scholarly journals Assessing Gene Expression and Methylation of KMT2D and IGF2 Genes in Patients with Non-Small Cell Lung Cancer

2018 ◽  
Vol 7 (1) ◽  
pp. 55
Author(s):  
Arash Matin Ahmadi ◽  
Hessamodin Ghasemi ◽  
Sajad Nooshin ◽  
Zoofa Zayani ◽  
Shohreh Zare Karizi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Methylation Level ◽  
Cpg Islands ◽  
Regulation Of Gene Expression ◽  
Tumor Development ◽  
Gene Promoter ◽  
Cancer Tissue ◽  
Lung Carcinogenesis ◽  
Igf2 Gene

Background: Aberrant promoter methylation of CpG islands is an important mechanism for regulation of gene expression. Recent data suggest that epigenetic abnormalities may occur very early in lung carcinogenesis. Systemic methylation changes may be a diagnostic marker for tumor development or prognosis. In this study, the expression and methylation of KMT2D and IGF2 genes were investigated in the lung cancer tissue compared to the adjacent normal tissue.Methods: The status of methylation of KMT2D and IGF2 genes were investigated in 30 patients with NSCLC after genomic DNA extraction using bisulfite treatment and MS-HRM method and the expression of these genes were checked by Real-Time PCR method in same samples.Results: For KMT2D gene, the expression and methylation level increased in 46.6% and 6.67% (respectively) for tumor samples comparison with normal samples (P>0.05). Also, for IGF2 gene 50% tumor samples overexpressed and 50% tumor samples showed that reduced expression comparison with the normal samples (P>0.05). In addition, 96.66% of tumor tissues did not show any change in methylation level for IGF2 gene promoter (P>0.05).Conclusion: This study showed that expression and methylation level of KMT2D and IGF2 genes did not change in NSCLC tumor samples compared to normal samples. However, this study was designed as a pilot study, and further investigations are required to confirm our findings.

scholarly journals Changes in the methylation level of microRNA genes as a factor of breast cancer development and progression

2021 ◽  
pp. 4-11
Author(s):  
Е.А. Филиппова ◽  
А.М. Бурденный ◽  
С.С. Лукина ◽  
Н.А. Иванова ◽  
И.В. Пронина ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Methylation Level ◽  
Molecular Subtype ◽  
Regulation Of Gene Expression ◽  
Epigenetic Mechanism ◽  
Cancer Tissue ◽  
Aberrant Methylation ◽  
Suppressor Genes ◽  
Mirna Genes

Введение. Метилирование как процесс эпигенетической регуляции экспрессии генов является важнейшим в поддержании геномной стабильности. В норме этот процесс определяет подавление активности онкогенов и поддержание работы супрессоров опухолевого роста. Другим важнейшим эпигенетическим регулятором являются микроРНК. Нарушения метилирования CpG-островков в промоторных районах генов, кодирующих микроРНК, являются важнейшим фактором онкогенеза. Цель - расширение спектра генов микроРНК гиперметилируемых при раке молочной железы и изучение их связи с метастазированием и иммуногистохимическим статусом опухоли. Методика. В настоящей работе был проведен отбор ряда генов микроРНК, изменяющих уровень метилирования при раке молочной железы. Методом количественной метилспецифичной ПЦР на представительной выборке из 70 парных образцов рака молочной железы изучен уровень метилирования 8 генов микроРНК, ассоциированных с раком молочной железы: MIR107, MIR124-2, MIR1258, MIR130B, MIR137, MIR191, MIR203А, MIR339. Результаты. Показано статистически значимое увеличение уровня метилирования в опухолевой ткани РМЖ по сравнению с гистологически нормальной тканью молочной железы для генов MIR107, MIR124-2, MIR1258, MIR130В, MIR137, MIR339 и снижение уровня метилирования для гена MIR191. Кроме того, показано статистически значимое увеличение уровня метилирования на III-IV (поздних) стадиях РМЖ для генов MIR107, MIR1258, MIR130В, MIR137, MIR339, в опухолях с большим размером - MIR107, MIR1258, MIR130В, MIR137, MIR339, с низким уровнем дифференцировки - MIR124-2, с наличием метастазов в лимфатические узлы - MIR107, MIR1258, MIR137, MIR339. Опухоли, не экспрессирующие рецептор прогестерона (PR), имеют статистически значимо более высокий уровень метилирования генов MIR137, MIR339. Заключение. Таким образом, определены новые молекулярные показатели прогрессии РМЖ и биомаркеры, которые могут быть использованы при дифференциальной диагностике молекулярного подтипа РМЖ. Background. Methylation, as an epigenetic mechanism for regulation of gene expression, is crucial for the genome stability. Normally, this process is characterized by the ability to silence the oncogene activity and to support the action of suppressor genes. MicroRNAs (miRNAs) are another key epigenetic regulator of gene expression. Aberrant methylation of CpG islands in promoter regions of the genes that code miRNAs is the most important oncogenic factor. Aim. To expand the spectrum of miRNA genes hypermethylated in breast cancer and to study their relationship with metastasis and immunohistochemical status of the tumor. Methods. MiRNA tumor suppressor genes were selected that changed their methylation level in breast cancer patients. Using the method of quantitative methylation-specific PCR, the methylation level of eight miRNA genes associated with breast cancer was studied on a representative set of 70 paired breast cancer samples: MIR107, MIR124-2, MIR1258, MIR130B, MIR137, MIR191, MIR203A, and MIR339. Results. The methylation level of the genes MIR-107, MIR124-2, MIR1258, MIR130B, MIR137, MIR339 was significantly higher in breast cancer tissue compared to normal breast tissue whereas for the gene MIR191, it was significantly lower. Also, the methylation levels of genes MIR107, MIR1258, MIR130B, MIR137, and MIR339 were significantly increased at stages III-IV (advanced) breast cancer; in large tumors, the methylation levels were increased for MIR107, MIR1258, MIR130B, MIR137, and MIR339; in poorly differentiated tumors, the methylation level was increased for MIR124-2; and in the presence of lymph node metastases, for MIR107, MIR1258, MIR-137, and MIR-339. Tumors not expressing the progesterone receptor (PR) had a higher methylation level of MIR137 and MIR339. Conclusion. The study determined new molecular indicators for breast cancer progression and identified biomarkers that may be used in the differential diagnosis of breast cancer molecular subtype.

scholarly journals Role of microRNAs in Lung Carcinogenesis Induced by Asbestos

2021 ◽  
Vol 11 (2) ◽  
pp. 97
Author(s):  
Rakhmetkazhy Bersimbaev ◽  
Olga Bulgakova ◽  
Akmaral Aripova ◽  
Assiya Kussainova ◽  
Oralbek Ilderbayev
Keyword(s):  
Lung Cancer ◽  
Expression Profile ◽  
Regulation Of Gene Expression ◽  
International Agency ◽  
Oxygen Species ◽  
Lung Carcinogenesis ◽  
Mrna Targets ◽  
The World ◽  
Post Transcriptional Regulation

MicroRNAs are a class of small noncoding endogenous RNAs 19–25 nucleotides long, which play an important role in the post-transcriptional regulation of gene expression by targeting mRNA targets with subsequent repression of translation. MicroRNAs are involved in the pathogenesis of numerous diseases, including cancer. Lung cancer is the leading cause of cancer death in the world. Lung cancer is usually associated with tobacco smoking. However, about 25% of lung cancer cases occur in people who have never smoked. According to the International Agency for Research on Cancer, asbestos has been classified as one of the cancerogenic factors for lung cancer. The mechanism of malignant transformation under the influence of asbestos is associated with the genotoxic effect of reactive oxygen species, which initiate the processes of DNA damage in the cell. However, epigenetic mechanisms such as changes in the microRNA expression profile may also be implicated in the pathogenesis of asbestos-induced lung cancer. Numerous studies have shown that microRNAs can serve as a biomarker of the effects of various adverse environmental factors on the human body. This review examines the role of microRNAs, the expression profile of which changes upon exposure to asbestos, in key processes of carcinogenesis, such as proliferation, cell survival, metastasis, neo-angiogenesis, and immune response avoidance.

Signal Transducer and Activator of Transcription6 Signaling Pathway in Tumor-Associated Macrophage Aggravates Lung Cancer Progression

2021 ◽  
Vol 11 (9) ◽  
pp. 1707-1713
Author(s):  
Jun Wan ◽  
Jian Wang ◽  
Qiurong Huang ◽  
Guanggui Ding ◽  
Xiean Ling
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
T Cell ◽  
Cancer Progression ◽  
Cancer Tissue ◽  
M2 Macrophage ◽  
Normal Tissues ◽  
Tumor Associated Macrophage ◽  
M1 Macrophage ◽  
And Migration

Lung cancer is a most common cancer worldwide. Tumor-associated macrophage (TAM) is known a key effector cell in tumor microenvironment. Meanwhile, STAT6 is crucial to cancer development. We aimed to determine the interaction between STAT6 and TAMs in lung cancer. In this work, firstly, we established mouse model of lung cancer. Then, immunofluorescence was performed to determine STAT6 and CD206 level in lung cancer tissue and adjacent normal tissues as well as model mice. RT-qPCR was applied to detect differentiation of macrophage and determine related gene expression. After treatment of siRNA of STAT6 or STAT6 inhibitor (AS1517499), Transwell assay and MTT were used to determine cell proliferation and migration. STAT6 was upregulated in lung cancer tissues while arginase was more active in M2 macrophage rather than M1 macrophage. Transfection of si-STAT6 not only decreased differentiation in M2 macrophage but also inhibited proliferative, migratory and invasive ability of cancer cells while AS1517499 led to reduced tumor growth. STAT6 inhibition caused decreased expression of M2 macrophages. Similarly, intratumoral T cell markers showed that CD8+T cell gene expression and CD4-mediated T cell marker FoxP3 was increased slightly. Taken altogether, macrophage-STAT6 promotes cell migration and proliferation in lung cancer.

scholarly journals D-GPM: A Deep Learning Method for Gene Promoter Methylation Inference

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 807 ◽  
Author(s):  
Pan ◽  
Liu ◽  
Wen ◽  
Liu ◽  
Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Deep Learning ◽  
Promoter Methylation ◽  
Methylation Level ◽  
Target Genes ◽  
Gene Promoter ◽  
Support Vector ◽  
Whole Genome ◽  
Expression Levels ◽  
Gene Expression Levels

Whole-genome bisulfite sequencing generates a comprehensive profiling of the gene methylation levels, but is limited by a high cost. Recent studies have partitioned the genes into landmark genes and target genes and suggested that the landmark gene expression levels capture adequate information to reconstruct the target gene expression levels. This inspired us to propose that the methylation level of the promoters in landmark genes might be adequate to reconstruct the promoter methylation level of target genes, which would eventually reduce the cost of promoter methylation profiling. Here, we propose a deep learning model called Deep-Gene Promoter Methylation (D-GPM) to predict the whole-genome promoter methylation level based on the promoter methylation profile of the landmark genes from The Cancer Genome Atlas (TCGA). D-GPM-15%-7000 × 5, the optimal architecture of D-GPM, acquires the least overall mean absolute error (MAE) and the highest overall Pearson correlation coefficient (PCC), with values of 0.0329 and 0.8186, respectively, when testing data. Additionally, the D-GPM outperforms the regression tree (RT), linear regression (LR), and the support vector machine (SVM) in 95.66%, 92.65%, and 85.49% of the target genes by virtue of its relatively lower MAE and in 98.25%, 91.00%, and 81.56% of the target genes based on its relatively higher PCC, respectively. More importantly, the D-GPM predominates in predicting 79.86% and 78.34% of the target genes according to the model distribution of the least MAE and the highest PCC, respectively.

scholarly journals MKL-1 regulates the stem cell marker. CD44 in breast cancer cells

2019 ◽  
Vol 78 ◽  
pp. 01002
Author(s):  
Zhou-Tong Dai ◽  
Ao Yao ◽  
Yuan Xiang ◽  
Jia Peng Li ◽  
Wei Guo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Malignant Tumors ◽  
Regulation Of Gene Expression ◽  
Gene Promoter ◽  
Expression Regulation ◽  
Stem Cell Marker ◽  
Luciferase Reporter ◽  
Regulation Mechanism ◽  
Luciferase Reporter Gene ◽  
Factors Affecting

CD44, cluster of differentiation 44 is a typical marker of stem cells. At present, it has been found that CD44 is prevalent in various human malignant tumors, but its expression regulation mechanism is still not clear. The initiation of gene expression, the modification of RNA levels, and the regulation of protein levels are the main factors affecting the expression level of genes, and the most critical one is the regulation of gene expression by signaling pathways. Up to now, there has been no report on the role of MKL-1 in the cloning of the cd44 promoter. Therefore, this study intends to clone the cd44 gene promoter, construct its luciferase reporter gene vector, transfect the MKL-1 overexpression vector, and analyze how it affects transcriptional activity, in order to further study the expression regulation of cd44. The mechanism provides a powerful tool in the future.

scholarly journals A natural sequence consisting of overlapping glucocorticoid-responsive elements mediates glucocorticoid, but not androgen, regulation of gene expression

2000 ◽  
Vol 350 (1) ◽  
pp. 123-129 ◽  
Author(s):  
Charbel MASSAAD ◽  
Michèle GARLATTI ◽  
Elizabeth M. WILSON ◽  
Françoise CADEPOND ◽  
Robert BAROUKI
Keyword(s):  
Gene Expression ◽  
Thymidine Kinase ◽  
Transcriptional Activation ◽  
Regulation Of Gene Expression ◽  
Gene Promoter ◽  
Mobility Shift ◽  
Liver And Kidney ◽  
Androgen Regulation ◽  
Responsive Element ◽  
Half Site

Cytosolic aspartate aminotransferase (cAspAT) is regulated by glucocorticoids in rat liver and kidney. Part of this regulation is mediated by an unusual glucocorticoid-responsive element (GRE)-like sequence called GRE A. GRE A is composed of two overlapping imperfect GREs, each comprising a conserved half-site (half-sites 1 and 4 respectively) and a poorly conserved half-site (half-sites 2 and 3 respectively). The sequence binds co-operatively two dimers of the glucocorticoid receptor (GR) and mediates efficient glucocorticoid regulation of gene expression. Analysis of deletions of the cAspAT gene promoter and subcloning of GRE A upstream of the thymidine kinase promoter indicate that this sequence is responsive to glucocorticoids, but not to androgens. Electrophoretic mobility shift assays indicate that the GRE A unit does not bind the androgen receptor (AR). The modification of three nucleotides in the poorly conserved half-sites 2 and 3, converting GRE A into two overlapping high-affinity GREs (ov-cGRE), resulted in co-operative binding of the AR. Furthermore, ov-cGRE efficiently mediated androgen regulation of the thymidine kinase promoter. A single base modification in half-site 2 or 3 in GRE A allowed the binding of the AR as one or two dimers respectively, and restored transcriptional activation by androgens only in the latter case. Thus the poor affinity of the AR for half-sites 2 and 3 prevented its binding to GRE A, indicating that the overlapping GRE A sequence of the cAspAT gene promoter discriminates a glucocorticoid-mediated from an androgen-mediated response.

scholarly journals Methylation level of CpG islands in GGH gene promoter in pediatric acute leukemia

PLoS ONE ◽  
2017 ◽  
Vol 12 (3) ◽  
pp. e0173472 ◽  
Author(s):  
Yue Li ◽  
Sixi Liu ◽  
Huihui Wang ◽  
Huirong Mai ◽  
Xiuli Yuan ◽  
...  
Keyword(s):  
Acute Leukemia ◽  
Methylation Level ◽  
Cpg Islands ◽  
Gene Promoter

Aberrant Epigenetic Regulation: A Central Contributor to Lung Carcinogenesis and a New Therapeutic Target

2013 ◽  
pp. e295-e300
Author(s):  
Rosalyn A. Juergens ◽  
Charles M. Rudin
Keyword(s):  
Lung Cancer ◽  
Clinical Trial ◽  
Histone Deacetylase ◽  
Histone Deacetylase Inhibitors ◽  
Early Stage ◽  
Single Agent ◽  
Objective Response ◽  
Gene Promoter ◽  
Epigenetic Therapy ◽  
Lung Carcinogenesis

Carcinogenesis is driven by a combination of genetic and epigenetic abnormalities. Aberrancies in gene promoter methylation patterns and histone acetylation are associated with silencing of tumor suppressor genes in lung cancer and other solid tumors. Identification of key epigenetic modifications has been shown to be prognostic in early-stage non-small cell lung cancer. Previous clinical trials aimed at modifying the epigenome with single-agent demethylating agents or histone deacetylase inhibitors given at maximally tolerated doses have provided disappointing results. A recent clinical trial using a combination of a demethylating agent and a histone deacetylase inhibitor at “epigenetically targeted” doses concomitantly has shown promising results, including a patient with a complete objective response. Biomarkers associated with this clinical trial suggest that patients who undergo robust demethylation, as detected in the peripheral blood after a month on treatment, identifies those who gain the most benefit from this novel treatment strategy. Based on observations of unusually durable responses to subsequent therapy after administration of combined epigenetic therapy, epigenetic therapy may also play a role in “priming” patients to better respond to standard cytotoxic therapy or immunotherapy. This manuscript will review the data on the role of epigenetics in lung cancer and the history of epigenetic treatments in lung cancer spanning over the last 40 years.

scholarly journals Features of Methylation and Gene Expression in the Promoter-Associated CpG Islands Using Human Methylome Data

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Xin Du ◽  
Leng Han ◽  
An-Yuan Guo ◽  
Zhongming Zhao
Keyword(s):  
Gene Expression ◽  
Methylation Level ◽  
Cpg Island ◽  
Expression Patterns ◽  
Cpg Islands ◽  
Gc Content ◽  
Gene Markers ◽  
A Genome ◽  
Genome Level ◽  
Lower Ratio

CpG islands are typically located in the 5′end of genes and considered as gene markers because they play important roles in gene regulation via epigenetic change. In this study, we compared the features of CpG islands identified by several major algorithms by setting the parameter cutoff values in order to obtain a similar number of CpG islands in a genome. This approach allows us to systematically compare the methylation and gene expression patterns in the identified CpG islands. We found that Takai and Jones’ algorithm tends to identify longer CpG islands but with weaker CpG island features (e.g., lower GC content and lower ratio of the observed over expected CpGs) and higher methylation level. Conversely, the CpG clusters identified by Hackenberg et al.’s algorithm using stringent criteria are shorter and have stronger features and lower methylation level. In addition, we used the genome-wide base-resolution methylation profile in two cell lines to show that genes with a lower methylation level at the promoter-associated CpG islands tend to express in more tissues and have stronger expression. Our results validated that the DNA methylation of promoter-associated CpG islands suppresses gene expression at the genome level.

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