Decrease of 5-hydroxymethylcytosine in primary cutaneous CD4+ small/medium sized pleomorphic T-cell lymphoproliferative disorder

Abstract Background: Primary cutaneous CD4+ small/medium-sized pleomorphic T-Cell lymphoproliferative disorder (PC-SMTLD) has been considered as a controversial dermatological disease that has been included in cutaneous T-cell lymphoma group, presenting most commonly as a solitary nodule and/or plaque with a specific and characteristic head and neck predilection. Due to the considerable overlap between PC-SMTLD and pseudolymphoma (PL), the differential diagnosis is often challenging. Methylation of DNA at position 5 of cytosine, and the subsequent reduction in intracellular 5-hydroxymethylcytosine (5-hmC) levels, is a key epigenetic event in several cancers, including systemic lymphomas. However, it has rarely been studied in cutaneous lymphomas. Objectives: The authors aimed to explore the role of differential 5-hmC immunostaining as a useful marker to distinguish PC-SMTLD from PL. Methods: Retrospective case series study with immunohistochemical and immunofluorescence analysis of 5-hmC was performed in PL and PC-SMTLD. Results: Significant decrease of 5-hmC nuclear staining was observed in PC-SMTLD when compared with PL (p<0.0001). By semi-quantitative grade integration, there were statistical differences in the final 5-hmC scores in the two study groups. The IF co-staining of 5-hmC with CD4 revealed a decrease of 5-hmC in CD4+ lymphocytes of PC-SMTLD. Study limitations: The small clinical sample size of the study. Conclusions: The immunorreactivity of 5-hmC in CD4+ lymphocytes was highly suggestive of a benign process as PL. Furthermore, the decrease of 5-hmC nuclear staining in PC-SMTLD indicated its lymphoproliferative status and helped to make the differential diagnosis with PL. © 2023 Sociedade Brasileira de Dermatologia. Published by Elsevier España, S.L.U. This is an open access article under the CC BY license (https://creativecommons.org/licenses/by/4.0/).

Application of vascular photobiomodulation therapy in individuals with low back pain and its relationship with global methylation / Aplicação da terapia por fotobiomodulação vascular em indivíduos com lombalgia e sua relação com a metilação global

ABSTRACT BACKGROUND AND OBJECTIVES: Low back pain is among the most disabling conditions worldwide, and among the epigenetic factors, methylation in CpG islands of gene promoter regions can modulate gene expression, potentially correlating with the development of the disease and providing insights into the choice of treatment. The objective of this study was to assess the efficacy of therapy using modified ILIB related to DNA methylation processes in low back pain. Secondary objectives of this study included investigating pain intensity, gender, sociodemographic data, and physical-functional profile. METHODS: This prospective study was conducted in a municipality in the southern region of Brazil. The sample consisted of 30 participants of both genders, with an average age of 41.77 years. The following aspects were analyzed: anthropometric characteristics, global methylation using the ELISA method, pain level, physical activity level, functional disabilities, and hesitancy level related to work and physical activity-related activities. RESULTS: A statistically significant association was observed between methylation levels before and after treatment application for the experimental and placebo groups (p < 0.005), demonstrating a mean responsiveness between methylation and treatment (d = 0.5). However, there were no other statistically significant associations correlated with the other work variables. CONCLUSION: The results obtained in this study suggest the need for further research related to the identification of specific genes in methylation, as well as the standardization of dosimetry used for transcutaneous ILIB laser application in the radial artery.

RESUMO JUSTIFICATIVA E OBJETIVOS: A lombalgia está entre as condições mais incapacitantes no mundo e; dentre os fatores epigenéticos, a metilação em ilhas CpG de regiões promotoras de genes pode modular a expressão gênica permitindo uma possível correlação ao desenvolvimento da doença, como também pode trazer esclarecimentos a respeito do tratamento a ser escolhido. O objetivo deste estudo foi verificar a eficácia da terapia através do uso do ILIB modificado relacionada ao processo de metilação de DNA na lombalgia. Os objetivos secundários deste estudo foram a investigação da intensidade da dor, sexo, dados sociodemográficos e perfil físico-funcional. MÉTODOS: Este estudo, desenvolvido em um município da região sul do Brasil, caracteriza-se como prospectivo. A amostra deste estudo foi composta por 30 participantes, de ambos os sexos, com idade média de 41,77 anos. Foram analisados os seguintes aspectos: características antropométricas, metilação global através do método ELISA, nível de dor, nível de atividade física, incapacidades funcionais e nível de hesitação para realizar atividades relacionada ao trabalho e atividade física. RESULTADOS: Observou-se associação estatisticamente significativa entre os níveis de metilação antes e a após aplicação do tratamento para grupo experimental e placebo (p<0,005) demostrando uma média responsividade entre as variáveis metilação e tratamento (d=0,5). No entanto, não houve nenhuma outra associação estatística correlacionada as demais variáreis do trabalho. CONCLUSÃO: Os resultados obtidos neste estudo sugerem que há necessidade mais estudos relacionados a identificação de genes específicos na metilação, além da necessidade de padronização de dosimetria utilizadas para aplicação do laser ILIB de forma transcutânea, em artéria radial.

Efecto de la epigenética en la artritis reumatoide / Effect of epigenetics on rheumatoid arthritis

La artritis reumatoide es una enfermedad autoinmune e inflamatoria que afecta de manera predominante a las articulaciones diartrodiales. En esta patología los factores ambientales o conductuales pueden actuar en sinergia con la predisposición genética, acelerando el inicio y la gravedad de la enfermedad. Este vínculo entre el medio ambiente y el genoma está mediado por marcas epigenéticas en el ácido desoxirribonucleico, incluyendo su metilación, la modificación de histonas y la regulación mediada por ácido ribonucleico no codificante. La epigenética puede generar cambios fenotípicos hereditarios, que no están determinados por modificaciones en la secuencia del ácido desoxirribonucleico y, en consecuencia, son reversibles. Por lo tanto la dieta, los medicamentos y otros factores ambientales, tendrían la capacidad de modularlos. La identificación de una desregulación epigenética específica, puede ofrecer una mayor comprensión de la fisiopatología de la enfermedad e influenciar positivamente en la prevención, diagnóstico y desarrollo de nuevas dianas terapéuticas.

Rheumatoid arthritis is an autoimmune and inflammatory disease that predominantly affects the diarthrodial joints. In this pathology, environmental or behavioral factors can act in synergy with genetic predisposition, accelerating the onset and severity of the disease. This link between the environment and the genome is mediated by epigenetic marks on deoxyribonucleic acid, including its methylation, histone modification, and noncoding ribonucleic acid-mediated regulation. Epigenetics can generate heritable phenotypic changes, which are not determined by modifications in the deoxyribonucleic acid sequence and are therefore reversible. Therefore, diet, medications and other environmental factors would have the ability to modulate them. The identification of a specific epigenetic dysregulation can offer a better understanding of the pathophysiology of the disease and positively influence the prevention, diagnosis and development of new therapeutic targets.

Epigenetics, hypersensibility and asthma: what do we know so far?

Abstract In this review, we describe recent advances in understanding the relationship between epigenetic changes, especially DNA methylation (DNAm), with hypersensitivity and respiratory disorders such as asthma in childhood. It is clearly described that epigenetic mechanisms can induce short to long-term changes in cells, tissues, and organs. Through the growing number of studies on the Origins of Health Development and Diseases, more and more data exist on how environmental and genomic aspects in early life can induce allergies and asthma. The lack of biomarkers, standardized assays, and access to more accessible tools for data collection and analysis are still a challenge for future studies. Through this review, the authors draw a panorama with the available information that can assist in the establishment of an epigenetic approach for the risk analysis of these pathologies.

Efectos de un programa de entrenamiento aeróbico en el tiempo de reacción y la metilación de ADN del gen SHANK3 en niños con trastorno de espectro autista: un estudio piloto / Effects of an Aerobic Training Program on Reaction Time and DNA Methylation of SHANK3 Gene in Children with Autism Spectrum Disorder: a Pilot Study

Introducción. El trastorno del espectro autista (TEA) es un trastorno del neurodesarrollo que provoca déficits en áreas cognitivas y motoras y es causado por varios mecanismos, entre ellos la regulación epigenética. Los procesos epigenéticos pueden verse influenciados por factores ambientales como el ejercicio físico. Objetivo. Analizar el efecto de un programa de ejercicio físico aeróbico (EFA) en el tiempo de reacción simple (TRS) y la metilación del ADN de la isla 2 del gen SHANK3 en niños con TEA. Materiales y métodos. Estudio cuasiexperimental realizado con un grupo de 9 niños (7-11 años) con TEA, que participaron en un programa de EFA de 10 semanas. Las diferencias en el TRS y la metilación de ADN fueron analizadas mediante la prueba de Kruskall-Wallis, considerando un nivel de significancia de p<0.05.Resultados. La mediana del TRS disminuyó después del programa de entrenamiento. Sin embargo, no se encontró una diferencia estadísticamente significativa (p=0.53). Se observó un patrón de hipermetilación en 11 de los dinucleótidos, tanto antes como después del entrenamiento, y se encontró una diferencia estadísticamente significativa en la posición CpG108 (p=0.032). Conclusión. Un programa de entrenamiento basado en EFA de intensidad moderada a vigorosa tiene el potencial de modificar el TRS y la metilación del ADN en niños con TEA. No obstante, es necesario realizar nuevos estudios con muestras más grandes y en los que se analicen más genes, para corroborar los resultados aquí descritos y fortalecer el conocimiento sobre el efecto del ejercicio en los procesos epigenéticos de esta población

Introduction. Autism spectrum disorder (ASD) is a neurodevelopmental disorder that produces cognitive and motor deficits and it is caused by several mechanisms, including epigenetic regulation. Epigenetic processes can be influenced by environ-mental factors such as physical exercise.Objective. To analyze the effect of an aerobic physical exercise (APE) program on simple reaction time (SRT) and DNA methylation of island 2 of the SHANK3 gene in children with ASD.Materials and methods. A quasi-experimental study was carried out on a group of 9 children (7-11 years old) with ASD, who participated in a 10-week APE program. Differences in SRT and DNA methylation were analyzed using the Kruskall-Wallis test by considering a significance level p<0.05.Results. The median SRT decreased after the training program. However, no sta-tistically significant difference was found (p = 0.53). A pattern of hypermethylation was observed in 11 dinucleotides, both before and after training, and a statistically significant difference was found in the CpG108 position (p = 0.032).Conclusion. A moderate to vigorous intensity of APE program has the potential to modify SRT and DNA methylation in children with ASD. However, it requires further studies with larger samples in which more genes are analyzed, to corroborate the results described here and strengthen knowledge about the effect of exercise on the epigenetic processes of this population

The critical importance of epigenetics in autoimmune-related skin diseases / 医学前沿

Autoimmune-related skin diseases are a group of disorders with diverse etiology and pathophysiology involved in autoimmunity. Genetics and environmental factors may contribute to the development of these autoimmune disorders. Although the etiology and pathogenesis of these disorders are poorly understood, environmental variables that induce aberrant epigenetic regulations may provide some insights. Epigenetics is the study of heritable mechanisms that regulate gene expression without changing DNA sequences. The most important epigenetic mechanisms are DNA methylation, histone modification, and noncoding RNAs. In this review, we discuss the most recent findings regarding the function of epigenetic mechanisms in autoimmune-related skin disorders, including systemic lupus erythematosus, bullous skin diseases, psoriasis, and systemic sclerosis. These findings will expand our understanding and highlight the possible clinical applications of precision epigenetics approaches.

Association Analysis Between Methylation of SCARB1 Gene Promoter and Coronary Heart Disease / 中国医学科学院学报

Objective To explore the relationship between scavenger receptor class B member 1 (SCARB1) gene promoter methylation and the pathogenesis of coronary artery disease. Methods A total of 120 patients with coronary heart disease treated in Renji Hospital affiliated to Shanghai Jiao Tong University School of Medicine from December 2018 to May 2020 were selected as the case group,while 140 gender and age matched healthy participants were randomly selected as the control group for a case-control study.The methylation status was detected by high-throughput target sequencing after bisulfite converting,and the methylation of CpG sites in the promoter region of SCARB1 gene was compared between the two groups. Results The case group showed higher methylation level of SCARB1+67 and lower methylation level of SCARB1+134 than the control group (both P<0.001),and the differences remained statistically significant in men (both P<0.001) and women (both P<0.001).The overall methylation level in the case group was lower than that in the control group [(80.27±2.14)% vs.(81.11±1.27)%;P=0.006],while this trend was statistically significant only in men (P=0.002). Conclusion The methylation of SCARB1 gene promotor is associated with the pathogenesis and may participate in the occurrence and development of coronary heart disease.

Age Estimation Based on DNA Methylation and Its Application Prospects in Forensic Medicine / 法医学杂志

With the improvement of DNA methylation detection techniques, studies on age-related methylation sites have found more age-specific ones across tissues, which improves the sensitivity and accuracy of age estimation. In addition, the establishment of various statistical models also provides a new direction for the age estimation of tissues from different sources. This review summarizes the related studies of age estimation based on DNA methylation from the aspects of detection technology, age-related cytosine phosphate guanine site and model selection in recent years.

Advances in the study of gene body methylation and tumors / 中华肝胆外科杂志

DNA methylation is an important epigenetic regulatory mechanism, including gene promoter methylation and gene body methylation. Abnormal DNA methylation is closely related to the development and progression of malignant tumors, and the correlation between promoter methylation and tumors has been more clearly described previously. However, with the in-depth study of genome-wide DNA methylation, it has been found that there are more extensive methylation levels in gene body regions, which also play an important role in tumor-related gene expression, cell differentiation and tumor development. In this paper, we review the effects of gene bodymethylation on tumors in recent years and provide clues for the research and application of gene body methylation in the field of tumors by elaborating the role and regulatory mechanism of gene body methylation on tumors.

Research progress of DNA methylation in idiopathic male infertility / 中国医师杂志

Male infertility is a multifactorial disease, of which the cause of male infertility cannot be determined, which is called idiopathic male infertility, and the incidence rate is gradually rising. Because its cause is unknown, it has become a major problem in the department of reproductive endocrinology. With the in-depth study of epigenetics, the diagnosis and treatment of idiopathic male infertility also has a new direction, especially the important role of DNA methylation in spermatogenesis and embryonic development. More and more gene fragments and loci have been found by scholars, which makes it possible to achieve accurate identification and targeted treatment. This article reviews and summarizes the research progress of DNA methylation related to idiopathic male infertility in recent years, aiming to further elaborate the pathogenesis of idiopathic male infertility and provide new ideas for clinical diagnosis and treatment.

Application of DNA methylation markers in the whole process management of cervical lesions / 中国医师杂志

DNA methylation plays an important role in the occurrence and development of cervical cancer. DNA methylation detection can be combined or complemented with human papillomavirus (HPV), cytology, etc., which is helpful to improve the accuracy of cervical cancer screening or reduce the rate of colposcopy referral. In this review, we focus on the significance of DNA methylation markers in cervical cancer screening and overall management.

Research progress on sex hormone-binding globulin involved in the occurrence and development of diabetes mellitus / 中国基层医药

Sex hormone-binding globulin (SHBG) is significantly associated with abnormal glucose metabolism. Low SHBG level is a risk factor for insulin resistance and the occurence of diabetes mellitus. SHBG is negatively correlated with the risk of type 2 diabetes mellitus and plays an important role in regulating insulin resistance while predicting its development. The genotype of SHBG has been found to be closely related to the occurrence of diabetes mellitus. Fatty liver and DNA methylation are also important factors mediating the relationship between SHBG and type 2 diabetes mellitus. The change in SHBG level may be related to insulin resistance by influencing hepatocyte nuclear factor 4a and regulating glucose transporter.

Expression of 5-methylcytosine and 5-hydroxymethylcytosine in bone tissue of rats with different types of skeletal fluorosis / 中华地方病学杂志

Objective:To learn about the levels of 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) in bone tissue of rats with different types of skeletal fluorosis and analyze their correlation.Methods:Thirty 4-week-old SPF grade healthy SD rats were selected. After adaptive feeding for 1 week, the rats were divided into control group (4 ml·kg -1·bw deionized water + standard maintenance diet), osteosclerosis group [20 mg·kg -1·bw sodium fluoride (NaF) + standard maintenance diet], and osteoporosis/osteomalacia group (20 mg·kg -1·bw NaF + low-calcium and low-protein partial diet) according to their body weight (100 - 120 g) by random number table method, with 10 rats in each group, half male and half female; gavaged 6 days each week and the experimental period was 5 months. At the end of the experiment, samples of rat heart blood and lower limb femur were collected. The contents of serum methyl donor S-adenosylmethionine (SAM) and its metabolite S-adenosylhomocysteine (SAH) in serum, and the levels of 5-mC and 5-hmC in bone tissue were measured by enzyme-linked immunosorbent assay (ELISA). Western blot was used to determine the expression of DNA methyltransferase (DNMTs) and DNA hydroxymethylase (TETs) in bone tissue of rats. The correlation between serum SAM content, SAM/SAH ratio and bone tissue 5-mC level, and between the bone tissue 5-mC level and 5-hmC level was analyzed. Results:Serum SAM [11.03 (7.06, 18.63), 3.96 (2.32, 9.09), 3.91 (2.35, 4.46) nmol/L], SAH content [(4.69 ± 0.55), (5.41 ± 1.13), (13.90 ± 1.09) ng/L], SAM/SAH ratio [2.58 (1.54, 4.12), 0.62 (0.52, 1.69), 0.14 (0.13, 0.15)] and bone tissue 5-mC [103.39 (97.37, 109.35), 52.50 (50.19, 68.13), 55.03 (49.97, 59.57) ng/L], 5-hmC levels [(32.61 ± 8.84), (56.96 ± 8.48), (20.34 ± 6.22) ng/L] in the control group, osteosclerosis group and osteoporosis/osteomalacia group were compared, and the differences were statistically significant beween three groups ( H/ F = 12.81, 284.24, 21.85, 19.37, 55.23, P < 0.01). Compared with the control group, the content of SAM, the ratio of SAM/SAH, the level of 5-mC in the osteosclerosis group and osteoporosis/osteomalacia group, and the level of 5-hmC in the osteoporosis/osteomalacia group were lower ( P < 0.05), while the content of SAH in the osteoporosis/osteomalacia group and the level of 5-hmC in the osteosclerosis group were higher ( P < 0.05). Compared with the osteosclerosis group, the content of SAH in the osteoporosis/osteomalacia group was higher, while the ratio of SAM/SAH and the level of 5-hmC were lower ( P < 0.05). Western blot showed that there were statistically significant differences in the expression levels of DNMT1, DNMT3A, DNMT3B, TET1 and TET2 protein in bone tissue of rats in the control group, osteosclerosis group, and osteoporosis/osteomalacia group ( F = 285.45, 345.58, 239.83, 311.52, 318.24, P < 0.001). Among them, the expression levels of DNMT1, DNMT3A and DNMT3B protein in the osteosclerosis group and osteoporosis/osteomalacia group were lower than those in the control group, and the expression levels of DNMT1, DNMT3A and DNMT3B protein in the osteosclerosis/osteomalacia group were lower than those in the osteosclerosis group ( P < 0.05); the expression levels of TET1 and TET2 protein in osteosclerosis group were higher than those in the control group and osteoporosis/osteomalacia group, and the expression levels of TET1 and TET2 protein in the osteoporosis/osteomalacia group were lower than those in the control group ( P < 0.05). The results of Spearman rank correlation analysis showed that the content of SAM and the ratio of SAM/SAH in the control group, osteosclerosis group and osteoporosis/osteomalacia group were positively correlated with the level of 5-mC in bone tissue ( rs = 0.89, 0.92, 0.81, 0.73, 0.87, 0.73, P < 0.05). The levels of 5-mC and 5-hmC in bone tissue of rats in each group were negatively correlated ( rs = - 0.69, - 0.68, - 0.72, P < 0.05). Conclusions:The level of 5-mC in bone tissue of osteosclerotic fluorosis rats is low, and the level of 5-hmC is high, while those of osteoporosis/osteomalacia fluorosis rats are lower. The difference of 5-mC level in bone tissue of rats with different types of skeletal fluorosis is not significant, which may be related to the difference of 5-hmC level in bone tissue.

Screening of DNA methylation sites and construction of differential methylation profiles in human hepatic stellate cells fibrosis and autophagy induced by sodium arsenite / 中华地方病学杂志

Objective:To analyze DNA methylation sites related to fibrosis and autophagy in human hepatic stellate cells (LX-2 cells) induced by sodium arsenite (NaAsO 2), and to screen specific methylation genes related to fibrosis and autophagy. Methods:Genome-wide DNA detection was performed using Illumina Infinium Methylation EPIC BeadChips (850K methylation chip) to derive differential methylation sites in LX-2 cells (control group) and the fibrosis and autophagy models of LX-2 cells induced by NaAsO 2(low, medium and high dose groups: the final concentrations were 5, 10, 15 μmol/L NaAsO 2, respectively, after 48 h intervention). Gene ontology (GO) function enrichment analysis and Kyoto encyclopedia of genes and genomes (KEGG) signaling pathway enrichment analysis were used to explore gene function. Results:The model of cell fibrosis and autophagy was established successfully in high dose group. The results of 850K methylation chip detection showed that there were 25 817 significant different methylation sites between the high dose group and the control group, including 12 083 hypermethylation sites and 13 734 hypomethylation sites. GO function enrichment analysis showed that the molecular functions of differentially methylated genes mainly included protein binding, ion binding, catalytic activity, enzyme binding. KEGG signaling pathway enrichment analysis showed that the pathways involved in differentially methylated genes mainly included metabolic pathway, cancer pathway, phosphatidylinositol-3-kinase-protein kinase B (PI3K-Akt) signaling pathway, endocytosis, and mitogen activated protein kinase (MAPK) signaling pathway. In the promoter region, 11 and 29 differentially methylated genes related to fibrosis and autophagy were screened, respectively.Conclusions:A large number of differential methylation sites exist in the process of NaAsO 2 induced fibrosis and autophagy of LX-2 cells. Specific methylation genes related to fibrosis and autophagy are screened out.

The pattern of alternative splicing and DNA methylation alteration and their interaction in linseed (Linum usitatissimum L) response to repeated drought stresses

BACKGROUND: Drought stress has significantly hampered agricultural productivity worldwide and can also result in modifications to DNA methylation levels. However, the dynamics of DNA methylation and its association with the changes in gene transcription and alternative splicing (AS) under drought stress are unknown in linseed, which is frequently cultivated in arid and semiarid regions. RESULTS: We analysed AS events and DNA methylation patterns in drought-tolerant (Z141) and drought-sensitive (NY-17) linseed under drought stress (DS) and repeated drought stress (RD) treatments. We found that the number of intron-retention (IR) and alternative 3' splice site (Alt3'SS) events were significantly higher in Z141 and NY-17 under drought stress. We found that the linseed response to the DS treatment was mainly regulated by transcription, while the response to the RD treatment was coregulated by transcription and AS. Whole genome-wide DNA methylation analysis revealed that drought stress caused an increase in the overall methylation level of linseed. Although we did not observe any correlation between differentially methylated genes (DMGs) and differentially spliced genes (DSGs) in this study, we found that the DSGs whose gene body region was hypermethylated in Z141 and hypomethylated in NY-17 were enriched in abiotic stress response Gene Ontology (GO) terms. This finding implies that gene body methylation plays an important role in AS regulation in some specific genes. CONCLUSION: Our study is the first comprehensive genome-wide analysis of the relationship between linseed methylation changes and AS under drought and repeated drought stress. Our study revealed different interaction patterns between differentially expressed genes (DEGs) and DSGs under DS and RD treatments and differences between methylation and AS regulation in drought-tolerant and drought-sensitive linseed varieties. The findings will probably be of interest in the future. Our results provide interesting insights into the association between gene expression, AS, and DNA methylation in linseed under drought stress. Differences in these associations may account for the differences in linseed drought tolerance.

Role of DNA methylation in the pathogenesis of ophthalmic diseases / 国际眼科杂志(Guoji Yanke Zazhi)

The occurrence and development of many eye diseases are closely related to genetic and environmental factors, among which epigenetic modification is an important bridge connecting genetic and environmental factors. It can affect the levels of related genes by influencing gene transcription or translation, thereby playing a role in the pathogenesis of ocular diseases. DNA methylation is an important part of epigenetic modification which is usually regulated by three processes: de novo methylation, maintenance methylation, and demethylation, and plays an essential role in regulating gene expression. At present, researchers have conducted that DNA methylation plays an important role in repair of damage to corneal endothelium, mitochondrial dynamics regulation and diabetic retinopathy, oxidative stress response and cataracts and other eye diseases, providing new ideas in the treatment of related ocular diseases. This study presented a brief review of the role of DNA methylation in the development of related ocular diseases and provided new perspectives and directions for the screening, diagnosis, and treatment of eye diseases.

Application value of SHOX2 and RASSF1A gene promoter region methylation detection for screening and diagnosis of early-stage lung adenocarcinoma / 肿瘤研究与临床

Objective:To investigate the value of SHOX2 and RASSF1A gene promoter region methylation detection for screening and diagnosis of early-stage lung adenocarcinoma.Methods:The mRNA sequencing data of 471 lung adenocarcinoma patients and corresponding methylation data of 413 cases were downloaded from The Cancer Genome Atlas (TCGA) database, the methylation levels of SHOX2 and RASSF1A gene promoter regions were calculated, and the difference in methy lation level between normal lung tissues and tumor tissues was analyzed. The clinical data of 54 patients with early-stage lung adenocarcinoma and 31 patients with benign lung tumors who underwent surgery at Drum Tower Hospital Affiliated to Nanjing University Medical School from January 2018 to January 2019 were retrospectively analyzed. The methylation status of SHOX2 and RASSF1A in tumor tissues and normal lung tissues (>5 cm from the edge of the tumor foci) (called clinical samples) was detect, and a positive methylation in the promoter region of either gene was considered as a combination of two genes methylation positivity. Using pathological diagnosis as the gold standard, the efficacy of gene methylation positivity in diagnosing early-stage lung adenocarcinoma was analyzed by receiver operating characteristic (ROC) curve. Patients with >80% of tumor cells in paraffin samples were screened, and mRNA high-throughput sequencing was performed in their tumor tissues and normal lung tissues. The relationship between positive methylation of the two genes and clinicopathological features was analyzed, and the correlation between the promoter region methylation level of the two genes and mRNA expression levels in clinical samples and TCGA database samples was analyzed by Spearman method. Gene set variance analysis (GSVA) method was used to analyze the differences in Kyoto Encyclopedia of Genes and Genomes enrichment pathways between two-gene methylation-positive clinical lung adenocarcinoma samples and corresponding methylation-negative lung adenocarcinoma.Results:In TCGA database, the SHOX2 promoter region methylation island contained 6 sequenced methylation sites, of which sites cg04532033 and cg01557547 methylation levels were higher in lung adenocarcinoma tissues than in normal lung tissues (both P < 0.05); the RASSF1A gene promoter region methylation island contained 11 sequenced methylation sites, and the methylation levels of 6 of these sites in lung adenocarcinoma tissues were higher than those in normal lung tissues (all P < 0.05). Compared with normal lung tissues, the methylation level of SHOX2 promoter region was higher in stage Ⅰ and Ⅱ lung adenocarcinoma tissues (both P < 0.05); the methylation level of RASSF1A promoter region was higher in all stages of lung adenocarcinoma ( P < 0.001). Among 54 patients with early-stage lung adenocarcinoma, 28 were positive for SHOX2 promoter region methylation in tumor tissues, 21 were positive for RASSF1A promoter region methylation, and 40 were positive for combined methylation of both genes; 31 benign lung nodules were negative for SHOX2 and RASSF1A methylation. ROC curve analysis showed that the sensitivity of positive SHOX2 promoter region methylation for diagnosing early-stage lung adenocarcinoma was higher than that of RASSF1A promoter region methylation positivity (51.8% vs. 38.9%), and the area under the curve (AUC) for diagnosis by two-gene methylation positivity was larger than that for diagnosis by SHOX2 or RASSF1A gene methylation positivity alone (0.870 vs. 0.759 and 0.694). The circulating thresholds (Ct) of SHOX2 and RASSF1A methylation tested by real-time fluorescence quantitative polymerase chain reaction (qRT-PCR) in stage Ⅰ and Ⅱ lung adenocarcinoma were lower than those in normal lung tissues (all P < 0.05); patients with two-gene methylation positivity were characterized by older age, longer tumor longest diameter and more advanced pathological stage compared with patients with two-gene methylation negativity (all P < 0.05). In clinical stage Ⅰ-Ⅱ lung adenocarcinoma samples, the Ct of SHOX2 and RASSF1A promoter region methylation tested by qRT-PCR was negatively correlated with their mRNA relative expression levels ( r=-0.43, P = 0.003; r = -0.48, P = 0.001); in TCGA database stage Ⅰ-Ⅱ lung adenocarcinoma samples, the level of SHOX2 promoter region methylation was negatively correlated with its mRNA relative expression level ( r = -0.23, P < 0.001), and the level of RASSF1A promoter region methylation was also negatively correlated with its mRNA relative expression level, but without statistical difference ( r = -0.05, P = 0.310). In two-gene promoter methylation-positive lung adenocarcinoma samples, the pathways related to folate metabolism and DNA stability were upregulated, and the pathways related to vasoconstriction and cell growth and differentiation were downregulated. Conclusions:The combined detection of SHOX2 and RASSF1A promoter region methylation can be used as an indicator for screening and diagnosis of early-stage lung adenocarcinoma. Abnormal promoter region methylation of the two genes may affect multiple tumor-related pathways and promote the occurrence and progression of early-stage lung adenocarcinoma.

Research update on DNA methylation in peripheral blood cells as a risk factor for coronary heart disease / 中华检验医学杂志

Coronary heart disease (CHD) is a kind of cardiovascular diseases originated from atherosclerosis (AS), and chronic inflammation is one of the pathological characteristics. The peripheral blood leukocytes, especially mononuclear cells, play an important role in the AS processes. Recently, in a series of Epigenome-Wide Association Studies (EWAS), multiple DNA differential methylation sites in peripheral blood cells were found to be statistically associated with CHD, which suggested that these DNA differential methylation sites might serve as new risk factors for CHD. The recognition of the variant of DNA methylation as a common epigenetic nucleic acid modification in the occurrence and development of CHD, is ongoing. DNA methylation has the potential to become warning biomarkers, which might provide new ideas and evidences for mechanistic studies of CHD.

Application of DNA methylation in detection of endometrial carcinoma in women with abnormal uterine bleeding at childbearing age / 中华检验医学杂志

Objective:This work aims to explore the application value of cervical exfoliated cell DNA (Cysteine dioxygenase type 1, CDO1 and CUGBP Elav-like family member 4, CELF4) methylation in the detection of endometrial cancer in women of childbearing age. Methods:From November 2021 to October 2022, a prospective study was conducted on a total number of 517 reproductive-age women with abnormal uterine bleeding who had surgical indications for hysteroscopy at the Xiangya Third Hospital of Central South University. The cervical exfoliated cells were collected for cytology, HPV (human papillomavirus) and gene methylation detection before operation. Clinical information of patients, level of tumor-related biomarkers, and endometrial thickness of transvaginal ultrasound (TVS) were also collected. Single factor regression method was used to analyze the high-risk factors of endometrial cancer. Receiver operating characteristic curve analysis was used to obtain the area under the curve(AUC), focusing on the screening efficacy of gene methylation test for endometrial cancer in women of childbearing age.Results:The age, body mass index (BMI)≥25 kg/m 2, endometrial thickness≥11 mm, CDO1 m ΔCt≤8.4, CELF4 m ΔCt≤8.8, and double gene methylation were associated with endometrial cancer in women of childbearing age, 1.16(1.08-1.25), 4.33(1.89-10.31), 9.49(3.88-26.69), 69.62(25.70-224.36), 23.64(9.66-63.99), 87.39(24.83-555.05), all P<0.05. The AUC was 0.90 (95% CI 0.83-0.97) of CDO1 m/ CELF4 m in diagnosing endometrial carcinoma was higher than others factors, with sensitivity and specificity of 91.7% (95% CI 80.6%-100%) and 88.8% (95% CI 86.0%-91.6%). TVS combined with DNA methylation detection further improved the sensitivity to 95.8% (95% CI 87.8%-100%), but could not improve the specificity 68.0% (95% CI 63.8%-72.1%). Conclusions:For women of childbearing age with abnormal uterine bleeding or abnormal vaginal discharge, the accuracy of cervical cytology DNA methyl detection of endometrial cancer is better than other non-invasive clinical programs. DNA methylation combined with TVS can improve the sensitivity of detection.

Advances in the role of epigenetics in tuberculosis / 中华微生物学和免疫学杂志

Tuberculosis (TB) is a chronic infectious disease caused by Mycobacterium tuberculosis ( Mtb) that seriously endangers human health. Mtb induces epigenetic changes in the host to regulate host genome transcription and immune response, which plays an important role in the growth and replication of Mtb and the development and outcome of TB. Since epigenetic regulation occurs early and is reversible, it has been extensively studied in the pathogenesis of various diseases and has great potential as a molecular target. This paper reviewed the epigenetic changes in host after Mtb infection, including DNA methylation and miRNA, and summarized the role of epigenetics in the pathogenesis of TB and the research progress in potential diagnostic markers.