Background: The dysregulation of various pathways and cellular processes contributes to the carci... more Background: The dysregulation of various pathways and cellular processes contributes to the carcinogenic transition from low-grade gliomas to high-grade gliomas. The altered tumor microenvironment, altered epigenetic state, and high mutation heterogeneity are critical factors in glial tumors. The morphogen retinoic acid (RA) controls the homeostasis, regeneration, and development of the brain. RA receptor (RAR) gene methylation has been shown in different types of glial tumors. Aims and Objectives: This study assessed the RARß gene as a potential therapeutic target in gliomas. Materials and Methods: Using in silico methods, potential drugs targeting the RARß gene were compared based on temozolomide’s effectiveness in treating gliomas. Results and Conclusion: Computational techniques can be used to identify drug-mediated pathways. This in silico study holds promise for RARB and RARB-targeted treatment strategies in gliomas.
Genetic and epigenetic factors have an important role during the development of osteoporosis. Rec... more Genetic and epigenetic factors have an important role during the development of osteoporosis. Receptor activator of nuclear factor-κ B (NF-κB) (RANK)/receptor activator of NF-κB ligand (RANKL) pathway is important for the bone remodeling, and NFATC1 and FOS are the downtargets of this pathway. Here, we report methylation status of NFATC1 and FOS genes in post- and premenopausal women. In this study, 30 premenopausal and 35 postmenopausal women were included. Methylation sensitive-high resolution melting (MS-HRM) analysis was used for identification of NFATC1 and FOS genes methylation. The NFATC1 gene was methylated in 11 of the 35 postmenopausal women, and the FOS gene was methylated in six of the postmenopausal women (p >0.005). Here, we found statistically significant association between unmethylation of the NFATC1 gene and postmenopausal status. This result explains the epigenetic regulation of osteoclasts during the menopausal transition, and for the first time, our results c...
Background: Obesity is a multifactorial disorder that is an important predisposing factor for a n... more Background: Obesity is a multifactorial disorder that is an important predisposing factor for a number of disorders. Genetic and epigenetic variations play important roles during the development of obesity. Method: DNA methylation is the most studied as one of the epigenetic modifications and is directly related to gene expression. Here, the methylation status of FSHR, PTH and ESRRA genes were investigated in obese patients to discover novel associations between DNA methylation and obesity phenotype. A total of 69 patients with obesity and 76 patients without obesity were enrolled in this study. DNA methylation in FSHR, PTH and ESRRA genes was analyzed. Result: There is a statistically significant association between the methylation status of ESRRA and fasting glucose (P=0.04) and BMI and methylation of the PTH gene (P=0.036) in obese subjects. In non-obese subjects, a statistically significant association was detected between adiponectin, resistin levels and FSHR methylation status...
Objective: The circadian system acts at whole levels of a woman’s life as a cornerstone: from fol... more Objective: The circadian system acts at whole levels of a woman’s life as a cornerstone: from follicle generation to the arrangement of hormonal balance; and the process from embryo implantation to birth. Methods: We compared the promoter methylation status of the circadian genes, BMAL1 and CLOCK, between pre-menopausal and postmenopausal women to find an epigenetic explanation in women with menopause. In this perspective, 56 postmenopausal women and 48 premenopausal women were enrolled in this study. Results: Menopause and methylation status of the BMAL1 or CLOCK genes did not show any statistically significant correlations (p˃0.05). Moreover, the correlation of the methylation pattern of the BMAL1 and CLOCK genes with age could not be detected (p˃0.05). Conclusion: The methylation status of the BMAL1 and CLOCK genes in menopause was characterized for the first time in our study. Further studies should shed light on this subject. Keywords: Menopause, BMAL1, CLOCK, MS-HRM, methylation
Annals of Medical and Health Sciences Research, 2022
From follicle generation to hormone production, and from pregnancy to
birth, the circadian system... more From follicle generation to hormone production, and from pregnancy to birth, the circadian system plays an essential role at every level in a woman's life. A woman's menstrual cycle is based on a monthly rhythm and menopause is among the main factors affecting this rhythm. It is important to note that the onset of menopause is influenced by both epigenetic alterations and changes in circadian rhythm. In this article, we discuss the role of epigenetic alterations in regulating the circadian gene network as well as the consequences of deteriorating circadian rhythms in menopause. Here, we provide evidence of how these findings can change the age of menopause, whether it is by the deterioration of circadian rhythms or by observing the epigenetic alterations that are taking place.
Colorectal cancer (CRC) is the leading cause of cancer death worldwide. A crucial
process that in... more Colorectal cancer (CRC) is the leading cause of cancer death worldwide. A crucial process that initiates and progresses CRC is various epigenetic and genetic changes occurring in colon epithelial cells. Recently, huge progress has been made to understand cancer epigenetics, especially regarding DNA methylation changes, histone modifications, dysregulation of miRNAs and noncoding RNAs. In the “epigenome” of colon cancer, abnormal methylation of genes that cause gene alterations or expression of miRNA has been reported in nearly all CRC; these findings can be encountered in the average CRC methylome. Epigenetic changes, known as driving events, are assumed to play a dominant part in CRC. Furthermore, as epigenetic changes in CRC become properly understood, these changes are being established as clinical biomarkers for therapeutic and diagnostic purposes. Progression in this area indicates that epigenetic changes will often be utilized in the future to prevent and treat CRC.
Coronavirus disease 2019 (COVID-2019) started in Wuhan, China, in December 2019. Angiotensin-conv... more Coronavirus disease 2019 (COVID-2019) started in Wuhan, China, in December 2019. Angiotensin-converting enzyme 2 (ACE2) receptor was one of the most important genes related to the entrance of the virus to the host. Until now, several variations have been identified in ACE2 and related transmembrane protease serine 2. Epigenetic modifications not only play an important role during the maintenance of genome and cellular homoeostasis but also for the etiopathophysiology of the virus infection. Studies showed methylation of ACE2 was changed to depend on host and age of the host during the viral infection.In this study, we provided an epigenetics point of view to the coronavirus infection. We highlight the importance of epigenetic modifications during viral replication and infection and their interaction with COVID-19 susceptibility and host viral response.
BACKGROUND Advancement in genetic technology has led to the identification of an increasing numbe... more BACKGROUND Advancement in genetic technology has led to the identification of an increasing number of genes in epilepsy. This will provide a huge information in clinical practice and improve diagnosis and treatment of epilepsy. METHODS this was a single-center retrospective cohort study of 80 patients who underwent NGS testing with customize epilepsy panel. RESULTS In total 54 out of 80 patients (67, 5%), pathogenic / likely pathogenic and variants of uncertain significance variants were identified according to ACMG criteria. Pathogenic or likely pathogenic variants (n=35) were identified in 29 out of 80 individuals (36.25%). Variants of uncertain significance (VOUS) (n=34) have identified in 28 out of 80 patients (35%). Pathogenic, likely pathogenic, and variants of uncertain significance (VOUS) were most frequently identified in TSC2 (n = 11), SCN1A (n = 6) and TSC1 (n = 5) genes. Other common genes were KCNQ2 (n = 3), AMT (n = 3), CACNA1H (n = 3), CLCN2 (n = 3), MECP2 (n = 2), ASAH1 (n = 2) and SLC2A1 (n = 2). CONCLUSIONS NGS based testing panels contributes the diagnosis of epilepsy and may change the clinical management by preventing unnecessary and potentially harmful diagnostic procedures and management in patients. Thus, our results highlighted the benefit of genetic testing in children suffered with epilepsy. This article is protected by copyright. All rights reserved.
Background: The dysregulation of various pathways and cellular processes contributes to the carci... more Background: The dysregulation of various pathways and cellular processes contributes to the carcinogenic transition from low-grade gliomas to high-grade gliomas. The altered tumor microenvironment, altered epigenetic state, and high mutation heterogeneity are critical factors in glial tumors. The morphogen retinoic acid (RA) controls the homeostasis, regeneration, and development of the brain. RA receptor (RAR) gene methylation has been shown in different types of glial tumors. Aims and Objectives: This study assessed the RARß gene as a potential therapeutic target in gliomas. Materials and Methods: Using in silico methods, potential drugs targeting the RARß gene were compared based on temozolomide’s effectiveness in treating gliomas. Results and Conclusion: Computational techniques can be used to identify drug-mediated pathways. This in silico study holds promise for RARB and RARB-targeted treatment strategies in gliomas.
Genetic and epigenetic factors have an important role during the development of osteoporosis. Rec... more Genetic and epigenetic factors have an important role during the development of osteoporosis. Receptor activator of nuclear factor-κ B (NF-κB) (RANK)/receptor activator of NF-κB ligand (RANKL) pathway is important for the bone remodeling, and NFATC1 and FOS are the downtargets of this pathway. Here, we report methylation status of NFATC1 and FOS genes in post- and premenopausal women. In this study, 30 premenopausal and 35 postmenopausal women were included. Methylation sensitive-high resolution melting (MS-HRM) analysis was used for identification of NFATC1 and FOS genes methylation. The NFATC1 gene was methylated in 11 of the 35 postmenopausal women, and the FOS gene was methylated in six of the postmenopausal women (p >0.005). Here, we found statistically significant association between unmethylation of the NFATC1 gene and postmenopausal status. This result explains the epigenetic regulation of osteoclasts during the menopausal transition, and for the first time, our results c...
Background: Obesity is a multifactorial disorder that is an important predisposing factor for a n... more Background: Obesity is a multifactorial disorder that is an important predisposing factor for a number of disorders. Genetic and epigenetic variations play important roles during the development of obesity. Method: DNA methylation is the most studied as one of the epigenetic modifications and is directly related to gene expression. Here, the methylation status of FSHR, PTH and ESRRA genes were investigated in obese patients to discover novel associations between DNA methylation and obesity phenotype. A total of 69 patients with obesity and 76 patients without obesity were enrolled in this study. DNA methylation in FSHR, PTH and ESRRA genes was analyzed. Result: There is a statistically significant association between the methylation status of ESRRA and fasting glucose (P=0.04) and BMI and methylation of the PTH gene (P=0.036) in obese subjects. In non-obese subjects, a statistically significant association was detected between adiponectin, resistin levels and FSHR methylation status...
Objective: The circadian system acts at whole levels of a woman’s life as a cornerstone: from fol... more Objective: The circadian system acts at whole levels of a woman’s life as a cornerstone: from follicle generation to the arrangement of hormonal balance; and the process from embryo implantation to birth. Methods: We compared the promoter methylation status of the circadian genes, BMAL1 and CLOCK, between pre-menopausal and postmenopausal women to find an epigenetic explanation in women with menopause. In this perspective, 56 postmenopausal women and 48 premenopausal women were enrolled in this study. Results: Menopause and methylation status of the BMAL1 or CLOCK genes did not show any statistically significant correlations (p˃0.05). Moreover, the correlation of the methylation pattern of the BMAL1 and CLOCK genes with age could not be detected (p˃0.05). Conclusion: The methylation status of the BMAL1 and CLOCK genes in menopause was characterized for the first time in our study. Further studies should shed light on this subject. Keywords: Menopause, BMAL1, CLOCK, MS-HRM, methylation
Annals of Medical and Health Sciences Research, 2022
From follicle generation to hormone production, and from pregnancy to
birth, the circadian system... more From follicle generation to hormone production, and from pregnancy to birth, the circadian system plays an essential role at every level in a woman's life. A woman's menstrual cycle is based on a monthly rhythm and menopause is among the main factors affecting this rhythm. It is important to note that the onset of menopause is influenced by both epigenetic alterations and changes in circadian rhythm. In this article, we discuss the role of epigenetic alterations in regulating the circadian gene network as well as the consequences of deteriorating circadian rhythms in menopause. Here, we provide evidence of how these findings can change the age of menopause, whether it is by the deterioration of circadian rhythms or by observing the epigenetic alterations that are taking place.
Colorectal cancer (CRC) is the leading cause of cancer death worldwide. A crucial
process that in... more Colorectal cancer (CRC) is the leading cause of cancer death worldwide. A crucial process that initiates and progresses CRC is various epigenetic and genetic changes occurring in colon epithelial cells. Recently, huge progress has been made to understand cancer epigenetics, especially regarding DNA methylation changes, histone modifications, dysregulation of miRNAs and noncoding RNAs. In the “epigenome” of colon cancer, abnormal methylation of genes that cause gene alterations or expression of miRNA has been reported in nearly all CRC; these findings can be encountered in the average CRC methylome. Epigenetic changes, known as driving events, are assumed to play a dominant part in CRC. Furthermore, as epigenetic changes in CRC become properly understood, these changes are being established as clinical biomarkers for therapeutic and diagnostic purposes. Progression in this area indicates that epigenetic changes will often be utilized in the future to prevent and treat CRC.
Coronavirus disease 2019 (COVID-2019) started in Wuhan, China, in December 2019. Angiotensin-conv... more Coronavirus disease 2019 (COVID-2019) started in Wuhan, China, in December 2019. Angiotensin-converting enzyme 2 (ACE2) receptor was one of the most important genes related to the entrance of the virus to the host. Until now, several variations have been identified in ACE2 and related transmembrane protease serine 2. Epigenetic modifications not only play an important role during the maintenance of genome and cellular homoeostasis but also for the etiopathophysiology of the virus infection. Studies showed methylation of ACE2 was changed to depend on host and age of the host during the viral infection.In this study, we provided an epigenetics point of view to the coronavirus infection. We highlight the importance of epigenetic modifications during viral replication and infection and their interaction with COVID-19 susceptibility and host viral response.
BACKGROUND Advancement in genetic technology has led to the identification of an increasing numbe... more BACKGROUND Advancement in genetic technology has led to the identification of an increasing number of genes in epilepsy. This will provide a huge information in clinical practice and improve diagnosis and treatment of epilepsy. METHODS this was a single-center retrospective cohort study of 80 patients who underwent NGS testing with customize epilepsy panel. RESULTS In total 54 out of 80 patients (67, 5%), pathogenic / likely pathogenic and variants of uncertain significance variants were identified according to ACMG criteria. Pathogenic or likely pathogenic variants (n=35) were identified in 29 out of 80 individuals (36.25%). Variants of uncertain significance (VOUS) (n=34) have identified in 28 out of 80 patients (35%). Pathogenic, likely pathogenic, and variants of uncertain significance (VOUS) were most frequently identified in TSC2 (n = 11), SCN1A (n = 6) and TSC1 (n = 5) genes. Other common genes were KCNQ2 (n = 3), AMT (n = 3), CACNA1H (n = 3), CLCN2 (n = 3), MECP2 (n = 2), ASAH1 (n = 2) and SLC2A1 (n = 2). CONCLUSIONS NGS based testing panels contributes the diagnosis of epilepsy and may change the clinical management by preventing unnecessary and potentially harmful diagnostic procedures and management in patients. Thus, our results highlighted the benefit of genetic testing in children suffered with epilepsy. This article is protected by copyright. All rights reserved.
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Papers by Prof. Dr. Rasime Kalkan
balance; and the process from embryo implantation to birth.
Methods: We compared the promoter methylation status of the circadian genes, BMAL1 and CLOCK, between pre-menopausal and postmenopausal women to find an epigenetic explanation in women with menopause. In this perspective, 56 postmenopausal women and 48
premenopausal women were enrolled in this study.
Results: Menopause and methylation status of the BMAL1 or CLOCK genes did not show any statistically significant correlations (p˃0.05).
Moreover, the correlation of the methylation pattern of the BMAL1 and CLOCK genes with age could not be detected (p˃0.05).
Conclusion: The methylation status of the BMAL1 and CLOCK genes in menopause was characterized for the first time in our study. Further
studies should shed light on this subject.
Keywords: Menopause, BMAL1, CLOCK, MS-HRM, methylation
birth, the circadian system plays an essential role at every level in a woman's
life. A woman's menstrual cycle is based on a monthly rhythm and
menopause is among the main factors affecting this rhythm. It is important to
note that the onset of menopause is influenced by both epigenetic alterations
and changes in circadian rhythm. In this article, we discuss the role of
epigenetic alterations in regulating the circadian gene network as well as the
consequences of deteriorating circadian rhythms in menopause. Here, we
provide evidence of how these findings can change the age of menopause,
whether it is by the deterioration of circadian rhythms or by observing the
epigenetic alterations that are taking place.
process that initiates and progresses CRC is various epigenetic and genetic changes
occurring in colon epithelial cells. Recently, huge progress has been made to understand cancer epigenetics, especially regarding DNA methylation changes, histone
modifications, dysregulation of miRNAs and noncoding RNAs. In the “epigenome” of
colon cancer, abnormal methylation of genes that cause gene alterations or expression
of miRNA has been reported in nearly all CRC; these findings can be encountered in the
average CRC methylome. Epigenetic changes, known as driving events, are assumed to
play a dominant part in CRC. Furthermore, as epigenetic changes in CRC become
properly understood, these changes are being established as clinical biomarkers for
therapeutic and diagnostic purposes. Progression in this area indicates that epigenetic
changes will often be utilized in the future to prevent and treat CRC.
balance; and the process from embryo implantation to birth.
Methods: We compared the promoter methylation status of the circadian genes, BMAL1 and CLOCK, between pre-menopausal and postmenopausal women to find an epigenetic explanation in women with menopause. In this perspective, 56 postmenopausal women and 48
premenopausal women were enrolled in this study.
Results: Menopause and methylation status of the BMAL1 or CLOCK genes did not show any statistically significant correlations (p˃0.05).
Moreover, the correlation of the methylation pattern of the BMAL1 and CLOCK genes with age could not be detected (p˃0.05).
Conclusion: The methylation status of the BMAL1 and CLOCK genes in menopause was characterized for the first time in our study. Further
studies should shed light on this subject.
Keywords: Menopause, BMAL1, CLOCK, MS-HRM, methylation
birth, the circadian system plays an essential role at every level in a woman's
life. A woman's menstrual cycle is based on a monthly rhythm and
menopause is among the main factors affecting this rhythm. It is important to
note that the onset of menopause is influenced by both epigenetic alterations
and changes in circadian rhythm. In this article, we discuss the role of
epigenetic alterations in regulating the circadian gene network as well as the
consequences of deteriorating circadian rhythms in menopause. Here, we
provide evidence of how these findings can change the age of menopause,
whether it is by the deterioration of circadian rhythms or by observing the
epigenetic alterations that are taking place.
process that initiates and progresses CRC is various epigenetic and genetic changes
occurring in colon epithelial cells. Recently, huge progress has been made to understand cancer epigenetics, especially regarding DNA methylation changes, histone
modifications, dysregulation of miRNAs and noncoding RNAs. In the “epigenome” of
colon cancer, abnormal methylation of genes that cause gene alterations or expression
of miRNA has been reported in nearly all CRC; these findings can be encountered in the
average CRC methylome. Epigenetic changes, known as driving events, are assumed to
play a dominant part in CRC. Furthermore, as epigenetic changes in CRC become
properly understood, these changes are being established as clinical biomarkers for
therapeutic and diagnostic purposes. Progression in this area indicates that epigenetic
changes will often be utilized in the future to prevent and treat CRC.