Gizem Calibasi

Relationship between Epidermal Growth Factor Receptor Gene Mutations and Clinicopathological Features in Patients with Non-Small Cell Lung Cancer in Western Turkey

BACKGROUND To investigate epidermal growth factor receptor (EGFR) gene mutations in patients with non- small cell lung cancer (NSCLC) and to analyze any relationship with clinicopathological features and prognosis. MATERIALS AND METHODS EGFR gene exons 18-21 in 48 specimens of paraffin-embedded tumor tissue from NSCLC patients were amplified by PCR, followed by direct sequencing and analysis of links to clinicopathological features and prognosis. RESULTS EGFR mutations were detected in 18 of 48 (42.6%) patients with NSCLC. There were 9 cases of mutations in exon 20, 7 in exon 19 and 2 in exon 21. Mutations were more frequently observed in women (5/7 pts, 71.4%) than in men (13/41 pts, 31.7%) (p=0.086) and in non-smokers (5/5 pts, 100%) than smokers (13/43 pts, 30.2%). There was negative correlation of EGFR mutations with smoking status (p=0.005). EGFR mutations were more frequently observed with adenocarcinoma histology (13/32 pts, 40.6%) than in other types (5/16 pts, 31.3%) (p=0.527). The patients with EGFR mutations had better survival than those with wild- type EGFR (p=0.08). There was no association of EGFR mutations with metastatic spread. CONCLUSIONS EGFR mutations in NSCLC were here demonstrated more frequently in females, non-smokers and adenocarcinoma histology in the western region of Turkey. Patients with EGFR mutations have a better prognosis.

KRAS mutation profile differences between rectosigmoid localized adenocarcinomas and colon adenocarcinomas

BACKGROUND Colorectal cancer has a heterogeneous nature that is influenced by the tumour site. Many improvements have been made in identifying and characterizing the genetic alterations between colon and rectal cancers. However, there is not enough information about KRAS mutational differences between rectosigmoid and colon cancers arising elsewhere in the large bowel. The aim of this study was to determine the differences in the frequency of KRAS genetic alterations between rectosigmoid cancers and colon cancers. METHODS Eighty-four patients diagnosed with colorectal cancer were included in this study. Genomic DNA was extracted from formalin-fixed paraffin-embedded tumour tissue sections. KRAS mutation analysis which was designed to detect the seven most common KRAS gene mutations (Gly12Ala, Gly12Asp, Gly12Arg, Gly12Cys, Gly12Ser, Gly12Val and Gly13Asp) was performed. Chi-square test was used to test the association between mutation status and other variables. RESULTS This study represents the first KRAS mutational results from Turkish rectosigmoid cancer patients. The KRAS mutation frequency of rectosigmoid tumours is higher (34.3%, 12/35) than that of colon-localized tumours (30.6%, 15/49). However, there is no significant correlation between the KRAS mutation status and tumour location (rectosigmoid and colon). CONCLUSIONS KRAS mutation analysis has a predictive and prognostic value in identifying tumours that may be resistant to treatment. Our study shows that differences in the biological behaviour of rectosigmoid and colon cancers should be considered. This finding highlights the importance of personalized cancer management, which could be assisted by cancer genotyping tools.

Dihydropyrimidine dehydrogenase 85T>C mutation is associated with ocular toxicity of 5-fluorouracil: a case report.

5-Fluorouracil (5-FU), the mainstay of solid tumor chemotherapy over the past 40 years, induces grade III–IV toxicities in up to 15% of patients with polymorphisms in the dihydropyrimidine dehydrogenase (DPYD), thymidylate synthase (TYMS), and methylenetetrahydrofolate reductase (MTHFR) genes. These toxicities include mucositis, neutropenia, nausea, diarrhea, myelosuppression, hand–foot syndrome, and rare ocular adverse effects. Here, we present the case of a female patient with rectal cancer who received 5-FU-based chemotherapy and developed grade III hand–foot syndrome and rare acute ocular adverse effects. Genetic analysis revealed that the patient had an 85T>C mutation in the DPYD gene resulting in a DPYD*9A allele. The clinical and molecular observations indicate that DPYD deficiency may be responsible for the severe ocular adverse effects observed in 5-FU-treated patients. Application of personalized therapy based on molecular testing should help clinicians provide the most effective chemotherapy agents and dose modifications for each patient, although further population-based pharmacogenetic trials for the 5-FU metabolism–related genes are necessary to minimize adverse effects and enhance clinical outcomes.

KRAS and BRAF mutation frequencies in a series of Turkish colorectal cancer patients

The prognostic value of KRAS and BRAF mutation in colorectal cancer (CRC) is very consistent. Several studies have demonstrated an association between these gene mutations and resistance to anti-EGFR based therapies. Wild type KRAS and BRAF is required for a response to CRC therapy. The aim of this study is to identify the frequency of KRAS and BRAF gene mutations in a series of Turkish CRC patients and to evaluate the relationship between the mutations and demographic features in the Turkish population. KRAS and BRAF mutations were analyzed in 220 colorectal tumor tissues. The mutation assays were performed with genomic DNA using automated microarray-based genotyping technology (Autogenomics Inc., Infinity Biofilm Chip Microarray, KRAS - BRAF Assay). Statistical analyses of the data were performed using SPSS (SPSS/Windows version 19.0, SPSS Inc., Chicago, IL, USA). In total, 33.2% of patients possessed a mutant KRAS genotype, and 6.7% of patients harbored BRAF mutations. The most common KRAS mutations were Gly12Asp and Gly12Val. All of the BRAF mutations were V600E. Patients with KRAS mutations did not harbor BRAF mutation. Female patients displayed an increased KRAS mutation frequency compared with male patients (P value =0.027). KRAS and BRAF gene alterations may determine the therapeutic response to anti-EGFR treatments. The utility of these markers was clarified by correlating genotyping studies with demographics and clinical findings. Cancer mutation profiles are influenced by cultural life style, environment and race/ethnicity. Genotype analysis could be used to select patients eligible for treatment. Patients should be classified according to genotypic subgroups for the selection of therapeutic agents.

Molecular Analysis of the KIT Gene in Gastrointestinal Stromal Tumors With Novel Mutations

Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract. KIT gene mutations have great importance for GISTs. This study evaluated the relationship between KIT mutations and GIST clinicopathologic features to define region-specific and population-specific differences. Genomic DNA was extracted from 60 GISTs, and polymerase chain reaction was performed for KIT gene exons 9, 11, 13, and 17. Polymerase chain reaction amplicons were sequenced in both directions. This study represents the first mutation data of the KIT gene in GISTs from a Turkish population and reports novel mutations. The mutation rate in exon 11 (46.7%) was remarkably higher than those of the other exons (8.3% for exon 9; 11.7% for exon 13; 1.7% for exon 17). There was an association between malignancy potential and the presence of KIT mutations (odds ratio=3.18). Cases with mutations in codons W557-K558 in exon 11 had 11-fold greater risk of malignancy when compared with those without a mutation in this exon (odds ratio=11). We report different mutations than those previously reported, which emphasizes the importance of personalized medicine that could be empowered by the use of bioinformatics tools in the diagnostic process and therapeutic approaches.

Techniques for Nucleic Acid Engineering: The Foundation of Gene Manipulation

Abstract The journey of nucleic acid isolation and characterization has been a long one starting in the late 1800s. DNA isolation has led the way due to its stable chemical characteristic. Since its initial implementation the demand of molecular studies has evolved rapidly into studying a wide range of nucleic acids, including all types of RNAs, mitochondrial DNA, and nucleic acid materials of other organisms. The scientific advancements and the “omics” era certainly brought new challenges, forcing the technology to go into an enormous advancement in a relatively short period. In the early 1900s the range of methods, the material, and the field of applications were limited. During, nearly, the last three decades the procedures became automated, standardized, economic, user-friendly, nonhazardous, and less time-consuming. The manual organic or inorganic procedures had left their place to more robust and reliable solid-phase extraction techniques. There are a wide range of samples in which high-quality and high-yield nucleic acid isolation is carried out. These samples vary from whole blood to different types of tissues, hair, bones, saliva, urine, and many more. We are going to explore the principles of nucleic acid isolation, the basics of chemistry behind the scenery, manual and advanced techniques of isolation and quality check, and the means of good laboratory practice.

Relationship of c-Kit Gene and Microsatellit Instability in the Pathogenesis of Wilms Tumors.

Hereditary nonpolyposis colon cancer (HNPCC), known as Lynch syndrome (LS), is caused by germline mutations in one of five genes that function in the DNA mismatch repair (MMR) process involving MLH1, MSH2, MSH6 or PMS2 (1,2). Patients with mutations in MMR genes exhibit microsatellite instability (MSI), a phenomenon in which errors in replication of highly repetitive sequences cannot be repaired, resulting in alteration of the length of repeat sequences and eventually genomic integrity (2). Mutational spectra for genes with high MSI frequencies vary between different cancers. Therefore, only marker genes of MSI are analyzed for evaluation of MMR genes. It has been demonstrated that patients with LS almost always exhibit MSI due to underlying defects in MMR genes and especially MLH1 and MSH2 (3).

Cetuximab alone has a dose-dependent antitumor effect in oral cavity cancer cells: an in vitro study

Yöntem: OCSCCCL (UPCI-SCC131) kültürü elde edildi ve xCELLigence RTCA SP cihaz› kullan›larak izlendi. Daha sonra yedi gruba bölüfltürüldü: (i) negatif kontrol: besiyeri+OCSCCCL, (ii) pozitif kontrol: besiyeri+OCSCCCL+sisplatin 10 μM/ml, (iii) besiyeri+OCSCCCL+setuksimab 25 μg/ml, (iv) besiyeri+OCSCCCL+setuksimab 50 μg/ml, (v) besiyeri+OCSCCCL+setuksimab 100 μg/ml, (vi) besiyeri+OCSCCCL+setuksimab 200 μg/ml, (vii) besiyeri+OCSCCCL+setuksimab 400 μg/ml. Hücre indeksi ve viyabilite istatistiksel aç›dan incelendi ve gruplar aras›nda karfl›laflt›r›ld›.

Hepatopathy-Thrombocytopenia Syndrome During Actinomycin D Treatment May Be Related to MDR1 (ABCB1) Gene Polymorphisms.

The antitumor agent actinomycin D has been used in the treatment of Wilms tumor for the past 40 years. Actinomycin D-induced hepatopathy-thrombocytopenia syndrome (HTS) is characterized as a rare syndrome. The mechanism underlying HTS may differ with individual multidrug resistance protein-1 (MDR1) genotype. The relationship between actinomycin D-related HTS and MDR1 gene mutations is presented in this case study of a pediatric patient with Wilms tumor. Our findings revealed that the girl had (-)1G>A, 1236C>T, 2677G>T, 3435C>T, and 61A>G MDR1 gene mutations. Understanding the function of genetic variants of MDR1 is an important aim for personalized cancer management.

Protein modelling of a novel KIT mutation (N567Y) in the gastrointestinal stromal tumour.

Dokuz Eylul University, Graduate School of Natural and Applied Sciences, Department of Chemistry, Izmir, Turkey Dokuz Eylul University, Institute of Health Sciences, Department of Basic Oncology, Izmir, Turkey Dokuz Eylul University, Faculty of Science, Department of Chemistry, Division of Biochemistry, Izmir, Turkey Dokuz Eylul University, Institute of Oncology, Department of Basic Oncology, Izmir, Turkey Dokuz Eylul University, Faculty of Medicine, Department of Biostatistics and Medical Informatics, Izmir, Turkey Dokuz Eylul University, Faculty of Medicine, Department of Medical Oncology, Izmir, Turkey