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Hill R, Madureira PA, Ferreira B, Baptista I, Machado S, Colaҫo L, Dos Santos M, Liu N, Dopazo A, Ugurel S, Adrienn A, Kiss-Toth E, Isbilen M, Gure AO, Link W. Retraction Note: TRIB2 confers resistance to anti-cancer therapy by activating the serine/threonine protein kinase AKT. Nat Commun 2023; 14:4341. [PMID: 37468494 DOI: 10.1038/s41467-023-40050-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023] Open
Affiliation(s)
- Richard Hill
- Department of Biomedical Sciences and Medicine (DCBM), University of Algarve, Campus de Gambelas, Faro, 8005-139, Portugal
- Centre for Biomedical Research (CBMR), University of Algarve, Campus de Gambelas, Faro, 8005-139, Portugal
- Brain Tumour Research Centre, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, PO1 2DT, Portsmouth, UK
| | - Patricia A Madureira
- Centre for Biomedical Research (CBMR), University of Algarve, Campus de Gambelas, Faro, 8005-139, Portugal
| | - Bibiana Ferreira
- Centre for Biomedical Research (CBMR), University of Algarve, Campus de Gambelas, Faro, 8005-139, Portugal
| | - Inês Baptista
- Centre for Biomedical Research (CBMR), University of Algarve, Campus de Gambelas, Faro, 8005-139, Portugal
| | - Susana Machado
- Centre for Biomedical Research (CBMR), University of Algarve, Campus de Gambelas, Faro, 8005-139, Portugal
| | - Laura Colaҫo
- Centre for Biomedical Research (CBMR), University of Algarve, Campus de Gambelas, Faro, 8005-139, Portugal
| | - Marta Dos Santos
- Centre for Biomedical Research (CBMR), University of Algarve, Campus de Gambelas, Faro, 8005-139, Portugal
| | - Ningshu Liu
- Bayer AG, Drug Discovery Oncology Research, Berlin, D-13342, Germany
| | - Ana Dopazo
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, 28029, Spain
| | - Selma Ugurel
- Department of Dermatology, University Hospital Essen, Essen, 45147, Germany
| | - Angyal Adrienn
- Department of Cardiovascular Science, University of Sheffield, Sheffield, S10 2RX, UK
| | - Endre Kiss-Toth
- Department of Cardiovascular Science, University of Sheffield, Sheffield, S10 2RX, UK
| | - Murat Isbilen
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, 06533, Turkey
| | - Ali O Gure
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, 06533, Turkey
| | - Wolfgang Link
- Department of Biomedical Sciences and Medicine (DCBM), University of Algarve, Campus de Gambelas, Faro, 8005-139, Portugal.
- Centre for Biomedical Research (CBMR), University of Algarve, Campus de Gambelas, Faro, 8005-139, Portugal.
- Algarve Biomedical Center (ABC), University of Algarve, Campus de Gambelas, Faro, 8005-139, Portugal.
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Sayan M, Arikan A, Isbilen M. In Silico Evaluation of SARS-CoV-2 K417N, L452R, and E484K Detection Assays Against Omicron Variants. New Microbiol 2023; 46:133-140. [PMID: 37247233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 05/29/2023] [Indexed: 05/31/2023]
Abstract
The study's objective was to assess whether the performance of the DIAGNOVITAL SARS-CoV-2 Mutation Detection Assays is affected by Omicron mutations. In silico evaluation of 67,717 Variant of Concern, Variant of Interest sequences and 6,612 sequences of the Omicron variants involving BA1., BA2., BA3 sub-lineages downloaded from the GISAID database by 17 December 2021, were performed. The sequences were aligned according to the reference genome MN908947.3 using MAFFT multiple sequence alignment software version 7. Our findings showed that among 6,612 Omicron, 41 Spike gene mutations with a frequency of ≥70% were identified. Some of the Omicron mutations (R408S, N440K, G446S, Q493S, Q498R) could affect the diagnostic performance of K417N, L452R, and E484K assays against the Omicron sub-lineages. However, L452R and K417N mutation tests allow differentiation of the Delta and Omicron variants mutation profile. The COVID-19 pandemic lasted longer than expected, and the rapid modification of diagnostic kits seems necessary to combat the pandemic.
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Affiliation(s)
- Murat Sayan
- Kocaeli University, Research and Education Hospital, PCR Unit, 41380, Kocaeli, Turkey
- Near East University, DESAM Research Institute, 99138, Nicosia, Northern Cyprus
| | - Ayse Arikan
- Near East University, DESAM Research Institute, 99138, Nicosia, Northern Cyprus
- Near East University, Faculty of Medicine, Department of Medical Microbiology and Clinical Microbiology, 99138, Nicosia, Northern Cyprus
| | - Murat Isbilen
- Acibadem Mehmet Ali Aydinlar University, Graduate School of Health Sciences, Department of Biostatistics and Bioinformatics, 34752, Istanbul, Turkey
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Bayirli-Turan D, Usanmaz M, Gorgun S, Yolcu E, Sahin C, Bilenoglu O, Isbilen M, Yildiz E. The Prevalence of Protein S Variant in Patients Diagnosed with COVID-19. Clin Lab 2022; 68. [PMID: 36250839 DOI: 10.7754/clin.lab.2022.211212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
BACKGROUND The rapid spread of the new severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) which causes the coronavirus disease 2019 (COVID-19) facilitated the emergence of numerous variants. The present study aimed to investigate the prevalence and change of important "S" protein variants such as N501Y, DelH69/ 70, and E484K in SARS CoV-2 PCR positive patients diagnosed with COVID-19 who have referred to a private hospital within the period that mutations were detected during COVID-19 pandemic. METHODS One hundred and eighty-seven patients who have been referred due to the suspicion of COVID-19 between December 2020 and April 2021 and in whom SARS-CoV-2 was detected positive in the PCR test were enrolled into the study. These patients were randomly selected among 285 patients detected in these months, among those with the most accurate graphics and data. The RNA material extracted from the nasopharyngeal swab samples taken from the patients was analyzed and specifically N501Y, del69-70, and E484K mutations were investigated through the Real-Time PCR method. RESULTS The mean age of the patients was 37.5 ± 14.1 years. Mutations were detected in 84 (44.9%) samples in total (N501Y + DelH69/70 by 81%, DelH69/70 by 7.1%, E484K by 7.1% and N501Y + E484K by 4.8%). There was no sample detected with the N501Y mutation. The mutation rate between December - February was detected between 1% and 8%, and the mutation rate increased to 39% to 44% in April and March. While DelH69/70 mutation was detected in December 2020 only, it was observed that N501Y + DelH69/70 variants became dominant as of February 2021, and E484K and N501Y + E484K variants started to appear in March and April. It was observed that the variant rates included DelH69/70 (p < 0.001), N501Y (p < 0.001), N501Y + DelH69/70 (p < 0.001), and N501Y + E484K (p = 0.01) mutations increased significantly according to the months. The E484K mu-tation was significantly higher in males (p = 0.037). There was no differences between mutation rates between the age groups. CONCLUSIONS Our findings indicate that the appearance of important SARS-CoV-2 variants gradually increases, that rates of mutation increase up to 40% within several months, that the N501Y + DelH69/70 variant gradually becomes to be dominant, and that different variations appear along with mutations.
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Sayan M, Arikan A, Isbilen M. Variant analysis of SARS-CoV-2 strains with phylogenetic analysis and the Coronavirus Antiviral and Resistance Database. J Comp Eff Res 2022; 11:157-167. [PMID: 35014556 PMCID: PMC8751628 DOI: 10.2217/cer-2021-0208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/12/2021] [Indexed: 01/16/2023] Open
Abstract
Aims: This study determined SARS-CoV-2 variations by phylogenetic and virtual phenotyping analyses. Materials & methods: Strains isolated from 143 COVID-19 cases in Turkey in April 2021 were assessed. Illumina NexteraXT library preparation kits were processed for next-generation ]sequencing. Phylogenetic (neighbor-joining method) and virtual phenotyping analyses (Coronavirus Antiviral and Resistance Database [CoV-RDB] by Stanford University) were used for variant analysis. Results: B.1.1.7-1/2 (n = 103, 72%), B.1.351 (n = 5, 3%) and B.1.525 (n = 1, 1%) were identified among 109 SARS-CoV-2 variations by phylogenetic analysis and B.1.1.7 (n = 95, 66%), B.1.351 (n = 5, 4%), B.1.617 (n = 4, 3%), B.1.525 (n = 2, 1.4%), B.1.526-1 (n = 1, 0.6%) and missense mutations (n = 15, 10%) were reported by CoV-RDB. The two methods were 85% compatible and B.1.1.7 (alpha) was the most frequent SARS-CoV-2 variation in Turkey in April 2021. Conclusion: The Stanford CoV-RDB analysis method appears useful for SARS-CoV-2 lineage surveillance.
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Affiliation(s)
- Murat Sayan
- Kocaeli University, Research & Education Hospital, PCR Unit, 41380, Kocaeli, Turkey
- Near East University, DESAM Research Institute, 99138, Nicosia, Northern Cyprus
| | - Ayse Arikan
- Near East University, DESAM Research Institute, 99138, Nicosia, Northern Cyprus
- Near East University, Department of Medical Microbiology & Clinical Microbiology, 99138, Nicosia, Northern Cyprus
| | - Murat Isbilen
- Acibadem Mehmet Ali Aydinlar University, Graduate School of Health Sciences, Department of Biostatistics & Bioinformatics, 34752, Istanbul, Turkey
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Kucukkaraduman B, Turk C, Fallacara AL, Isbilen M, Senses KM, Ayyildiz ZO, Akbar MW, Lotem M, Botta M, Gure AO. Predictive Gene Signature for Pyrazolopyrimidine Derivative c-Src Inhibitor 10a Sensitivity in Melanoma Cells. ACS Med Chem Lett 2020; 11:928-932. [PMID: 32435407 DOI: 10.1021/acsmedchemlett.9b00679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 02/18/2020] [Indexed: 11/29/2022] Open
Abstract
Melanoma is a highly aggressive cancer with poor prognosis. Although more than 80% of melanomas harbor an activating mutation in genes within the MAPK pathway, which are mutually exclusive, usefulness of therapies targeting MAPK pathway are impeded by innate and/or acquired resistance in most patients. In this study, using melanoma cells, we report the efficacy of a recently developed pyrazolo[3,4-d]pyrimidine derived c-Src inhibitor 10a and identify a molecular signature which is predictive of 10a chemosensitivity. We show that the expression of TMED7, PLOD2, XRCC5, and NSUN5 are candidate biomarkers for 10a sensitivity. Although an undifferentiated/mesenchymal/invasive status of melanoma cells is associated with resistance to 10a, we show here for the first time that melanoma cells can be sensitized to 10a via treatment with valproic acid, a histone deacetylase inhibitor.
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Affiliation(s)
- Baris Kucukkaraduman
- Department of Molecular Biology and Genetics, Bilkent University, Ankara 06800, Turkey
| | - Can Turk
- Faculty of Medicine, Department of Medical Microbiology, Lokman Hekim University, Ankara 06510, Turkey
| | - Anna L. Fallacara
- Department of Biotechnology, Chemistry and Pharmacy, “Department of Excellence 2018-2022”, University of Siena, Via Aldo Moro 2, Siena 53100, Italy
| | - Murat Isbilen
- DNAFect Genetics Consulting R&D and Biotechnology Inc., Kocaeli 41470, Turkey
| | - Kerem M. Senses
- Department of Molecular Biology and Genetics, Zonguldak Bulent Ecevit University, Zonguldak 67100, Turkey
| | - Zeynep O. Ayyildiz
- Department of Genome Sciences and Molecular Biotechnology, Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35340, Turkey
| | - Muhammad W. Akbar
- Department of Molecular Biology and Genetics, Bilkent University, Ankara 06800, Turkey
| | - Michal Lotem
- Sharett Institute of Oncology, Hadassah Hebrew University Hospital, Ein Karem Campus, Jerusalem 91120, Israel
| | - Maurizio Botta
- Department of Biotechnology, Chemistry and Pharmacy, “Department of Excellence 2018-2022”, University of Siena, Via Aldo Moro 2, Siena 53100, Italy
| | - Ali O. Gure
- Department of Molecular Biology and Genetics, Bilkent University, Ankara 06800, Turkey
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Akbar MW, Isbilen M, Belder N, Canli SD, Kucukkaraduman B, Turk C, Sahin O, Gure AO. A Stemness and EMT Based Gene Expression Signature Identifies Phenotypic Plasticity and is A Predictive but Not Prognostic Biomarker for Breast Cancer. J Cancer 2020; 11:949-961. [PMID: 31949498 PMCID: PMC6959010 DOI: 10.7150/jca.34649] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 11/03/2019] [Indexed: 01/05/2023] Open
Abstract
Aims: Molecular heterogeneity of breast cancer results in variation in morphology, metastatic potential and response to therapy. We previously showed that breast cancer cell line sub-groups obtained by a clustering approach using highly variable genes overlapped almost completely with sub-groups generated by a drug cytotoxicity-profile based approach. Two distinct cell populations thus identified were CSC(cancer stem cell)-like and non-CSC-like. In this study we asked whether an mRNA based gene signature identifying these two cell types would explain variation in stemness, EMT, drug sensitivity, and prognosis in silico and in vitro. Main methods:In silico analyses were performed using publicly available cell line and patient tumor datasets. In vitro analyses of phenotypic plasticity and drug responsiveness were obtained using human breast cancer cell lines. Key findings: We find a novel gene list (CNCL) that can generate both categorical and continuous variables corresponding to the stemness/EMT (epithelial to mesenchymal transition) state of tumors. We are presenting a novel robust gene signature that unites previous observations related either to EMT or stemness in breast cancer. We show in silico, that this signature perfectly predicts behavior of tumor cells tested in vitro, and can reflect tumor plasticity. We thus demonstrate for the first time, that breast cancer subtypes are sensitive to either Lapatinib or Midostaurin. The same gene list is not capable of predicting prognosis in most cohorts, except for one that includes patients receiving neo-adjuvant taxene therapy. Significance: CNCL is a robust gene list that can identify both stemness and the EMT state of cell lines and tumors. It can be used to trace tumor cells during the course of phenotypic changes they undergo, that result in altered responses to therapeutic agents. The fact that such a list cannot be used to identify prognosis in most patient cohorts suggests that presence of factors other than stemness and EMT affect mortality.
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Affiliation(s)
- Muhammad Waqas Akbar
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Murat Isbilen
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey.,DNAFect Genetics Consulting R&D and Biotechnology Inc., Kocaeli, Turkey
| | - Nevin Belder
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Secil Demirkol Canli
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey.,Molecular Pathology Application and Research Center, Hacettepe University, Ankara, Turkey
| | - Baris Kucukkaraduman
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Can Turk
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Ozgur Sahin
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Ali Osmay Gure
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
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Demirkol S, Gomceli I, Isbilen M, Dayanc BE, Tez M, Bostanci EB, Turhan N, Akoglu M, Ozyerli E, Durdu S, Konu O, Nissan A, Gonen M, Gure AO. A Combined ULBP2 and SEMA5A Expression Signature as a Prognostic and Predictive Biomarker for Colon Cancer. J Cancer 2017; 8:1113-1122. [PMID: 28607584 PMCID: PMC5463424 DOI: 10.7150/jca.17872] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 03/05/2017] [Indexed: 01/08/2023] Open
Abstract
Background: Prognostic biomarkers for cancer have the power to change the course of disease if they add value beyond known prognostic factors, if they can help shape treatment protocols, and if they are reliable. The aim of this study was to identify such biomarkers for colon cancer and to understand the molecular mechanisms leading to prognostic stratifications based on these biomarkers. Methods and Findings: We used an in house R based script (SSAT) for the in silico discovery of stage-independent prognostic biomarkers using two cohorts, GSE17536 and GSE17537, that include 177 and 55 colon cancer patients, respectively. This identified 2 genes, ULBP2 and SEMA5A, which when used jointly, could distinguish patients with distinct prognosis. We validated our findings using a third cohort of 48 patients ex vivo. We find that in all cohorts, a combined ULBP2/SEMA5A classification (SU-GIB) can stratify distinct prognostic sub-groups with hazard ratios that range from 2.4 to 4.5 (p≤0.01) when overall- or cancer-specific survival is used as an end-measure, independent of confounding prognostic parameters. In addition, our preliminary analyses suggest SU-GIB is comparable to Oncotype DX colon(®) in predicting recurrence in two different cohorts (HR: 1.5-2; p≤0.02). SU-GIB has potential as a companion diagnostic for several drugs including the PI3K/mTOR inhibitor BEZ235, which are suitable for the treatment of patients within the bad prognosis group. We show that tumors from patients with worse prognosis have low EGFR autophosphorylation rates, but high caspase 7 activity, and show upregulation of pro-inflammatory cytokines that relate to a relatively mesenchymal phenotype. Conclusions: We describe two novel genes that can be used to prognosticate colon cancer and suggest approaches by which such tumors can be treated. We also describe molecular characteristics of tumors stratified by the SU-GIB signature.
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Affiliation(s)
- Secil Demirkol
- Department of Molecular Biology and Genetics, Bilkent University, Cankaya, Ankara, Turkey
| | - Ismail Gomceli
- Department of Gastroenterological Surgery, Antalya Education and Research Hospital, Antalya, Turkey
| | - Murat Isbilen
- Department of Molecular Biology and Genetics, Bilkent University, Cankaya, Ankara, Turkey
| | | | - Mesut Tez
- Fifth Department of Surgery, Ankara Numune Training and Research Hospital, Ankara, Turkey
| | - Erdal Birol Bostanci
- Department of Gastroenterological Surgery, Yuksek Ihtisas Training and Research Hospital, Ankara, Turkey
| | - Nesrin Turhan
- Department of General and Oncological Surgery - Surgery C, The Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Musa Akoglu
- Department of Gastroenterological Surgery, Yuksek Ihtisas Training and Research Hospital, Ankara, Turkey
| | - Ezgi Ozyerli
- Department of Molecular Biology and Genetics, Bilkent University, Cankaya, Ankara, Turkey
| | - Sevi Durdu
- Department of Molecular Biology and Genetics, Bilkent University, Cankaya, Ankara, Turkey
| | - Ozlen Konu
- Department of Molecular Biology and Genetics, Bilkent University, Cankaya, Ankara, Turkey
| | - Aviram Nissan
- Department of General and Oncological Surgery - Surgery C, The Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Mithat Gonen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ali Osmay Gure
- Department of Molecular Biology and Genetics, Bilkent University, Cankaya, Ankara, Turkey
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8
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Senses KM, Ghasemi M, Akbar MW, Isbilen M, Fallacara AL, Frankenburg S, Schenone S, Lotem M, Botta M, Gure AO. Phenotype-based variation as a biomarker of sensitivity to molecularly targeted therapy in melanoma. Medchemcomm 2017; 8:88-95. [PMID: 28670440 PMCID: PMC5488266 DOI: 10.1039/c6md00466k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 10/11/2016] [Indexed: 12/13/2022]
Abstract
Transcriptomic phenotypes defined for melanoma have been reported to correlate with sensitivity to various drugs. In this study, we aimed to define a minimal signature that could be used to distinguish melanoma sub-types in vitro, and to determine suitable drugs by which these sub-types can be targeted. By using primary melanoma cell lines, as well as commercially available melanoma cell lines, we find that the evaluation of MLANA and INHBA expression is as capable as one based on a combined analysis performed with genes for stemness, EMT and invasion/proliferation, in identifying melanoma subtypes that differ in their sensitivity to molecularly targeted drugs. Using this approach, we find that 75% of melanoma cell lines can be treated with either the MEK inhibitor AZD6244 or the HSP90 inhibitor 17AAG.
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Affiliation(s)
- Kerem M. Senses
- Department of Molecular Biology and Genetics
, Bilkent University
,
06800 Ankara
, Turkey
.
| | - Mehdi Ghasemi
- Department of Molecular Biology and Genetics
, Bilkent University
,
06800 Ankara
, Turkey
.
| | - Muhammad W. Akbar
- Department of Molecular Biology and Genetics
, Bilkent University
,
06800 Ankara
, Turkey
.
| | - Murat Isbilen
- Department of Molecular Biology and Genetics
, Bilkent University
,
06800 Ankara
, Turkey
.
| | - Anna L. Fallacara
- Department of Biotechnology
, Chemistry and Pharmacy
, University of Siena
,
53100 Siena
, Italy
| | - Shoshana Frankenburg
- Sharett Institute of Oncology
, Hadassah Hebrew University Hospital
,
Ein Karem Campus
, 91120 Jerusalem
, Israel
| | - Silvia Schenone
- Department of Pharmacy
, University of Genoa
,
16132 Genoa
, Italy
| | - Michal Lotem
- Sharett Institute of Oncology
, Hadassah Hebrew University Hospital
,
Ein Karem Campus
, 91120 Jerusalem
, Israel
| | - Maurizio Botta
- Department of Biotechnology
, Chemistry and Pharmacy
, University of Siena
,
53100 Siena
, Italy
| | - Ali O. Gure
- Department of Molecular Biology and Genetics
, Bilkent University
,
06800 Ankara
, Turkey
.
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Akgun H, Metintas S, Ak G, Demirkol S, Aydın R, Isbilen M, Gure A, Metintas M. P3.03-039 Prognostic Biomarkers for Malignant Pleural Mesothelioma Treated with Chemotherapy. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2016.11.1938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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Senses KM, Gonen M, Barutcu AR, Kalaylioglu Z, Isbilen M, Konu O, Chen YT, Altorki NK, Gure AO. Cancer-testis gene expression is associated with the methylenetetrahydrofolate reductase 677 C>T polymorphism in non-small cell lung carcinoma. BMC Med Genet 2013; 14:97. [PMID: 24063603 PMCID: PMC3849821 DOI: 10.1186/1471-2350-14-97] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 09/20/2013] [Indexed: 11/13/2022]
Abstract
Background Tumor-specific, coordinate expression of cancer-testis (CT) genes, mapping to the X chromosome, is observed in more than 60% of non-small cell lung cancer (NSCLC) patients. Although CT gene expression has been unequivocally related to DNA demethylation of promoter regions, the underlying mechanism leading to loss of promoter methylation remains elusive. Polymorphisms of enzymes within the 1-carbon pathway have been shown to affect S-adenosyl methionine (SAM) production, which is the sole methyl donor in the cell. Allelic variants of several enzymes within this pathway have been associated with altered SAM levels either directly, or indirectly as reflected by altered levels of SAH and Homocysteine levels, and altered levels of DNA methylation. We, therefore, asked whether the five most commonly occurring polymorphisms in four of the enzymes in the 1-carbon pathway associated with CT gene expression status in patients with NSCLC. Methods Fifty patients among a cohort of 763 with NSCLC were selected based on CT gene expression status and typed for five polymorphisms in four genes known to affect SAM generation by allele specific q-PCR and RFLP. Results We identified a significant association between CT gene expression and the MTHFR 677 CC genotype, as well as the C allele of the SNP, in this cohort of patients. Multivariate analysis revealed that the genotype and allele strongly associate with CT gene expression, independent of potential confounders. Conclusions Although CT gene expression is associated with DNA demethylation, in NSCLC, our data suggests this is unlikely to be the result of decreased MTHFR function.
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Affiliation(s)
- Kerem M Senses
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey.
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