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Naturally Occurring Histone Deacetylase (HDAC) Inhibitors in the Treatment of Cancers
Published in Namrita Lall, Medicinal Plants for Cosmetics, Health and Diseases, 2022
Sujatha Puttalingaiah, Murthy V. Greeshma, Mahadevaswamy G. Kuruburu, Venugopal R. Bovilla, SubbaRao V. Madhunapantula
Epigenetic regulation of gene expression is one of the key mechanisms by which the expression of genes is controlled through the modification of histones (Stephens et al., 2013). Histones are a family of basic proteins (11,300–15,400 Daltons) found as a part of the nucleosome, which is the fundamental structural and functional unit of the chromatin (Kujirai et al., 2016). Nucleosomes are disc-shaped particles of 11 nm in diameter with a 5.7 nm height and are made up of 146 base pairs of DNA consisting of eight histone proteins viz., H2A, H2B, H3, H4 (2 units of each), and appear as beads on a string (McGinty and Tan, 2015).
Genetics at the Cell Level
Published in Carlos Simón, Carmen Rubio, Handbook of Genetic Diagnostic Technologies in Reproductive Medicine, 2022
Valentina Lorenzi, Roser Vento-Tormo
Because single-cell sequencing methods require cells to be dissociated, information about the spatial location of each cell within the tissue of origin is inevitably lost. Knowledge of how the cells are spatially organized in the tissue, however, is crucial to fully understanding cellular identity. Indeed, both the “absolute” location of a cell within the tissue and its relative position compared to other cells are often linked to the cell's function. Combining such information with single-cell gene expression data, measured by RNA-seq, also allows the inference of complex interactions, such as cell-cell communication. Currently, scRNA-seq data can be integrated with either image-based or sequencing-based spatial data.
RNA-seq Analysis
Published in Altuna Akalin, Computational Genomics with R, 2020
Gene expression is a term used to describe the contribution of a gene to the overall functions and phenotype of a cell through the activity of the molecular products, which are encoded in the specific nucleotide sequence of the gene. RNA is the primary product encoded in a gene, which is transcribed in the nucleus of a cell. A class of RNA molecules, messenger RNAs, are transported from the nucleus to the cytoplasm, where the translation machinery of the cell translates the nucleotide sequence of the mRNA into proteins. The functional protein repertoire in a given cell is the primary factor that dictates the shape, function, and phenotype of a cell. Due to the prime roles of proteins for a cell’s fate, most molecular biology literature is focused on protein-coding genes. However, a bigger proportion of a eukaryotic gene repertoire is reserved for non-coding genes, which code for RNA molecules that are not translated into proteins, yet carry out many important cellular functions. All in all, the term gene expression refers to the combined activity of protein-coding or non-coding products of a gene.
Overview of gene expression techniques with an emphasis on vitamin D related studies
Published in Current Medical Research and Opinion, 2023
Jeffrey Justin Margret, Sushil K. Jain
Several studies have compared the gene expression patterns between different cell types. The effect of astemizole treatment in mice showed similar gene expression patterns in heart tissue and PBMC48. Min et al.49 studied gene expression patterns in five different cell types from six individuals and found higher gene expression in PAXgene cells (cells that stabilize intercellular RNA of all cell types in WB) than in others, suggesting the suitability of PAXgene cells for large scale epidemiological studies. Most of the genes were expressed differently across three RNAs isolated from lymphoblastoid cell lines (LCL), WB using PAXgene tubes, and PBMC studied to identify the biomarkers related to cardiovascular disease. However, their association with each of the traits was also different, which emphasizes the importance of selecting suitable cells for gene expression studies50. Gene expression profiling of advanced heart failure patients showed similar patterns in WB and PBMC. Although PBMC was more accurate in predicting high-risk groups, WB cells were better at predicting moderate and high-risk groups51.
Association between the Genetic Polymorphisms of CCL2, CCL5, CCL8, CCR2, and CCR5 with Chronic Hepatitis C Virus Infection in the Chinese Han Population
Published in Immunological Investigations, 2022
Lin-Nan Shao, Shi-Hang Zhou, Ni Wang, Shu-Ting Zhang, Ming Liu
Transcriptional factors regulate gene expression by binding to the promoter region (Sun et al. 2017). To further clarify the association between rs1024610 polymorphism in the CCL2 promoter region and CCL2 production, we performed transient transfection studies. In dual-luciferase reporter assays, the luciferase activity associated with the rs1024610 allele T construct was higher than that associated with the A allele construct, although this difference was not statistically significant (P = .072). This finding is consistent with our previous results showing that rs1024610 does not influence plasma levels of CCL2. Nevertheless, prediction of potential transcription factors using the online software, JASPAR (http://jaspar.genereg.net/), revealed that when the A allele was converted to T, the number of potential binding transcription factors increased from VENTX alone to VENTX and PAX3. Thus, we conjectured that the difference in luciferase activity may be more significant if HEK293 cells were stimulated by some ligands; however, further research is required to confirm this hypothesis.
Comparing immunotherapies to other frequently used treatments of gastric cancer
Published in Expert Review of Clinical Pharmacology, 2021
Debora Basile, Francesca Simionato, Lorenzo Calvetti, Alessandro Cappetta, Annalisa Pesavento, Marta Mongillo, Giandomenico Roviello, Gerardo Rosati, Gemma Rossi, Giuseppe Aprile
Gene expression profile consists of genes in a cell with a peculiar signature indicative of immune responses. In melanoma and non-small-lung cancer patients, the gene expression profile of IFN- gamma signaling was associated with response to checkpoint inhibitors [115,116]. Several trials have also evaluated the role of a gene signature in GC patients. In the KEYNOTE-012 trial, the IFN-gamma signature tested in melanoma patients has been tested. No statistical improvement was observed in terms of ORR; however, a trend toward better response was reported in patients with high expression [117]. Interestingly, in the KEYNOTE-059, the INF-gamma signature was associated with ORR in patients receiving pembroliuzmab [18]. Similar results were shown in the Check-mate032 by analyzing a four-gene inflammatory signature [109].