DNA methylation detection methods used in colorectal cancer

Zhan, Yuxia; Luo, Guanghua

doi:10.12998/wjcc.v7.i19.2916

Cited by 11 publications

(6 citation statements)

References 90 publications

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“…But what is interesting to note is that present research is directed towards identifying aberrant DNA methylation patterns. Detection of such CpG island methylator phenotype can be clinically used for early diagnosis as well as prognosis of colorectal cancer (Reviewed in [ 95 ]). Reduced DNA methylation in lymphocytes of healthy postmenopausal women have also been linked to folate deficiency [ 41 ].…”

Section: Maternal Dietary and Supplementary Intakesmentioning

confidence: 99%

DNA methylation and regulation of gene expression: Guardian of our health

Dhar

Saha

Mitra

et al. 2021

Nucleus

123

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One of the most critical epigenetic signatures present in the genome of higher eukaryotes is the methylation of DNA at the C-5 position of the cytosine ring. Based on the sites of DNA methylation in a locus, it can serve as a repressive or activation mark for gene expression. In a crosstalk with histone modifiers, DNA methylation can consequently either inhibit binding of the transcription machinery or generate a landscape conducive for transcription. During developmental phases, the DNA methylation pattern in the genome undergoes alterations as a result of regulated balance between de novo DNA methylation and demethylation. Resultantly, differentiated cells inherit a unique DNA methylation pattern that fine tunes tissue-specific gene expression. Although apparently a stable epigenetic mark, DNA methylation is actually labile and is a complex reflection of interaction between epigenome, genome and environmental factors prior to birth and during progression of life. Recent findings indicate that levels of DNA methylation in an individual is a dynamic outcome, strongly influenced by the dietary environment during germ cell formation, embryogenesis and post birth exposures. Loss of balances in DNA methylation during developmental stages may result in imprinting disorders, while at any later stage may lead to increased predisposition to various diseases and abnormalities. This review aims to provide an outline of how our epigenome is uniquely guided by our lifetime of experiences beginning in the womb and how understanding it better holds future possibilities of improvised clinical applications.

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Section: Maternal Dietary and Supplementary Intakesmentioning

confidence: 99%

DNA methylation and regulation of gene expression: Guardian of our health

Dhar

Saha

Mitra

et al. 2021

Nucleus

123

View full text Add to dashboard Cite

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“…The classical approach by quantitative real-time polymerase chain reaction (Methy-Light) evaluates hypermethylation in a five-marker panel ( CACNA1G , CDKN2A (p16), CRABP1 , MLH1 , and NEUROG1 ) [ 28 , 29 ]. However, the MS-MLPA technique has already been validated as a reliable and cost-effective method for CIMP assessing in CRC in several studies, with similar overall accuracy [ 30 , 31 , 32 , 33 ]. Moreover, MS-MLPA analyzes the same five markers as Methy-Light, adding IGF2, SOSC1 , and RUNX3 for CIMP analysis.…”

Section: Discussionmentioning

confidence: 99%

Effects of Somatic Methylation in Colonic Polyps on Risk of Developing Metachronous Advanced Colorectal Lesions

Murcia

Martínez-Roca

Juárez

et al. 2021

Cancers

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The utility of molecular markers for predicting the risk of metachronous advanced colorectal lesions (MACLs) remains poorly investigated. We examined the relationship between somatic hypermethylation in polyps at baseline and the risk of developing MACL. This retrospective cohort study included 281 consecutive patients with colonic polyps who were enrolled between 2007 and 2009 and followed-up until 2014. MACLs were defined as adenomas of ≥10 mm, high-grade dysplasia, or with a villous component; and serrated lesions of ≥10 mm or with dysplasia. In total, 595 polyps were removed at baseline colonoscopy and analyzed for pathological characteristics and CpG island methylator phenotype (CIMP) using the MS-MLPA (Methylation-Specific -- Multiplex Ligation-dependent Probe Amplification) technique. Forty-five patients (16.0%) showed at least one CIMP+ polyp. MACL risk was higher in patients with CIMP+ polyps (odds ratio (OR), 4.50; 95% CI, 1.78–11.4; p = 0.002). Patients with CIMP+ polyps also exhibited shorter time to MACL development (33.8 months vs. 50.1 months; p < 0.001), even with adjustment for polyp size and number (OR, 2.40; 95% CI, 1.33–4.34). Adding CIMP analysis improved the sensitivity (57.0% to 70.9%), negative predictive value (71.1% to 77.3%), and overall accuracy (49.8% to 52.0%) for MACL risk estimation. These results highlight that CIMP may be a useful marker for endoscopic surveillance.

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“…With the rapid development of complex molecular biology techniques (e.g., qRT-PCR, in situ hybridization (ISH), RNA/DNA sequencing, NGS, and DNA methylation detection methods), there is a constant search for new biomarkers of cellular proliferation with potential diagnostic, prognostic, and/or predictive significance in cancers including CRC [ 115 , 236 , 259 , 263 , 264 , 265 , 266 , 267 , 268 , 269 , 270 , 271 , 272 , 273 , 274 , 275 , 276 , 277 , 278 ].…”

Section: Methods To Assess Cell Proliferation In Colorectal Cancermentioning

confidence: 99%

“…Detection methods for DNA methylation in CRC include methylation-specific polymerase chain reaction (MSR), DNA sequencing (e.g., bisulfide sequencing, pyrosequencing), methylation-specific high resolution melting curve analysis (MS-HRM), and MethyLight assay (reviewed in [ 278 ]).…”

Section: Methods To Assess Cell Proliferation In Colorectal Cancermentioning

confidence: 99%

Prognostic Biomarkers of Cell Proliferation in Colorectal Cancer (CRC): From Immunohistochemistry to Molecular Biology Techniques

Kasprzak

2023

Cancers

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Colorectal cancer (CRC) is one of the most common and severe malignancies worldwide. Recent advances in diagnostic methods allow for more accurate identification and detection of several molecular biomarkers associated with this cancer. Nonetheless, non-invasive and effective prognostic and predictive testing in CRC patients remains challenging. Classical prognostic genetic markers comprise mutations in several genes (e.g., APC, KRAS/BRAF, TGF-β, and TP53). Furthermore, CIN and MSI serve as chromosomal markers, while epigenetic markers include CIMP and many other candidates such as SERP, p14, p16, LINE-1, and RASSF1A. The number of proliferation-related long non-coding RNAs (e.g., SNHG1, SNHG6, MALAT-1, CRNDE) and microRNAs (e.g., miR-20a, miR-21, miR-143, miR-145, miR-181a/b) that could serve as potential CRC markers has also steadily increased in recent years. Among the immunohistochemical (IHC) proliferative markers, the prognostic value regarding the patients’ overall survival (OS) or disease-free survival (DFS) has been confirmed for thymidylate synthase (TS), cyclin B1, cyclin D1, proliferating cell nuclear antigen (PCNA), and Ki-67. In most cases, the overexpression of these markers in tissues was related to worse OS and DFS. However, slowly proliferating cells should also be considered in CRC therapy (especially radiotherapy) as they could represent a reservoir from which cells are recruited to replenish the rapidly proliferating population in response to cell-damaging factors. Considering the above, the aim of this article is to review the most common proliferative markers assessed using various methods including IHC and selected molecular biology techniques (e.g., qRT-PCR, in situ hybridization, RNA/DNA sequencing, next-generation sequencing) as prognostic and predictive markers in CRC.

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DNA methylation detection methods used in colorectal cancer

Cited by 11 publications

References 90 publications

DNA methylation and regulation of gene expression: Guardian of our health

DNA methylation and regulation of gene expression: Guardian of our health

Effects of Somatic Methylation in Colonic Polyps on Risk of Developing Metachronous Advanced Colorectal Lesions

Prognostic Biomarkers of Cell Proliferation in Colorectal Cancer (CRC): From Immunohistochemistry to Molecular Biology Techniques

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