DNA Methylation in Solid Tumors: Functions and Methods of Detection

Martisova, Andrea; Holcakova, Jitka; Izadi, Nasim; Sebuyoya, Ravery; Hrstka, Roman; Bartošík, Martin

doi:10.3390/ijms22084247

Cited by 81 publications

(53 citation statements)

References 143 publications

(152 reference statements)

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“…First, owing to the 5mC regulators being critical in the progression of cancer [ 33 , 34 , 35 ], we recognized 21 5mC regulatory genes by consulting the literature [ 31 , 36 ]. The mRNA expression of 21 5mC regulatory genes and 13413 lncRNAs were downloaded from the TCGA database.…”

Section: Resultsmentioning

confidence: 99%

5mC-Related lncRNAs as Potential Prognostic Biomarkers in Colon Adenocarcinoma

Huang

Wang

et al. 2022

Biology

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Globally, colon adenocarcinoma (COAD) is one of the most frequent types of malignant tumors. About 40~50% of patients with advanced colon adenocarcinoma die from recurrence and metastasis. Long non-coding RNAs (lncRNAs) and 5-methylcytosine (5mC) regulatory genes have been demonstrated to involve in the progression and prognosis of COAD. The goal of this study was to explore the biological characteristics and potential predictive value of 5mC-related lncRNA signature in COAD. In this research, The Cancer Genome Atlas (TCGA) was utilized to obtain the expression of genes and somatic mutations in COAD, and Pearson correlation analysis was used to select lncRNAs involved in 5mC-regulated genes. Furthermore, we applied univariate Cox regression and Lasso Cox regression to construct 5mC-related lncRNA signature. Then Kaplan–Meier survival analysis, principal components analysis (PCA), receiver operating characteristic (ROC) curve, and a nomogram were performed to estimate the prognostic effect of the risk signature. GSEA was utilized to predict downstream access of the risk signature. Finally, the immune characteristics and immunotherapeutic signatures targeting this risk signature were analyzed. In the results, we obtained 1652 5mC-related lncRNAs by Pearson correlation analysis in the TCGA database. Next, we selected a risk signature that comprised 4 5mC-related lncRNAs by univariate and Lasso Cox regression. The prognostic value of the risk signature was proven. Finally, the biological mechanism and potential immunotherapeutic response of the risk signature were identified. Collectively, we constructed the 5mC-related lncRNA risk signature, which could provide a novel prognostic prediction of COAD patients.

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Section: Resultsmentioning

confidence: 99%

5mC-Related lncRNAs as Potential Prognostic Biomarkers in Colon Adenocarcinoma

Huang

Wang

et al. 2022

Biology

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“…In advances in CC knowledge, genomics has served to clarify mutations/polymorphisms that generate susceptibility to the development of the disease, and the effect of DNA methylation in CpG-rich promoter regions, such as hypomethylation, general loss of methylation during CC carcinogenesis, and gene silencing by hypermethylation of tumor suppressor genes [140].…”

Section: Genomicsmentioning

confidence: 99%

“…It is heritable and does not change the DNA sequence. Hypermethylation of tumor suppressor genes has been widely characterized as one of the first steps in human carcinogenesis [140].…”

Section: Genomicsmentioning

confidence: 99%

Understanding Cervical Cancer through Proteomics

Martínez-Rodríguez

Limones-González

Mendoza-Almanza

et al. 2021

Cells

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Cancer is one of the leading public health issues worldwide, and the number of cancer patients increases every day. Particularly, cervical cancer (CC) is still the second leading cause of cancer death in women from developing countries. Thus, it is essential to deepen our knowledge about the molecular pathogenesis of CC and propose new therapeutic targets and new methods to diagnose this disease in its early stages. Differential expression analysis using high-throughput techniques applied to biological samples allows determining the physiological state of normal cells and the changes produced by cancer development. The cluster of differential molecular profiles in the genome, the transcriptome, or the proteome is analyzed in the disease, and it is called the molecular signature of cancer. Proteomic analysis of biological samples of patients with different grades of cervical intraepithelial neoplasia (CIN) and CC has served to elucidate the pathways involved in the development and progression of cancer and identify cervical proteins associated with CC. However, several cervical carcinogenesis mechanisms are still unclear. Detecting pathologies in their earliest stages can significantly improve a patient’s survival rate, prognosis, and recurrence. The present review is an update on the proteomic study of CC.

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“…DNA methylation is another epigenetic mechanism that has been extensively investigated in the process of cervical carcinogenesis. Most studies used LBC samples to examine the methylation profiles of promoters of tumor suppressor genes in CC [ 60 , 61 ], as well as LSILs and HSILs [ 62 , 63 ]. Methylation rates usually correlated with the disease stage (being highest in invasive carcinomas).…”

Section: Cervical Precancerous Lesionsmentioning

confidence: 99%

New Trends in the Detection of Gynecological Precancerous Lesions and Early-Stage Cancers

Holcakova

Bartošík

Anton

et al. 2021

Cancers

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The prevention and early diagnostics of precancerous stages are key aspects of contemporary oncology. In cervical cancer, well-organized screening and vaccination programs, especially in developed countries, are responsible for the dramatic decline of invasive cancer incidence and mortality. Cytological screening has a long and successful history, and the ongoing implementation of HPV triage with increased sensitivity can further decrease mortality. On the other hand, endometrial and ovarian cancers are characterized by a poor accessibility to specimen collection, which represents a major complication for early diagnostics. Therefore, despite relatively promising data from evaluating the combined effects of genetic variants, population screening does not exist, and the implementation of new biomarkers is, thus, necessary. The introduction of various circulating biomarkers is of potential interest due to the considerable heterogeneity of cancer, as highlighted in this review, which focuses exclusively on the most common tumors of the genital tract, namely, cervical, endometrial, and ovarian cancers. However, it is clearly shown that these malignancies represent different entities that evolve in different ways, and it is therefore necessary to use different methods for their diagnosis and treatment.

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DNA Methylation in Solid Tumors: Functions and Methods of Detection

Cited by 81 publications

References 143 publications

5mC-Related lncRNAs as Potential Prognostic Biomarkers in Colon Adenocarcinoma

5mC-Related lncRNAs as Potential Prognostic Biomarkers in Colon Adenocarcinoma

Understanding Cervical Cancer through Proteomics

New Trends in the Detection of Gynecological Precancerous Lesions and Early-Stage Cancers

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