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BACKGROUND: Low-grade gliomas (LGG) are a variety of brain tumors that show different clinical outcomes. The methylation of the GSTM5 gene has been noted in the development of LGG, however, its prognostic importance remains uncertain. OBJECTIVE: The objective of this study was to examine the correlation between GSTM5 DNA methylation and clinical outcomes in individuals diagnosed with LGG. METHODS: Analysis of GSTM5 methylation levels in LGG samples was conducted using data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. The overall survival based on GSTM5 methylation status was evaluated using Kaplan-Meier curves. The DNA methylation heatmap for particular CpG sites in the GSTM5 gene was visualized using the "pheatmap" R package. RESULTS: The study analyzed that LGG tumors had higher levels of GSTM5 methylation than normal tissues. There was an inverse relationship discovered between GSTM5 expression and methylation. LGG patients with hypermethylation of GSTM5 promoter experienced a positive outcome. Age, grade, and GSTM5 methylation were determined as independent prognostic factors in LGG through both univariate and multivariate Cox regression analyses. CONCLUSION: Methylation of GSTM5 DNA, specifically at certain CpG sites, is linked to a positive outlook in patients with LGG. Utilizing the "pheatmap" R package to visualize GSTM5 methylation patterns offers important information for identifying prognostic markers and therapeutic targets in low-grade gliomas.
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Laser therapy has shown promising outcomes in treating infantile hemangiomas. However, the molecular mechanisms underlying laser treatment for IH remain incompletely elucidated. This study aimed to unravel the molecular mechanisms of laser therapy in IH treatment. We evaluated the inhibitory effects of laser treatment on the proliferation and promotion of apoptosis in human hemangioma endothelial cells (HemECs) through cell counting kit-8 (CCK-8) assay, Hoechst 33342 staining, and flow cytometric analysis. Transcriptome sequencing analysis of HemECs following laser treatment revealed a significant decrease in the expression level of the GSTM5 gene. The qRT-PCR and western blot analysis also showed that GSTM5 expression in HemECs was downregulated compared to human umbilical vein endothelial cells (HUVECs), and concomitantly, the p62-Nrf2 pathway was suppressed. Using siRNA to downregulate GSTM5 expression, we observed that inhibiting GSTM5 expression could restrain cell proliferation, elevate intracellular ROS levels, and induce apoptosis in HemECs. Furthermore, upon inhibition of the p62-Nrf2 pathway using p62-specific siRNA, a significant decrease in GSTM5 expression and an elevation in intracellular ROS levels were noted in laser-treated HemECs. These findings suggested that laser treatment may operate by inhibiting the p62-Nrf2 pathway, thereby downregulating GSTM5 expression, elevating ROS levels, and consequently inducing apoptosis in HemECs.
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Hemangioma , Lasers de Estado Sólido , Humanos , Fator 2 Relacionado a NF-E2 , Espécies Reativas de Oxigênio , Transcriptoma , Hemangioma/genética , Hemangioma/radioterapia , Células Endoteliais da Veia Umbilical Humana , RNA Interferente PequenoRESUMO
Background: A diabetic foot ulcer (DFU) is a serious, long-term condition associated with a significant risk of disability and mortality. However, research on its biomarkers is still limited. This study utilizes bioinformatics and machine learning methods to identify immune-related biomarkers for DFU and validates them through external datasets and animal experiments. Methods: This study used bioinformatics and machine learning to analyze microarray data from the Gene Expression Omnibus (GEO) database to identify key genes associated with DFU. Animal experiments were conducted to validate these findings. This research employs the datasets GSE68183 and GSE80178 retrieved from the GEO database as the training dataset for building a gene machine learning model, and after conducting differential analysis on the data, this study used package glmnet and package e1071 to construct LASSO and SVM-RFE machine learning models, respectively. Subsequently, we validated the model using the training set and validation set (GSE134431). We conducted enrichment analysis, including GSEA and GSVA, on the model genes. We also performed immune functional analysis and immune-related analysis on the model genes. Finally, we conducted immunohistochemistry (IHC) validation on the model genes. Results: This study identifies GSTM5 as a potential immune-related key target in DFU using machine learning and bioinformatics methods. Subsequent validation through external datasets and IHC experiments also confirms GSTM5 as a critical biomarker for DFU. The gene may be associated with T cells regulatory (Tregs) and T cells follicular helper, and it influences the NF-κB, GnRH, and MAPK signaling pathway. Conclusion: This study identified and validated GSTM5 as a biomarker for DFU. This finding may potentially provide a target for immune therapy for DFU.
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Genome-wide chromosomal microarray is extensively used to detect copy number variations (CNVs), which can diagnose microdeletion and microduplication syndromes. These small unbalanced chromosomal structural rearrangements ranging from 1 kb to 10 Mb comprise up to 15% of human mutations leading to monogenic or contiguous genomic disorders. Albeit rare, CNVs at 1p13.3 cause a variety of neurodevelopmental disorders (NDDs) including development delay (DD), intellectual disability (ID), autism, epilepsy, and craniofacial anomalies (CFA). Most of the 1p13.3 CNV cases reported in the pre-microarray era encompassed a large number of genes and lacked the demarcating genomic coordinates, hampering the discovery of positional candidate genes within the boundaries. In this study, we present four subjects with 1p13.3 microdeletions displaying DD, ID, autism, epilepsy, and CFA. In silico comparative genomic mapping with three previously reported subjects with CNVs and 22 unreported DECIPHER CNV cases has resulted in the identification of four different sub-genomic loci harboring five positional candidate genes for DD, ID, and CFA at 1p13.3. Most of these genes have pathogenic variants reported, and their interacting genes are involved in NDDs. RT-qPCR in various human tissues revealed a high expression pattern in the brain and fetal brain, supporting their functional roles in NDDs. Interrogation of variant databases and interacting protein partners led to the identification of another set of 11 potential candidate genes, which might have been dysregulated by the position effect of these CNVs at 1p13.3. Our studies define 1p13.3 as a genomic region harboring 16 NDD candidate genes and underscore the critical roles of small CNVs in in silico comparative genomic mapping for disease gene discovery. Our candidate genes will help accelerate the isolation of pathogenic heterozygous variants from exome/genome sequencing (ES/GS) databases.
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BACKGROUND: Glutathione-S transferases (GSTs) comprise a series of critical enzymes involved in detoxification of endogenous or xenobiotic compounds. Among several GSTs, Glutathione S-transferases mu (GSTM) has been implicated in a number of cancer types. However, the prognostic value and potential functions of the GSTM family genes have not been investigated in lung adenocarcinoma (LUAD). METHODS: We examined the expression of GSTM5 in LUAD and identified associations among GSTM5 expression, clinicopathological features, survival data from the Cancer Genome Atlas (TCGA). The correlation between GSTM5 DNA methylation and its expression was analyzed using the MEXPRESS tool and UCSC Xena browser. The methylation status of GSTM5 in the promoter region in lung cancer cells was measured by methylation-specific PCR (MSP). After 5-aza-2'-deoxycytidine treatment of lung cancer cells, expression of GSTM5, cell proliferation and migration were assessed by RT-PCR, CCK-8 and transwell assays, respectively. RESULTS: The results showed that GSTM5 was abnormally down-regulated in LUAD patients' tissues, and patients with low GSTM5 expression level had significantly shorter OS. Cox regression analyses revealed that GSTM5 was associated with overall survival (OS) of LUAD patients, which expression was an independent prognostic indicator in terms of OS (hazard ratio: 0.848; 95% CI: 0.762-0.945; P = 0.003). In addition, we found the promoter region of GSTM5 was hypermethylated in the tumor tissue compared with adjacent normal tissues, and the average methylation level of GSTM5 were moderately correlated with its expression. Moreover, methylation-specific PCR also showed that the GSTM5 gene promoter was hypermethylated in lung cancer cells, and treatment with 5-Aza-CdR can restore the gene expression and inhibit cell proliferation and migration. Finally, Gene Set Enrichment Analysis (GSEA) revealed that low GSTM5 expression was significantly related to DNA repair pathways. CONCLUSION: Our data demonstrate that low GSTM5 expression and its high DNA methylation status may act as a novel putative molecular target gene for LUAD.
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Adenocarcinoma de Pulmão , Neoplasias Pulmonares , Adenocarcinoma de Pulmão/patologia , Biomarcadores Tumorais/genética , Biomarcadores Tumorais/metabolismo , DNA/metabolismo , Metilação de DNA , Decitabina , Regulação Neoplásica da Expressão Gênica , Glutationa/metabolismo , Glutationa Transferase , Humanos , Neoplasias Pulmonares/patologia , Prognóstico , Transferases/genética , Transferases/metabolismoRESUMO
Acute myeloid leukaemia (AML) is a very heterogeneous malignancy in which standard treatment is based on chemotherapy. Resistance to chemotherapeutic agents remains a big problem in AML, because negatively influences patient overall survival. Several resistance mechanisms have been described, the best of which is the process of drug removal from the cell and/or nucleus by membrane transport proteins. The aim of the study was to investigate the effect of polymorphism of genes coding ABCC3, GSTM5 involved in the transport and metabolism of drugs. For this purpose 95 newly diagnosed AML patients and 125 healthy controls were genotyped. We showed that ABCC3 rs4148405 and GSTM5 rs3754446, but not ABCC33 rs4793665, affected overall survival in Polish AML patients.
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Transportadores de Cassetes de Ligação de ATP/genética , Glutationa Transferase/genética , Leucemia Mieloide Aguda/epidemiologia , Leucemia Mieloide Aguda/genética , Adulto , Idoso , Idoso de 80 Anos ou mais , Estudos de Casos e Controles , Intervalo Livre de Doença , Feminino , Genótipo , Humanos , Masculino , Pessoa de Meia-Idade , Polônia/epidemiologia , Polimorfismo de Nucleotídeo Único , Taxa de Sobrevida , Adulto JovemRESUMO
Cellular mosaicism due to monoallelic autosomal expression (MAE), with cell selection during development, is becoming increasingly recognized as prevalent in mammals, leading to interest in understanding its extent and mechanism(s). We report here use of clonal cell lines derived from the CNS of adult female [Formula: see text] hybrid (C57BL/6 X JF1) mice to characterize MAE as neural stem cells (nscs) differentiate to astrocyte-like cells (asls). We found that different subsets of genes show MAE in the two populations of cells; in each case, there is strong enrichment for genes specific to the respective developmental state. Genes that exhibit MAE are 22% of nsc-specific genes and 26% of asl-specific genes. Moreover, the promoters of genes with MAE have reduced CpG dinucleotides but increased CpG differences between the two parental mouse strains. Extending the study of variability to wild populations of mice, we found evidence for balancing selection as a contributing force in evolution of those genes showing developmental specificity (i.e., expressed in either nsc or asl), not just for genes showing MAE. Furthermore, we found that genes showing skewed allelic expression (SKE) were similarly enriched among cell type-specific genes and also showed a heightened probability of balancing selection. Thus, developmental stage-specific genes and genes with MAE or SKE seem to make up overlapping classes subject to selection for increased diversity. The implications of these results for development and evolution are discussed in the context of a model with stochastic epigenetic modifications taking place only during a relatively brief developmental window.
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Sistema Nervoso Central/fisiologia , Regulação da Expressão Gênica no Desenvolvimento/genética , Genes Controladores do Desenvolvimento/genética , Seleção Genética/genética , Alelos , Animais , Astrócitos/fisiologia , Diferenciação Celular/genética , Feminino , Camundongos , Camundongos Endogâmicos C57BL , Células-Tronco Neurais/fisiologia , Regiões Promotoras Genéticas/genéticaRESUMO
Major depressive disorder (MDD) is a prevalent debilitating psychiatric mood that contributes to increased rates of disability and suicide. However, the pathophysiology underlying MDD remains poorly understood. A growing number of studies have associated dysfunction of the prefrontal cortex (PFC) with depression, but no proteomic study has been conducted to assess PFC protein expression in a preclinical model of depression. Using the chronic unpredictable mild stress (CUMS) rat model of depression, differential protein expression between the PFC proteomes of CUMS and control rats was assessed through two-dimensional electrophoresis followed by matrix-assisted laser desorption ionization-time of flight-tandem mass spectrometry. Differential protein expression was analyzed for Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway over-representation. Four differential proteins were selected for Western blotting validation. Twenty-nine differential proteins were identified in the PFC of CUMS rats relative to control rats. Through KEGG analysis, energy and glutathione metabolic pathways were determined to be the most significantly altered biological pathways. Two of the four differential proteins selected for Western blotting validation - glyoxalase 1 and dihydropyrimidinase-related protein 2 - were found to be significantly downregulated in CUMS relative to control rats. In conclusion, proteomic analysis reveals that energy and glutathione metabolism are the most significantly altered biological pathways in the CUMS rat model of depression. Further investigation on these processes and proteins in the PFC is key to a better understanding of the underlying pathophysiology of MDD.
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Depressão/metabolismo , Modelos Animais de Doenças , Metabolismo Energético/fisiologia , Glutationa/metabolismo , Córtex Pré-Frontal/metabolismo , Proteômica/métodos , Animais , Depressão/psicologia , Masculino , Distribuição Aleatória , Ratos , Ratos Sprague-Dawley , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodosRESUMO
Parkinson disease (PD) is a degenerative movement disorder that results from the destruction of dopaminergic neurons in the midbrain substantia nigra. Both genetic and environmental factors contribute to PD risk, and likely to age at diagnosis. Among 258 newly diagnosed non-Hispanic Caucasian cases from Group Health Cooperative in western Washington State, we assessed whether diagnosis age was associated with 1,327 single nucleotide polymorphisms in genes related to central nervous system function, oxidative stress, inflammation or metal transport. We conducted linear regression to assess the age difference per variant allele while adjusting for sex and smoking. Of the polymorphisms associated with PD diagnosis age (ptrend<0.05), three demonstrated similar associations among 64 PD cases from the University of Washington Neurology Clinic, were not similarly associated (pinteraction<0.05) with age in general among 436 unrelated non-Hispanic Caucasian controls from the source population, and were predicted to be functional according to a public National Institute of Environmental Health Sciences polymorphism database. The most robust association was for rs10889162, a polymorphism in a predicted transcription factor binding site -582 bp from CYP2J2 arachidonic acid epoxygenase. Each variant allele was associated with 5.04 years older diagnosis age (95% confidence interval 2.28-7.80, p=0.0003). This association did not vary by sex or smoking history. Polymorphisms in predicted microRNA binding sites in GSTM5 and SLC11A2 were also associated with >2-year differences in diagnosis age. These results await confirmation in other series of incident cases, but suggest that selected genes and environmental exposures may influence PD diagnosis age.
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BACKGROUND: Myelodysplastic syndrome (MDS) is a preleukemic condition that transforms into acute myeloid leukemia. However, the genetic events underlying this transformation remain poorly understood. Aberrant DNA methylation may play a causative role in the disease and its prognosis. Thus, we compared the DNA methylation profiles in refractory anemia with excess blast (RAEB) to those in refractory cytopenia with multilineage dysplasia (RCMD). METHODS: Bone marrow samples were collected from 20 patients with primary MDS (9 with RAEB and 11 with RCMD), and peripheral blood samples were collected from 4 healthy controls. These samples were assessed using a commercial whole genome-wide methylation assay. Methylation-specific polymerase chain reaction (PCR) was used to detect the methylation of candidate gene promoters in RAEB and RCMD. RESULTS: Microarray data revealed significant hypermethylation in 69 genes within RAEB but not RCMD. Candidate genes were mapped to 5 different networks, and network 1 had the highest score due to its involvement in gene expression, cancer, and cell cycle. Five genes (GSTM5, BIK, CENPH, RERG, and ANGPTL2) were associated with malignant disease progression. Among them, the methylated promoter pairs of GSTM5 (55.5% and 20%), BIK (20% and 0%), and ANGPTL2 (44.4% and 10%) were observed more frequently in RAEB. CONCLUSION: DNA methylation of GSTM5, BIK, and ANGPTL2 may induce epigenetic silencing and contribute to the increasing blasts and resulting MDS progression; however, the functions of these genes were not determined. Further study focusing on epigenetic silencing using various detection modalities is required.