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Çırak Balta M, Erdoğdu İH, Oktay E, Çulhac N. Comparison of molecular analysis results determined by next-generation sequencing to immunohistochemical indicators and clinicopathological parameters in prostate adenocarcinomas. INDIAN J PATHOL MICR 2024:00004270-990000000-00130. [PMID: 38427749 DOI: 10.4103/ijpm.ijpm_361_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 07/21/2023] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND Prostate cancer is a common cancer in males, frequently leading to mortality. Multiple genetic factors play roles in prostate cancer pathogenesis. Demonstration of pathological pathways and customised treatment options have been possible with next-generation sequencing. AIM In this study, we aimed to evaluate the relationships of the changes in the prostate cancer pathways genes with the pathological, immunohistochemical and the clinical parameters. STUDY DESIGN Retrospective cross-sectional study. Materials and Methods: Among the prostate needle biopsy materials investigated in Adnan Menderes University Faculty of Medicine, Department of Pathology, thirty-one cases, who had been analysed using the next-generation sequencing system, were included in this study. RESULTS As a result of statistical analysis, a significant relationship was found between the pathogenic mutation detected in androgen receptor and Breast Cancer Gene 2 genes and tumour volume. In all cases with a pathogenic mutation in the androgen receptor gene, a pathogenic mutation in the Protein Tyrosine Phosphatase and Tensin Homolog gene was also observed and a significant relationship was found between them. Castration resistance was observed in cases with high tumour volume, and a statistically significant difference was found. A statistically significant relationship was found between tumour volume and Ki-67 expression. In addition, a significant relationship was observed between the castration resistance and Ki-67, c-erbB2 expressions. A statistically significant relationship was found between Ki-67 and c-erbB2. CONCLUSION Regarding prognosis prediction and treatment, identifying the molecular changes in genes playing roles in prostate cancer with next-generation sequencing is very important.
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Affiliation(s)
| | | | - Esin Oktay
- Department of Oncology, Aydın Adnan Menderes University, Aydın, Turkey
| | - Nil Çulhac
- Department of Pathology, Aydın Adnan Menderes University, Aydın, Turkey
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Erdoğdu İH, Örenay-Boyacıoğlu S, Boyacıoğlu O, Kahraman-Çetin N, Kacar-Döger F, Yavaşoğlu İ, Bolaman AZ. Evaluation of New Generation Sequencing (NGS)-Based Somatic Gene Variations and Real-Time Polymerase Chain Reaction (PCR)-Based Gene Fusions in Elderly and Young Acute Leukemia Patients: A Retrospective View. J Pers Med 2024; 14:140. [PMID: 38392574 PMCID: PMC10890296 DOI: 10.3390/jpm14020140] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/15/2024] [Accepted: 01/24/2024] [Indexed: 02/24/2024] Open
Abstract
Malignant diseases occurring in elderly patients follow a different course from younger patients and show different genetic structures. Therefore, in this retrospective study, the somatic gene variant profile and fusion gene profiles of elderly and young acute leukemia patients were determined to draw attention to the existing genetic difference, and the results were compared. In this study, the records of 204 acute leukemia patients aged 18+ who were referred to the Molecular Pathology Laboratory from the Hematology Clinic between 2018 and 2022 were reviewed retrospectively. Fusion gene detection in patients was performed with the HemaVision®-28Q Panel. The NGS Myeloid Neoplasms Panel was conducted using the MiniSEQ NGS platform according to the manufacturer's protocol. When all cases are evaluated together, the most frequently diagnosed acute leukemia is acute myeloid leukemia (85.8%). Both groups had a similar fusion gene profile; however, the fusion burden was higher in the elderly group. When the groups were evaluated in terms of somatic gene variations, there were differences between the groups, and the variation load was higher in the elderly group. Considering the different somatic gene variation profiles, it is understood that the genetic structure of tumor cells is different in elderly patients compared to young cases.
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Affiliation(s)
- İbrahim Halil Erdoğdu
- Department of Molecular Pathology, Faculty of Medicine, Aydin Adnan Menderes University, Aydin 09010, Türkiye
| | - Seda Örenay-Boyacıoğlu
- Department of Medical Genetics, Faculty of Medicine, Aydin Adnan Menderes University, Aydin 09010, Türkiye
| | - Olcay Boyacıoğlu
- Faculty of Engineering, Aydin Adnan Menderes University, Aydin 09010, Türkiye
| | - Nesibe Kahraman-Çetin
- Department of Molecular Pathology, Faculty of Medicine, Aydin Adnan Menderes University, Aydin 09010, Türkiye
| | - Füruzan Kacar-Döger
- Department of Molecular Pathology, Faculty of Medicine, Aydin Adnan Menderes University, Aydin 09010, Türkiye
| | - İrfan Yavaşoğlu
- Department of Hematology, Faculty of Medicine, Aydin Adnan Menderes University, Aydin 09010, Türkiye
| | - Ali Zahit Bolaman
- Department of Hematology, Faculty of Medicine, Aydin Adnan Menderes University, Aydin 09010, Türkiye
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Osman S, Kahraman Çetin N, Erdoğdu İH, Meteoğlu İ. Mutation Profile via Next-Generation Sequencing in Patients with Colorectal Adenocarcinoma and Its Clinicopathological Correlation. Turk J Gastroenterol 2023; 34:1124-1133. [PMID: 37737217 PMCID: PMC10724784 DOI: 10.5152/tjg.2023.22682] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 01/29/2023] [Indexed: 09/23/2023]
Abstract
BACKGROUND/AIMS Recent studies that reveal the molecular profiles of colorectal carcinomas have demonstrated tumor heterogeneity. Characterization of colorectal carcinoma-specific genomic alterations is essential for developing more successful and targeted treat- ment protocols. Moreover, it is vital in elucidating the pathogenesis and mechanisms of resistance against treatment and predicting prognosis. MATERIALS AND METHODS The study included 73 cases diagnosed with colorectal carcinomas and subjected to molecular analysis by the next-generation sequencing. The association between the clinicopathologic parameters and pathogenic mutations detected in 32 genes was evaluated. RESULTS Pathogenic mutations were determined in a total of 24 genes. The Cell Division Cycle 27 (CDC27), Kirsten rat sarcoma viral proto-oncogene (KRAS), serine/threonine protein kinase B-raf (BRAF), phosphatase and tensin homolog, breast cancer 2 (BRCA2), and phosphotidylinositol-4,5-biphosphate 3-kinase (PIK3CA) mutations were determined at higher rates, with the adenomatous polypo- sis coli mutation determined at a lower rate than in the literature. There were significant positive correlations between CDC27 and phosphatase and tensin homolog (PTEN), PTEN and BRCA2, and PTEN and adenomatous polyposis coli (APC) concomitant muta- tions, whereas negative correlations were present between BRAF and KRAS. Statistically significant relationships were present between KRAS exon 2 and mucinous morphology, PIK3CA and absence of perineural invasion, BRAF and tumor differentiation/localization, MutS homolog 3 (MSH3) and tumor diameter, and BRCA2 and absence of lymph node metastasis. CONCLUSION It is necessary to have a comprehensive database of genomic alterations of colorectal carcinomas to interpret mutations more accurately clinically. There are no studies on the frequency of mutations in colorectal carcinomas in the Turkish population; thus, follow-up and treatment protocols are organized following the European and American databases and guidelines. A comprehensive study of the colorectal carcinoma patients' mutation profile in the Turkish patient cohort by the next-generation sequencing method will help to provide significant therapeutic, prognostic, and predictive data and design more successful treatment and follow-up strategies.
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Affiliation(s)
- Sibel Osman
- Department of Pathology, Aydın Adnan Menderes University Faculty of Medicine, Aydın, Turkey
| | - Nesibe Kahraman Çetin
- Department of Pathology, Aydın Adnan Menderes University Faculty of Medicine, Aydın, Turkey
| | - İbrahim Halil Erdoğdu
- Department of Pathology, Aydın Adnan Menderes University Faculty of Medicine, Aydın, Turkey
| | - İbrahim Meteoğlu
- Department of Pathology, Aydın Adnan Menderes University Faculty of Medicine, Aydın, Turkey
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Kaçar Döger F, Erdoğdu İH, Çırak Balta M, Bolaman AZ, Yavaşoğlu İ. Molecular Response Assessment in Patients with Chronic Myeloid Leukemia; Clinicopathological Retrospective Research. meandros 2022. [DOI: 10.4274/meandros.galenos.2022.63497] [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: 12/30/2022]
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Özçalımlı A, Erdoğdu İH, Turgutkaya A, Yavaşoğlu İ, Döger FK, Bolaman AZ. The evaluation of gene mutation profiles by next-generation sequencing in diffuse large B-cell lymphoma. Int J Lab Hematol 2022; 45:310-316. [PMID: 36576110 DOI: 10.1111/ijlh.14012] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/13/2022] [Indexed: 12/29/2022]
Abstract
OBJECTIVE Diffuse large B cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma. Although it is a clinically and biologically heterogeneous disease, it is usually treated with R-CHOP chemotherapy. Here, we aimed to investigate gene expression frequency with next-generation sequencing (NGS) and the relation of gene mutations with remission and relapse status in patients with DLBCLs. MATERIALS AND METHODS We investigated gene mutation profiles by NGS in patients with DLBCL-NOS and analyzed the correlation between gene mutations and response and relapse rates and other clinical indices. RESULTS Twenty-eight of forty patients were evaluated. The most commonly mutated genes were ANKRD, BRCA1, BRCA2, EZH2, KMTC2, MYC, MYD88, NF1, NOTCH1, PMS2, PTEN, and WRN. The relapse rate was found higher in DLBCL patients with ANKRD26, BRCA2, MYD88, and NOTCH1 mutations. Also, remission duration was found shorter in patients with ANKRD26, BRCA2, and MYD88 mutations. CONCLUSIONS Our study demonstrates that the presence of some genetic mutations is effective on prognosis in patients with DLBCL. NGS-based evaluation of DLBCL treatment can be used in the future.
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Affiliation(s)
- Azime Özçalımlı
- Internal Medicine Department, Adnan Menderes University, Aydın, Turkey
| | | | | | - İrfan Yavaşoğlu
- Hematology Department, Adnan Menderes University, Aydın, Turkey
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Kahraman Çetin N, Erdoğdu İH, Bozkurt E, Meteoğlu İ. Evaluation of the Mutation Profile via Next-Generation Sequencing in a Turkish Population With Non-small Cell Lung Cancer. Balkan Med J 2021; 38:382-391. [PMID: 34860166 PMCID: PMC8880901 DOI: 10.5152/balkanmedj.2021.21049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background Lung cancer is the most common cancer type worldwide, with non-small cell lung cancer being the most frequently studied. Identifying of cancer-related genes in non-small cell lung cancer is crucial for developing individualized treatment, particularly as mutation profiles can vary by country and ethnicity. Aims To identify comprehensive mutation profiles in a cohort of Turkish patients with non-small cell lung cancer using the next-generation sequencing. Study Design Retrospective cross-sectional study. Methods In total, 72 cancer-related genes and 4149 variants were recorded in the non-small cell lung cancer panel, and their relationship with clinical and histopathological features was investigated through next-generation sequencing. Results Among 507 patients, 420 (82.8%) were males and 87 (17.2%) were females. Percentages of phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (11%), B-Raf proto-oncogene, serine/threonine kinase (8%), and neurofibromatosis type 1 (6%) mutations were higher than those reported in the literature. Males had a higher rate of Kirsten rat sarcoma 2 viral oncogene homolog mutations (P = .102), whereas epidermal growth factor receptor mutations were statistically more common in females (P = .001). Multiple variants of strong significance were identified in 6.3% patients diagnosed with adenocarcinoma, most of whom were smokers. Kirsten rat sarcoma 2 viral oncogene homolog and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha mutations were most commonly observed. Conclusion This study shows that Turkish patients have higher rates of PIK3CA, BRAF and NF1 mutations compared to the literature. Studies to determine the molecular profile specific to Turkish people will guide clinicians in treatment and contribute significantly to determining priorities in diagnosis.
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Affiliation(s)
- Nesibe Kahraman Çetin
- Department of Pathology, Aydın Adnan Menderes University School of Medicine, Aydın, Turkey
| | - İbrahim Halil Erdoğdu
- Department of Pathology, Aydın Adnan Menderes University School of Medicine, Aydın, Turkey
| | - Emin Bozkurt
- Department of Veterinary, Eldivan Vocational School of Health Services, Çankırı Karatekin University, Çankırı, Turkey
| | - İbrahim Meteoğlu
- Department of Pathology, Aydın Adnan Menderes University School of Medicine, Aydın, Turkey
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Bilak Ş, Çevik MÖ, Erdoğdu İH, Bağış H. Expression of Vitamin D Receptor and Vitamin D Receptor Gene Polymorphisms (BsmI, FokI, and TaqI) in Patients with Pterygium. Arq Bras Oftalmol 2021; 84:241-248. [PMID: 33567021 DOI: 10.5935/0004-2749.20210032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 04/02/2020] [Indexed: 11/20/2022] Open
Abstract
PURPOSE This study aimed to determine the role of vitamin D receptor in the pathogenesis of pterygium. The vitamin D receptor eexpression levels in pterygium tissue, blood vitamin D levels, and frequency of selected vitamin D receptor gene polymorphisms (BsmI, FokI, and TaqI) were compared between patients with pterygium and healthy participants. METHODS The study included patients with pterygiumeee (n=50) and healthy volunteers (n=50). The serum vitamin D levels were measured for both groups. Immunohistochemical staining for vitamin D receptor ewas performed on sections obtained from the pterygium and adjacent healthy conjunctival tissues of the same individuals. The genomic existence of vitamin D receptor epolymorphisms (BsmI, FokI, and TaqI) were analyzed in DNA obtained from venous blood of participants using polymerase chain reaction and restriction fragment length polymorphism methods. RESULTS There was no difference found between the serum vitamin D levels of patients with pterygium and healthy controls. However, tissue expression of vitamin D receptor was higher in the pterygium endothelial cells of micro-vessels (p=0.002), subepithelial stromal (p=0.04), and intravascular inflammatory cells (p=0.0001), in comparison with the adjacent healthy conjunctival tissue. Moreover, while the BBtt haplotype was 2-fold higher, the bbTt haplotype was 2.5-fold lower, and the BbTT haplotype was 2.25-fold lower in the control group than in the pterygium group (p<0.001). CONCLUSIONS Vitamin D serum levels did not differ between the healthy and pterygium groups. Vitamin D receptor expression was increased in the pterygium tissue versus the adjacent healthy tissue. However, vitamin D receptor polymorphism analysis in patients with pterygium did not reveal any significant difference in BsmI, FokI, or TaqI polymorphisms in comparison with the healthy volunteers.
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Affiliation(s)
- Şemsettin Bilak
- Department of Ophthalmology, School of Medicine, Adıyaman University, Adıyaman, Turkey
| | - Muhammer Özgür Çevik
- Department of Medical Genetics, School of Medicine, Adıyaman University, Adıyaman, Turkey
| | - İbrahim Halil Erdoğdu
- Department of Pathology, School of Medicine, Adnan Menderes University, Aydın, Turkey
| | - Haydar Bağış
- Department of Medical Genetics, School of Medicine, Adıyaman University, Adıyaman, Turkey
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Abstract
Biobanks are units where high quality and long-term protection of biomaterials is maintained. This system, in which biological materials and data are systematically recorded and stored, is a unique resource for the study of the pathophysiology of disease, the development of diagnostic biomarkers, and working with human tissues for the potential discovery of targeted therapeutic agents. At this point, the pathology unit plays a unifying and complementary role between the clinical and core disciplines and offers optimal management of the patients' biomaterials for diagnostic and research projects. The aim of this article is to present general information with regard to a biobank constructed for the storage of tumor tissue and blood biospecimens. Ethical issues (informed consent, protection of confidentiality and privacy, and secondary use of biospecimens) and the information technology system (collection, systematic recording, backup and protection of clinical information) are important issues in biobanking. The selection of freezers to be used in storage (mechanical freezers, liquid-vapor nitrogen tanks), and if mechanical freezers are preferred the establishment of the relevant infrastructure and support team (such as additional power units for protection from power outages), the preservation of materials by aliquoting in different freezers, ensuring financing so as to afford the cost of the infrastructure, and implementation of all these dynamics while adhering to international guidelines are of the utmost importance.
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Affiliation(s)
- Canan Kelten Talu
- Department of Molecular Pathology, Graduate School of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Muhammed Hasan Toper
- Department of Molecular Pathology, Graduate School of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - Yasemin Şahin
- Department of Molecular Pathology, Graduate School of Health Sciences, Dokuz Eylul University, Izmir, Turkey
| | - İbrahim Halil Erdoğdu
- Department of Molecular Pathology, Graduate School of Health Sciences, Dokuz Eylul University, Izmir, Turkey
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