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Identifying Breast Cancer Treatment Biomarkers Using Transcriptomics
Published in Shazia Rashid, Ankur Saxena, Sabia Rashid, Latest Advances in Diagnosis and Treatment of Women-Associated Cancers, 2022
Since DNA methylation changes can enhance DNA damage processes in our genome. Therefore, tracing DNA damage or repair-related pathways in differentially methylated regions with simple analysis like gene set enrichment analysis can provide a bird’s-eye view of the carcinogenic gene action or pathways (Subramanian et al., 2005).
Methods in molecular exercise physiology
Published in Adam P. Sharples, James P. Morton, Henning Wackerhage, Molecular Exercise Physiology, 2022
Adam P. Sharples, Daniel C. Turner, Stephen Roth, Robert A. Seaborne, Brendan Egan, Mark Viggars, Jonathan C. Jarvis, Daniel J. Owens, Jatin G. Burniston, Piotr P. Gorski, Claire E. Stewart
DNA sequencing reads are then separated by the unique index used during library preparation, to ascertain which data (or DNA reads) is derived from which experimental sample. Once collated, these DNA reads are then ready to undergo computational pipelines, which will commonly follow processes outlined below: Initial quality control of the sequencing reads to ensure that the sequencing process was performed adequately.Trimming of sequencing reads to remove misleading, biased or poor-quality parts of each DNA sequencing read, so that only a region of high-quality reliable data is left on each sequencing read.Alignment to the genome of interest (e.g. humans/homo sapiens, mouse/mus musculus).Followed by experiment-specific analyses. This may include the identification of differentially methylated regions (DMRs) and differentially methylated CpG sites (DMCpGs), also known as differentially methylation positions (DMPs) or loci (DML), between two different conditions and/or across different time points.
Beckwith–Wiedemann Syndrome
Published in Dongyou Liu, Handbook of Tumor Syndromes, 2020
Jirat Chenbhanich, Sirisak Chanprasert, Wisit Cheungpasitporn
Of the approximately 100 imprinted genes known to date, most are clustered together, with each cluster containing 2–15 genes and varying in size from <100 kb to several megabases [6]. The establishment of imprints—“the imprinting cycle”—is sophisticated and needs to be reset at each generation [8]. The expression of genes in the imprinting cluster is controlled by discreet DNA segments called imprinting control region (ICR). In the primordial germ cells, human epigenome undergoes extensive reprogramming, where global erasure of DNA methylation occurs and parent-specific imprints are removed. During gametogenesis, ICRs are differentially methylated in either paternal or maternal germline. Following fertilization, these marked regions are robustly protected against a wave of genome-wide demethylation and subsequent de novo methylation. These differentially methylated regions later regulate the paternally or maternally expressed alleles of many genes in the same region during human development. Dysregulation of imprinting will result in imprinting disorders, of which the most well-known are 15q11-13-associated Prader–Willi syndrome and Angelman syndrome, and 11p15.5-associated BWS and Silver−Russell syndrome.
Dysregulated translational factors and epigenetic regulations orchestrate in B cells contributing to autoimmune diseases
Published in International Reviews of Immunology, 2023
Ming Yang, Ping Yi, Jiao Jiang, Ming Zhao, Haijing Wu, Qianjin Lu
DNA methylation of HLA-DRB1 in MS monocytes could mediate genetic susceptibility to MS [224]. Numerous differentially methylated positions (DMPs) were found in B cells of MS patients, followed by monocytes and T cells [225]. It has been reported that DMPs (hypermethylation) are located in promoters of lymphotoxin alpha (LTA) locus of B cells, and smaller differentially methylated regions (DMRs) localize in four MS-related genes (SLC44A2, LTBR, CARD11 and CXCR5), suggesting the association of DNA methylation with MS risk and therapeutic response [42]. High disease heterogeneous results in low reproducibility of DMPs, so larger cohort studies are needed to validate specific locus and understand potential significance in treatment. Furthermore, upregulated hsa-miR-424 downregulated IRF1 and CXCL10 in CD19+B cells, that could suppress proliferation and promote apoptosis, according to a transcriptome analysis focusing on therapy-free RRMS patients [57].
Searching for DNA methylation in patients triple-negative breast cancer: a liquid biopsy approach
Published in Expert Review of Molecular Diagnostics, 2023
Irsa Shoukat, Christopher R. Mueller
In one study, DNA methylation profiling stratified TNBC into three distinct clusters associated with better or worse prognosis and identified differentially methylated regions (DMRs) associated with overall survival[69]. Between the three, the hypomethylated cluster was associated with better survival within the first five years post-diagnosis, while the medium-methylated profile had the worst survival (n = 73). This assay was validated using data on breast tumor samples from The Cancer Genome Atlas project (TCGA) Illumina 450k breast cohort and could stratify TNBCs and non-TNBCs with a sensitivity of 0.72, specificity of 0.94 and area under the curve (AUC) (receiver operating characteristic) of 0.90[78]. Delving deeper, the same group identified altered DNA methylation in TNBC-specific genes that leads to progression of secondary disease[79]. These studies were some of the first to highlight that DNA methylation could be used to stratify TNBC subtypes and provide prognostic indicators; however, it requires tissue sampling and warrants further clinical investigation in larger independent cohort studies.
Long non-coding RNA MEG3 and its genetic variant rs941576 are associated with rheumatoid arthritis pathogenesis in Egyptian patients
Published in Archives of Physiology and Biochemistry, 2022
Alaa S. Wahba, Maha E. Ibrahim, Noha M. Mesbah, Samy M. Saleh, Dina M. Abo-elmatty, Eman T. Mehanna
Maternally expressed gene 3 (MEG3) is a tumour suppressor lncRNA of the imprinted Delta-like homolog 1 (DLK1)–MEG3 locus which is located on human 14q32 chromosome (Benetatos et al.2011). This locus contains paternally expressed protein-coding genes, DLK1, Retrotransposon-like protein 1(RTL1) and thyroxine 5-deiodinase (DIO3) and maternally expressed non-coding RNAs, consisting of the lncRNA MEG3, several microRNAs and small nucleolar RNAs (da Rocha et al.2008). Methylation of two differentially methylated regions (DMRs) on the paternal allele, one located upstream of the MEG3 transcription start site (IG-DMR), and the other overlapping with the promoter of the MEG3 (MEG3-DMR) maintains reciprocal imprinting between protein-coding genes and non-coding RNAs (Benetatos et al.2011).