic imbalances of six neuroblastoma cell lines using the multiplex ligation-dependent probe amplification (MLPA) technique and the microRNA (miRNA) expression profiles of the cell lines by a microarray study. According to MLPA results, we aimed to assess the miRNA expression profiles of the cell lines harboring 11q and 1p deletions. The cell lines with 1p deletions revealed statistically significant higher levels of expression for 29 miRNAs in contrast to the cell lines without 1p deletion in microarray study. We also performed GO enrichment analysis for predicted targets of the differentially expressed miRNAs. According to GO enrichment analysis, miRNAs that showed the high change in expression was associated with neuronal differentiation. We showed that hsa-miR-494, hsa-miR-495, and hsa-miR-543 target most of mRNAs in neuronal differentiation pathway. Although limited to the cell lines, our results highly suggest that NBs with different segmental chromosome abnormalities may have different dysregulated miRNA expression signatures that target the genes involved in neuronal differentiation.

Is There A Systemic Inflammatory Effect of Cholesteatoma?

Introduction Inflammation causes squamous epithelial transformation of the mucosa in the middle ear cavity and plays a role in the onset, growth, spread, and recurrence of cholesteatoma. Objectives The objective of this study is to investigate the systemic inflammatory effect in chronic otitis with cholesteatoma. Methods The study included a total of 311 patients comprising 156 patients with a pathology diagnosis of cholesteatoma and a control group of 155 with no active inflammation. The Neutrophil-to-lymphocyte Ratio (NLR) was calculated by dividing the neutrophil value by the lymphocyte value. Results The mean NLR was 1.94 ± 0.91 in the patients with cholesteatoma and 1.94 ± 0.85 in the control group. We determined no statistically significant difference between the groups in respect of NLR (p = 0.983). We calculated the NLR as 2.01 ± 1.00 in patients with ossicle erosion and 1.82 ± 0.69 in those without ossicle erosion, 1.86 ± 0.85 in patients with bone erosion and 1.98 ± 0.95 in those without bone erosion. We determined no statistical difference between these values (p = 0.175). Conclusion The results of this study showed that NLR had no predictive value in respect of bone erosions and associated complications in patients with cholesteatoma. The inflammatory effect of cholesteatoma is not systemic but remains more local.

Novel Zinc Finger Protein Gene 469 (ZNF469) Variants in Advanced Keratoconus.

PURPOSE: Common polymorphic variants upstream of Zinc finger protein gene 469 (ZNF469) have been associated with central corneal thickness. Rare ZNF469 variants have been shown in keratoconus patients. The aim of the current study was to investigate the frequency of ZNF 469 gene variants in rapidly progressive advance keratoconus patients who underwent corneal transplant surgery by the age of 30, compared to their frequency in the normal Turkish population. METHODS: A search in a patient database was performed to identify patients with a rapidly progressive keratoconus requiring corneal transplant surgery by the age of 30 in at least one eye. Twenty-six advance keratoconus patients (study group) and 109 health subjects (control group) were included in the study. Blood samples were donated, and genomic DNA was extracted. The entire coding sequence of the ZNF469 gene including the 84 bp of the putative intron was amplified using PCR primers and analyzed using next generation sequencing (NGS). RESULTS: Fifteen single nucleotide polymorphisms previously reported and registered to the dbSNP database were detected in the study group. The allele frequencies of these polymorphisms were higher in the keratoconus group compared to the control group and to the ExAC genome database. Three new missense heterozygote variants and one new synonym variant were detected in keratoconus group. According to prediction software, the P873T and Q2188H variants were shown to be non-tolerated, whereas G3424S could be tolerated. The synonymous variant R1060R is not predicted to lead to abnormal splicing by Human Splicing Finder in silico analysis. CONCLUSION: New detected ZNF 469 P873T and Q2188H heterozygote coding variants in isolated advance keratoconus patients may be associated with the disease pathogenesis.

The Detection of Genetic Parameters for Prognostic Stratification of Neuroblastoma Using Multiplex Ligation-Dependent Probe Amplification Technique.

BACKGROUND: Neuroblastoma (NB) is a neoplasm of the sympathetic nervous system and the most frequent extra cranial solid tumor of early childhood. These tumors display a wide range of clinical behavior and are characterized by complex chromosomal changes, some of which are associated with distinct clinical phenotypes. We investigated the contribution of genetic variables to staging and histology by logistic regression analyses. METHODS: We used multiplex ligation-dependent probe amplification (MLPA) to detect segmental genomic imbalances and gene copy number changes in 202 primary NBs. RESULTS: Cases with NB were categorized into four distinct groups based on the genomic changes. Group 1 (48 cases, 23.7%) contained tumors with a 1p deletion and/or MYCN gene amplification (MNA). Group 2 included 46 cases (22.8%) with 3p and/or 11q deletions without 1p deletion and MYCN gene amplification. Tumors harboring at least two commonly observed deletions with or without MNA were classified as Group 3 (25 cases, 12.4%). Tumors with chromosomal imbalance other than MYCN gene amplification and 1p, 3p, and 11q deletions were in Group 4 (83 cases, 41.1%). MYCN gene amplification and 17q gain were significant predisposing factors for unfavorable histology. Significant correlations were detected between 1p deletion and MYCN gene amplification; 3p and 11q deletions; and 11q deletion and 17q gain. CONCLUSION: MLPA can be used effectively to simultaneously detect multiple genomic imbalances and these changes can be utilized to classify neuroblastomas by prognostic subtypes. The genetic changes detected in NB in this study and their associations with clinical characteristics are in line with previously published reports.

Chromosomal aberrations in benign prostatic hyperplasia patients.

PURPOSE: To investigate the chromosomal changes in patients with benign prostatic hyperplasia (BPH). MATERIALS AND METHODS: A total of 54 patients diagnosed with clinical BPH underwent transurethral prostate resection to address their primary urological problem. All patients were evaluated by use of a comprehensive medical history and rectal digital examination. The preoperative evaluation also included serum prostate-specific antigen (PSA) measurement and ultrasonographic measurement of prostate volume. Prostate cancer was detected in one patient, who was then excluded from the study. We performed conventional cytogenetic analyses of short-term cultures of 53 peripheral blood samples obtained from the BPH patients. RESULTS: The mean (±standard deviation) age of the 53 patients was 67.8±9.4 years. The mean PSA value of the patients was 5.8±7.0 ng/mL. The mean prostate volume was 53.6±22.9 mL. Chromosomal abnormalities were noted in 5 of the 53 cases (9.4%). Loss of the Y chromosome was the most frequent chromosomal abnormality and was observed in three patients (5.7%). There was no statistically significant relationship among age, PSA, prostate volume, and chromosomal changes. CONCLUSIONS: Loss of the Y chromosome was the main chromosomal abnormality found in our study. However, this coexistence did not reach a significant level. Our study concluded that loss of the Y chromosome cannot be considered relevant for the diagnosis of BPH as it is for prostate cancer. Because BPH usually occurs in aging men, loss of the Y chromosome in BPH patients may instead be related to the aging process.

Amplification of Cellular Oncogenes in Solid Tumors.

The term gene amplification refers to an increase in copy number of a gene. Upregulation of gene expression through amplification is a general mechanism to increase gene dosage. Oncogene amplifications have been shown in solid human cancers and they are often associated with progression of cancer. Defining oncogene amplification is useful since it is used as a prognostic marker in clinical oncology nowadays, especially v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (HER2) targeted agents are used in breast cancer patients with high level of HER2 overexpression as a therapeutic approach. However, patients without HER2 overexpression do not appear to benefit from these agents. We concluded that determination of oncogene amplification in solid tumors is an important factor in treatment of human cancers with many unknowns. We have referred to PubMed and some databases to prepare this article.

The Importance of the Neutrophil-Lymphocyte Ratio in Patients with Idiopathic Peripheral Facial Palsy.

Objective. The purpose of this study was to investigate whether or not there was a correlation between the neutrophil-to-lymphocyte ratio (NLR) value and the severity of idiopathic peripheral facial palsy (IPFP) and to determine whether or not NLR could be used as an early predictive parameter in the prognosis of IPFP patients. Material and Method. This retrospective study was conducted on 146 patients who were diagnosed with IPFP. The control group comprised 140 patients. Patients with IPFP were categorized according to the House-Brackmann grading system (HBS). The NLR value was obtained by dividing the neutrophil value by the lymphocyte value. Results. In the IPFP group, the mean NLR value was 3.63 ± 2.74 and, in the control group, 1.84 ± 0.78. The mean NLR value was significantly higher in IPFP patients than in the control subjects (p < 0.0001). The mean NLR value in group A (Grades I-II ) was 2.61 ± 2.28, in group B (Grades III-IV) 3.22 ± 2.65, and in group C (Grades V-VI) 10.69 ± 6.30. Conclusion. We determined that as the severity of IPFP increased, the NLR value increased. The NLR value can be used as a prognostic factor in the early prediction of IPFP prognosis.

Copy number status and mutation analyses of anaplastic lymphoma kinase (ALK) gene in 90 sporadic neuroblastoma tumors.

Somatic and germline mutations of the anaplastic lymphoma kinase (ALK) gene were recently described in neuroblastoma (NB). In this study, we investigated the association of ALK copy number alterations with copy number status 2p24.1 amplicon harboring DEAD box polypeptide 1 (DDX1), MYCN and neuroblastoma-amplified (NAG) genes in 90 primary tumors of sporadic NB cases by multiplex ligation-dependent probe amplification (MLPA). We also performed mutation analysis of ALK gene by directly sequencing the exons 20-28 which cover the region that encodes juxtamembrane and kinase domains. A total of 39 (43.3%) NB cases revealed copy numbers alterations of ALK gene. There was highly significant association of ALK copy number gains with gains of one or more of the genes at 2p24.1 (DDX1, MYCN or NAG) in MYCN unamplified tumors (P<0.000). In addition, 15 of 17 MYCN amplified cases (88.2%) had aberrant ALK status. Solitary gain of ALK with normal copy number status of all other genes was observed only in one case. DNA sequencing of exons 20-28 of ALK revealed two different nucleotide changes in three cases leading to amino acid substitutions of F1245V and R1275Q in tyrosine kinase domain. In conclusion, the frequency of ALK mutations in NB is low and solitary copy number change of it is rarely observed.

Is There A System Inflammatory Effect of Cholesteatoma?

Abstract Introduction Inflammation causes squamous epithelial transformation of the mucosa in the middle ear cavity and plays a role in the onset, growth, spread, and recurrence of cholesteatoma. Objectives The objective of this study is to investigate the systemic inflammatory effect in chronic otitis with cholesteatoma. Methods The study included a total of 311 patients comprising 156 patients with a pathology diagnosis of cholesteatoma and a control group of 155 with no active inflammation. The Neutrophil-to-lymphocyte Ratio (NLR) was calculated by dividing the neutrophil value by the lymphocyte value. Results The mean NLR was 1.94 ± 0.91 in the patients with cholesteatoma and 1.94 ± 0.85 in the control group. We determined no statistically significant difference between the groups in respect of NLR (p = 0.983). We calculated the NLR as 2.01 ± 1.00 in patients with ossicle erosion and 1.82 ± 0.69 in those without ossicle erosion, 1.86 ± 0.85 in patients with bone erosion and 1.98 ± 0.95 in those without bone erosion. We determined no statistical difference between these values (p = 0.175). Conclusion The results of this study showed that NLR had no predictive value in respect of bone erosions and associated complications in patients with cholesteatoma. The inflammatory effect of cholesteatoma is not systemic but remains more local.