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Karachanak-Yankova S, Serbezov D, Mihaylova M, Nikolova D, Balabanski L, Damyanova V, Antonova O, Staneva R, Ganev M, Spasova V, Rukova B, Nesheva D, Josifovska S, Stancheva M, Belejanska D, Petrova M, Mehrabian S, Traykov L, Hadjidekova S, Toncheva D. Detection of pathogenic variants in Alzheimer’s disease related genes in Bulgarian patients by pooled whole-exome sequencing. BIOTECHNOL BIOTEC EQ 2023. [DOI: 10.1080/13102818.2022.2155572] [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: 01/11/2023] Open
Affiliation(s)
- Sena Karachanak-Yankova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
- Department of Genetics, Faculty of Biology, Sofia University ‘St. Kliment Ohridski’, Sofia, Bulgaria
| | - Dimitar Serbezov
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Marta Mihaylova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Dragomira Nikolova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | | | - Vera Damyanova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Olga Antonova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Rada Staneva
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Mihail Ganev
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Victoria Spasova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Blaga Rukova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Desislava Nesheva
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Slavica Josifovska
- Department of Molecular Biology, Genetics and Microbiology, Faculty of Natural Sciences and Mathematics, ‘Ss. Cyril and Methodius’ University, Skopje, North Macedonia
| | - Mikaela Stancheva
- Department of Genetics, Faculty of Biology, Sofia University ‘St. Kliment Ohridski’, Sofia, Bulgaria
| | - Diana Belejanska
- Department of Neurology, University Hospital ‘Alexandrovska’, Sofia, Bulgaria
| | - Mariya Petrova
- Department of Neurology, University Hospital ‘Alexandrovska’, Sofia, Bulgaria
| | - Shima Mehrabian
- Department of Neurology, University Hospital ‘Alexandrovska’, Sofia, Bulgaria
| | - Latchezar Traykov
- Department of Neurology, University Hospital ‘Alexandrovska’, Sofia, Bulgaria
| | - Savina Hadjidekova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Draga Toncheva
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
- Bulgarian Academy of Sciences, Sofia, Bulgaria
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Doltchinkova V, Lozanova S, Rukova B, Nikolov R, Ivanova E, Roumenin C. Electrokinetic properties of healthy and β-thalassemia erythrocyte membranes under in vitro exposure to static magnetic field. Front Chem 2023; 11:1197210. [PMID: 37927566 PMCID: PMC10620691 DOI: 10.3389/fchem.2023.1197210] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 09/18/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction: The current understanding of the biological impacts of a static magnetic field (SMF) is restricted to the direct interactions of the magnetic field with biological membranes. The electrokinetic (zeta) potential is an electrochemical property of erythrocyte surfaces which was negatively charged in physiological media after SMF exposure (0.1‒2.0 T). Methods: The novel data about electrokinetic parameters of the erythrocytes is determined by microelectrophoresis after SMF-exposure in norm and heterozygous β-thalassemia. The methods of light scattering, lipid peroxidation, fluorescence microscopy are used. Results: The electrokinetic potential of erythrocytes in norm is increased after SMF intensities due to enhanced negatively exposed charges on the outer surface of the membrane accompanied by an increase in light scattering where changes in cell morphology are observed. Conversely, a decrease in the zeta potential of β-thalassemia erythrocytes upon SMF-treatment was determined because of the reduction in the surface electrical charge of the membranes, where a significant decrease in light scattering at 1.5 T and 2.0 T was recorded. Exposure to SMF (0.5-2.0 T) was associated with an increase in the malondialdehyde content in erythrocytes. Biophysical studies regarding the influence of SMF on the electrostatic free energy of cells shows an increase in negative values in healthy erythrocytes, which corresponds to the implementation of a spontaneous process. This is also the process in β-thalassemia cells after SMF exposure with lower negative values of free electrostatic energy than erythrocytes in norm. Discussion: The effect of static magnetic field (SMF 0.1-2.0 T) on the electrokinetic and morphological characteristics of erythrocytes in norm and β-thalassemia is determined and correlated with the increase/reduction in surface charge and shrinkage/swelling of the cells, respectively. Lipid peroxidation of healthy and β-thalassemia erythrocytes caused an enhancement of lipid peroxidation because of the higher concentrations of TBARS products in cellular suspension. SMF (0.1‒2.0 T) altered the spontaneous chemical processes with negative values of electrostatic free energy of erythrocytes in norm and β-thalassemia accompanied by a lower FITC-Concanavalin A binding affinity to membrane receptors (SMF 2.0 T). The electrokinetic properties of human erythrocytes in norm and β-thalassemia upon SMF treatment and their interrelationship with the structural-functional state of the membrane were reported. The presented work would have future fundamental applications in biomedicine.
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Affiliation(s)
- Virjinia Doltchinkova
- Department of Biophysics and Radiobiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Siya Lozanova
- Institute of Robotics “St. Ap. and Gospeller Matthew”, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Blaga Rukova
- Department of Medical Genetics, Medical University of Sofia, Sofia, Bulgaria
| | - Rumin Nikolov
- Faculty of Mechanical Engineering, Technical University, Sofia, Bulgaria
| | - Elitsa Ivanova
- Department of Biophysics and Radiobiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Chavdar Roumenin
- Institute of Robotics “St. Ap. and Gospeller Matthew”, Bulgarian Academy of Sciences, Sofia, Bulgaria
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Antonova O, Rukova B, Mladenov B, Rangelov S, Hammoudeh Z, Nesheva D, Staneva R, Spasova V, Grigorov E, Hadjidekova S, Slavov C, Toncheva D. Expression profiling of muscle invasive and non-invasive bladder tumors for biomarkers identification related to drug resistance, sensitivity and tumor progression. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1778528] [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: 10/24/2022] Open
Affiliation(s)
- Olga Antonova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Blaga Rukova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Boris Mladenov
- Department of Urology, UMBALSM “N. I. Pirogov,” Sofia, Bulgaria
| | - Simeon Rangelov
- Department of Urology, University Hospital “Tsaritsa Yoanna,” Sofia, Bulgaria
| | - Zora Hammoudeh
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Desislava Nesheva
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Rada Staneva
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Viktoria Spasova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Evgeni Grigorov
- Department of Pharmaceutical Sciences and Pharmaceutical Management, Faculty of Pharmacy, Medical University of Varna “Prof. Dr. Paraskev Stoyanov,” Varna, Bulgaria
| | - Savina Hadjidekova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Chavdar Slavov
- Department of Urology, University Hospital “Tsaritsa Yoanna,” Sofia, Bulgaria
| | - Draga Toncheva
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
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Staneva RG, Balabanski L, Dimova I, Rukova B, Hadjidekova S, Dimitrov P, Simeonov V, Ivanov S, Vagarova R, Malinov M, Cukuranovic R, Stefanovic V, Polenakovic M, Djonov V, Galabov A, Toncheva D. Genetic, Genomic and Epigenomic Studies of Balkan Endemic Nephropathy (Ben). ACTA ACUST UNITED AC 2016; 36:101-8. [PMID: 27442376 DOI: 10.1515/prilozi-2015-0058] [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: 11/15/2022]
Abstract
BEN is a primary, chronic tubulointerstitial nephritis characterized with chronic anemia, absence of edema, xantoderma, normal blood pressure and normal findings on the fundus oculi. The disease is distributed in restricted areas in Bulgaria, Romania, Croatia, Bosnia, Former Yugoslavia. Despite numerous studies on genetic and environmental factors and their possible involvement in BEN, its etiopathogenesis still remains elusive. Our recent study aim to elucidate the possible epigenetic component in BEN development. Whole genome DNA array methylation analysis was applied to compare the methylation profiles of male and female BEN patients from endemic regions in Bulgaria and Serbia and healthy controls. All three most prominent candidate genes with aberrations in the epigenetic profile discovered with this study are involved in the inflammatory/immune processes and oncogenesis. These data are in concordance with the reported pathological alterations in BEN. This research supports the role of epigenetic changes in BEN pathology. Exome sequencing of 22.000 genes with Illumina Nextera Exome Enrichment Kit revealed three mutant genes (CELA1, HSPG2, and KCNK5) in BEN patients which encode proteins involved in basement membrane/extracellular matrix and vascular tone, tightly connected to process of angiogenesis. We suggest that an abnormal process of angiogenesis plays a key role in the molecular pathogenesis of BEN.
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Stoynev N, Dimova I, Rukova B, Hadjidekova S, Nikolova D, Toncheva D, Tankova T. Gene expression in peripheral blood of patients with hypertension and patients with type 2 diabetes. J Cardiovasc Med (Hagerstown) 2015; 15:702-9. [PMID: 23337395 DOI: 10.2459/jcm.0b013e32835dbcc8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
AIM To evaluate the expression of atherosclerosis-associated genes in patients with hypertension and type 2 diabetes mellitus. MATERIAL AND METHODS Twenty-seven patients (14 men, 13 women), mean age 43.26 ± 11.69 years, were included in the study, which was divided into three groups: group 1 - patients with newly diagnosed hypertension and normal glucose tolerance (n = 9), group 2 - normotensive individuals with newly diagnosed type 2 diabetes (n = 9), and control group - normotensive individuals with normal glucose tolerance (n = 9). Gene expression analysis was performed with Human Atherosclerosis RT2 Profiler PCR Array. RESULTS In patients with hypertension, we found eight genes with increased expression - FABP3, FAS, FN1, IL1R2, LPL, SERPINE1, TGFB1, and VCAM1. Decreased expression was observed for two genes - SELPLG and SERPINEB2. In patients with type 2 diabetes we found seven up-regulated genes - APOE, BAX, MMP1, NFKB1, PDGFB, SPP1, and TGFB2, whereas no specifically down-regulated genes were observed. Three genes - KLF2, PDGFRB, and PPARD were found to be expressed only in groups 1 and 2. CONCLUSION Hypertension is associated with increased expression of FABP3, FAS, FN1, IL1R2, LPL, SERPINE1, TGFB1, and VCAM1 and decreased expression of SELPLG and SERPINEB2. The up-regulation of FAS, FN1, SERPINE1, TGFB1, and VCAM1 might be associated with an increased cardiovascular risk. Type 2 diabetes is associated with increased expression of APOE, BAX, MMP1, NFKB1, PDGFB, SPP1, and TGFB2. KLF2 and PPARD might be part of protective mechanisms that limit target organ damage in both disease conditions. Expression of PDGFRB might play an important role in the pathogenesis of both hypertension and type 2 diabetes.
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Affiliation(s)
- Nikolay Stoynev
- aDepartment of Diabetology, Clinical Center of Endocrinology bDepartment of Medical Genetics cDepartment of Physiology, Medical University Sofia, Bulgaria
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Al Zeyadi M, Dimova I, Ranchich V, Rukova B, Nesheva D, Hamude Z, Georgiev S, Petrov D, Toncheva D. Whole genome microarray analysis in non-small cell lung cancer. BIOTECHNOL BIOTEC EQ 2015; 29:111-118. [PMID: 26019623 PMCID: PMC4433918 DOI: 10.1080/13102818.2014.989179] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [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: 10/24/2014] [Accepted: 11/10/2014] [Indexed: 11/09/2022] Open
Abstract
Lung cancer is a serious health problem, since it is one of the leading causes for death worldwide. Molecular–cytogenetic studies could provide reliable data about genetic alterations which could be related to disease pathogenesis and be used for better prognosis and treatment strategies. We performed whole genome oligonucleotide microarray-based comparative genomic hybridization in 10 samples of non-small cell lung cancer. Trisomies were discovered for chromosomes 1, 13, 18 and 20. Chromosome arms 5p, 7p, 11q, 20q and Хq were affected by genetic gains, and 1p, 5q, 10q and 15q, by genetic losses. Microstructural (<5 Mbp) genomic aberrations were revealed: gains in regions 7p (containing the epidermal growth factor receptor gene) and 12p (containing KRAS) and losses in 3p26 and 4q34. Based on high amplitude of alterations and small overlapping regions, new potential oncogenes may be suggested: NBPF4 (1p13.3); ETV1, AGR3 and TSPAN13 (7p21.3-7p21.1); SOX5 and FGFR1OP2 (12p12.1-12p11.22); GPC6 (13q32.1). Significant genetic losses were assumed to contain potential tumour-suppressor genes: DPYD (1p21.3); CLDN22, CLDN24, ING2, CASP3, SORBS2 (4q34.2-q35.1); DEFB (8p23.1). Our results complement the picture of genomic characterization of non-small cell lung cancer.
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Affiliation(s)
- Mohammad Al Zeyadi
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia , Sofia , Bulgaria
| | - Ivanka Dimova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia , Sofia , Bulgaria
| | - Vladislav Ranchich
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia , Sofia , Bulgaria
| | - Blaga Rukova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia , Sofia , Bulgaria
| | - Desislava Nesheva
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia , Sofia , Bulgaria
| | - Zora Hamude
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia , Sofia , Bulgaria
| | - Sevdalin Georgiev
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia , Sofia , Bulgaria
| | - Danail Petrov
- Clinic of Thoracic Surgery, Medical University of Sofia , Sofia , Bulgaria
| | - Draga Toncheva
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia , Sofia , Bulgaria
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Rukova B, Staneva R, Hadjidekova S, Stamenov G, Milanova V, Toncheva D. Whole genome methylation analyses of schizophrenia patients before and after treatment. BIOTECHNOL BIOTEC EQ 2014; 28:518-524. [PMID: 26019538 PMCID: PMC4434134 DOI: 10.1080/13102818.2014.933501] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/05/2014] [Indexed: 12/12/2022] Open
Abstract
The aetiology of schizophrenia is still unknown but it involves both heritable and non-heritable factors. DNA methylation is an inheritable epigenetic modification that stably alters gene expression. It takes part in the regulation of neurodevelopment and may be a contributing factor to the pathogenesis of brain diseases. It was found that many of the antipsychotic drugs may lead to epigenetic modifications. We have performed 42 high-resolution genome-wide methylation array analyses to determine the methylation status of 27,627 CpG islands. Differentially methylated regions were studied with samples from 20 Bulgarian individuals divided in four groups according to their gender (12 males/8 females) and their treatment response (6 in complete/14 in incomplete remission). They were compared to two age and sex matched control pools (110 females in female pool/110 males in male pool) before and after treatment. We found significant differences in the methylation profiles between male schizophrenia patients with complete remission and control male pool before treatment (C16orf70, CST3, DDRGK1, FA2H, FLJ30058, MFSD2B, RFX4, UBE2J1, ZNF311) and male schizophrenia patients with complete remission and control male pool after treatment (AP1S3, C16orf59, KCNK15, LOC146336, MGC16384, XRN2) that potentially could be used as target genes for new therapeutic strategies as well as markers for good treatment response. Our data revealed major differences in methylation profiles between male schizophrenia patients in complete remission before and after treatment and healthy controls which supports the hypothesis that antipsychotic drugs may play a role in epigenetic modifications.
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Affiliation(s)
- Blaga Rukova
- Department of Medical Genetics, Medical University of Sofia , Sofia , Bulgaria
| | - Rada Staneva
- Department of Medical Genetics, Medical University of Sofia , Sofia , Bulgaria
| | - Savina Hadjidekova
- Department of Medical Genetics, Medical University of Sofia , Sofia , Bulgaria
| | | | - Vihra Milanova
- Department of Psychiatry, Medical University of Sofia , Sofia , Bulgaria
| | - Draga Toncheva
- Department of Medical Genetics, Medical University of Sofia , Sofia , Bulgaria
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Damyanova V, Dimova I, Savov A, Nesheva D, Hadjidekova S, Rukova B, Jivkova R, Nikolova V, Vatev I, Toncheva D. Comprehensive Genomic Study in Patients with Idiopathic Azoospermia and Oligoasthenoteratozoospermia. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2012.0092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Avdjieva-Tzavella D, Hadjidekova S, Rukova B, Nesheva D, Litvinenko I, Hristova-Naydenova D, Simeonov E, Tincheva R, Toncheva D. Detection of Genomic Imbalances by Array-Based Comparative Genomic Hybridization in Bulgarian Patients with Autism Spectrum Disorders. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2012.0097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Balabanski L, Antov G, Dimova I, Ivanov S, Nacheva M, Gavrilov I, Nesheva D, Rukova B, Hadjidekova S, Malinov M, Toncheva D. Next-generation sequencing of BRCA1 and BRCA2 in breast cancer patients and control subjects. Mol Clin Oncol 2014; 2:435-439. [PMID: 24772314 DOI: 10.3892/mco.2014.251] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [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: 05/29/2013] [Accepted: 11/22/2013] [Indexed: 01/09/2023] Open
Abstract
Breast cancer is currently the most common type of cancer in females. The majority of the hereditary forms of breast cancer are caused by mutations in the BRCA1 and BRCA2 genes, whose main function is the DNA repair of double-strand breaks. Genetic testing of females with a family history of breast cancer is recommended to determine their hereditary predisposition for this type of cancer. The variants with no clear clinical significance may represent a diagnostic challenge when performing targeted resequencing. In this study, DNA samples were obtained from 24 breast cancer patients (mean age, 35±10 years) with a positive family history and from 71 age-matched healthy controls. Informed consent was obtained from all the subjects. Sequence-targeted BRCA1 and BRCA2 libraries were prepared using the TruSeq Custom Amplicon method and sequenced on the Illumina MiSeq system. A wide range of variants were identified in the BRCA1 and BRCA2 genes. Two pathological/presumably pathological variants were detected in the breast cancer patient group: a mutation in BRCA2 at the chromosomal (chr) position chr13:32890665, which affected the first position of the 5' splice region following exon 2; and a mutation in BRCA1 at chr17:41219635, causing an in-frame triple nucleotide deletion of valine 1688 (8.3%). In the patient and control groups, 7 likely polymorphic variants and 13 common variants were detected in the BRCA1 and BRCA2 genes. To the best of our knowledge, this study was the first to identify 3 common polymorphisms in BRCA2, characteristic solely of the Bulgarian population, including chr13:32973737, T/-, a single-nucleotide polymorphism (SNP) within the 3'-UTR of exon 27; chr13:32973280, A/-, a mononucleotide deletion within the 5'-UTR of exon 27; and chr13:32973924, T/-, a mononucleotide deletion downstream of the gene sequence. To the best of our knowledge, this study was the first to apply next-generation sequencing of the BRCA1 and BRCA2 genes in a Bulgarian population, prompting further investigation for local founder mutations and variants characteristic for this particular region.
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Affiliation(s)
| | - Georgi Antov
- Bulgarian Academy of Sciences, Institute of Genetics 'Academician Doncho Kostov', 1113 Sofia
| | - Ivanka Dimova
- Department of Medical Genetics, Medical University of Sofia, 1431 Sofia
| | | | - Maria Nacheva
- Specialized Hospital for Active Treatment in Oncology, 1756 Sofia, Bulgaria
| | - Ivan Gavrilov
- Specialized Hospital for Active Treatment in Oncology, 1756 Sofia, Bulgaria
| | - Desislava Nesheva
- Department of Medical Genetics, Medical University of Sofia, 1431 Sofia
| | - Blaga Rukova
- Department of Medical Genetics, Medical University of Sofia, 1431 Sofia
| | | | | | - Draga Toncheva
- Genomic Laboratory, Malinov Hospital, 1680 Sofia; ; Department of Medical Genetics, Medical University of Sofia, 1431 Sofia
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Staneva R, Rukova B, Hadjidekova S, Nesheva D, Antonova O, Dimitrov P, Simeonov V, Stamenov G, Cukuranovic R, Cukuranovic J, Stefanovic V, Polenakovic M, Dimova I, Hlushchuk R, Djonov V, Galabov A, Toncheva D. Whole genome methylation array analysis reveals new aspects in Balkan endemic nephropathy etiology. BMC Nephrol 2013; 14:225. [PMID: 24131581 PMCID: PMC3852817 DOI: 10.1186/1471-2369-14-225] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [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] [Received: 04/15/2013] [Accepted: 10/11/2013] [Indexed: 11/17/2022] Open
Abstract
Background Balkan endemic nephropathy (BEN) represents a chronic progressive interstitial nephritis in striking correlation with uroepithelial tumours of the upper urinary tract. The disease has endemic distribution in the Danube river regions in several Balkan countries. DNA methylation is a primary epigenetic modification that is involved in major processes such as cancer, genomic imprinting, gene silencing, etc. The significance of CpG island methylation status in normal development, cell differentiation and gene expression is widely recognized, although still stays poorly understood. Methods We performed whole genome DNA methylation array analysis on DNA pool samples from peripheral blood from 159 affected individuals and 170 healthy individuals. This technique allowed us to determine the methylation status of 27 627 CpG islands throughout the whole genome in healthy controls and BEN patients. Thus we obtained the methylation profile of BEN patients from Bulgarian and Serbian endemic regions. Results Using specifically developed software we compared the methylation profiles of BEN patients and corresponding controls and revealed the differently methylated regions. We then compared the DMRs between all patient-control pairs to determine common changes in the epigenetic profiles. SEC61G, IL17RA, HDAC11 proved to be differently methylated throughout all patient-control pairs. The CpG islands of all 3 genes were hypomethylated compared to controls. This suggests that dysregulation of these genes involved in immunological response could be a common mechanism in BEN pathogenesis in both endemic regions and in both genders. Conclusion Our data propose a new hypothesis that immunologic dysregulation has a place in BEN etiopathogenesis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Draga Toncheva
- Department of Medical Genetics, Medical University of Sofia, 1421 2Zdrave str, Sofia, Bulgaria.
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Stamenov G, Hadjidekova S, Rukova B, Persenska S. P-3 Application of array-based comparative genomic hybridization for whole genome screening of first-trimester spontaneous abortions. Reprod Biomed Online 2013. [DOI: 10.1016/s1472-6483(13)60066-8] [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: 11/16/2022]
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Damyanova V, Dimitrova-Dikanarova D, Hadjidekova S, Savov A, Nesheva D, Rukova B, Vatev I, Toncheva D. [Genomic study in patients with idiopathic azoospermia and oligoasthenoteratozoospermia]. Akush Ginekol (Sofiia) 2013; 52:27-34. [PMID: 24501866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Genome disbalances are related to the different types of infertility and they play a role in the treatment of human infertility. Comparative genome hybridization (CGH) combined with microchips is a modern high resolution technique for all human chromosomes investigations. We analysed the genome disbalances in 16 blood samples of men with an idiopathic oligoastenozoospermia or azoospermia using CGH and microchips for the whole human genome. Our data showed a few affected loci, including: 3q26.32 deletion accompanied by 14q11.1 deletion, 9q12 deletion, 5q35.1 amplification, 7p22.3 amplification and 17q12-17q21.2 amplification. In this study we have match the deletions: in two patients in the same area in the 8 chromosome, as well as in 5 patients in 14 chromosome. The deleted region contains 25 genes. Two of them (SPAG11B and SPAG11A) are associated with stages of spermatogenesis and in particular formation and maturation of the spermatozoa. These genes play a role during spermatogenesis and fertilization. Loss. chr.14q11.2 (EDDM3A and EDDM3B) affected the proteins that are synthesized and secreted by epididymal epithelial cells that has been found up-regulated in epididimis of nonobstructive azoospermic men. Our results displayed the significance of CGH and microchip analysis as a promising area of research with serious clinical application for resolving the problems of the male infertility and still have an important annex for selecting the most appropriate methods for the treatment in these patients as a perspective scientific field of investigations with a clinical appliance.
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Hadjidekova S, Rukova B, Avdjieva-Tzavella D, Nesheva D, Tincheva R, Toncheva D. Comparison of Two Microarray CGH Platforms for Genome-Wide Copy Number Profilings: Oligo-Based Arrays Versus Bacterial Artificial Chromosome Arrays. BIOTECHNOL BIOTEC EQ 2011. [DOI: 10.5504/bbeq.2011.0064] [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: 11/27/2022] Open
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Cherneva R, Georgiev O, Dimova I, Rukova B, Petrov D, Toncheva D. EGFR and hTERT Expression as a Diagnostic Approach for Non-small Cell Lung Cancer in High Risk Groups. Biomark Cancer 2010; 2:57-63. [PMID: 24179385 PMCID: PMC3783287 DOI: 10.4137/bic.s3383] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Objective: The early detection of NSCLC is of importance because it provides chances for better outcomes. The aim of the study was to explore the clinical utility of EGFR and hTERT mRNA expression as markers for diagnosis of NSCLC. Methods: EGFR and hTERT mRNA were quantified by quantative reverse transcription real time polymerase chain reaction in plasma of 45 non-small cell lung cancer (NSCLC) and 40 chronic obstructive pulmonary disease (COPD) patients, selected by certain spirometric characteristics that made them at high risk of developing lung cancer in future. Results: The gene expression level of each gene was calculated and given as a relative quantity—RQ. EGFR gene expression was found in all lung cancer patients. The mean level of expression was RQ = 29.39. hTERT mRNA could be detected in 88% of patients. The mean expression ratio in them was RQ = 17.31. Only 50% of the high risk patients turned to be positive for EGFR. The level of their expression was RQ = 2.09. The plasma levels of hTERT could be detected in 17 (42.5%) patients of the high risk COPD group. Their mean level of expression was RQ = 1.02. A statistically significant difference in EGFR and hTERT mRNA expression could be observed between the two groups of patients—p = 0.0001. Conclusion: EGFR and hTERT mRNA are potential markers for lung cancer diagnosis, whose clinical importance should be replicated in a larger cohort of patients.
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