GLAD-PCR Assay of DNA Methylation Markers Associated with Colorectal Cancer

Evdokimov, Alexey A.; Нетесова, Н. А.; Сметанникова, Н. А.; Abdurashitov, M. A.; Akishev, A G

doi:10.4172/0974-8369.1000342

Cited by 5 publications

(8 citation statements)

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“…The list of genes with aberrant methylated sites in tumors of gastric cancer ( Table 3 ) significantly differs from the earlier obtained list of genes in colorectal cancer [ 13 ]. The sfrp2 gene is an exception; its regulatory region’s methylation in tumor DNA is observed in both cases with almost the same frequency (72% for colorectal cancer).…”

Section: Discussionmentioning

confidence: 59%

“…Identification of RCGY sites in DNA from GC tissues for a GLAD-PCR analysis. At this step, we used ten random DNA samples from gastric cancer tissues to select the most frequently methylated RCGY sites within the regulatory regions of tumor suppressor genes as described earlier [ 12 , 13 ]…”

Section: Resultsmentioning

confidence: 99%

“…Tissue samples obtained during surgery were placed in a test tube containing a RNA-later solution and refrigerated for 24 h at +4°C, then transferred to a freezer and stored at –20°C [ 12 ].…”

Section: Methodsmentioning

confidence: 99%

“…By using hybrid primers corresponding to the terminal tetranucleotides obtained after the hydrolysis of the NNR(5mC)↓GYNN sequence, all RCGY sites – located within ~ 200 bp of the hybridization site of the fluorescent probe – in the regulatory region of each gene were analyzed. The lowest cycle threshold (Cq) value meant maximum methylation of the R(5mC)GY site [ 12 , 13 ].…”

Section: Methodsmentioning

confidence: 99%

“…Recently, we have studied the methylation of the tumor suppressor genes in DNA samples derived from colorectal cancer tissues using the GLAD-PCR assay. Abnormal methylation of the RCGY sites in the fbn1 , cnrip1 , adhfe1 , ryr2 , sept9I , and eid3 genes was proved for more than 75% of the tumor DNA samples [ 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

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GLAD-PCR assay of R(5mC)GY sites in the regulatory region of tumor-suppressor genes associated with gastric cancer

et al. 2020

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At early stages of carcinogenesis, the regulatory regions of some tumor suppressor genes become aberrantly methylated at RCGY sites, which are substrates of DNA methyltransferase Dnmt3. Identification of aberrantly methylated sites in tumor DNA is considered to be the first step in the development of epigenetic PCR test systems for early diagnosis of cancer. Recently, we have developed a GLAD-PCR assay, a method for detecting the R(5mC)GY site in the genome position of interest even at significant excess of DNA molecules with a non-methylated RCGY site in this location. The aim of the present work is to use the GLAD-PCR assay to detect the aberrantly methylated R(5mC)GY sites in the regulatory regions of tumor suppressor genes (brinp1, bves, cacna2d3, cdh11, cpeb1, epha7, fgf2, galr1, gata4, hopx, hs3st2, irx1, lrrc3b, pcdh10, rprm, runx3, sfrp2, sox17, tcf21, tfpi2, wnt5a, zfp82, and znf331) in DNA samples obtained from gastric cancer (GC) tissues. The study of the DNA samples derived from 29 tumor and 25 normal gastric tissue samples demonstrated a high diagnostic potential of the selected RCGY sites in the regulatory regions of the irx1, cacna2d3, and epha7 genes; the total indices of sensitivity and specificity for GC detection being 96.6% and 100%, respectively.

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Section: Discussionmentioning

confidence: 59%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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GLAD-PCR assay of R(5mC)GY sites in the regulatory region of tumor-suppressor genes associated with gastric cancer

et al. 2020

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Molecular subtypes based on DNA methylation predict prognosis in colon adenocarcinoma patients

Yang

2019

Aging

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Tumor heterogeneity makes early diagnosis and effective treatment of colon adenocarcinoma difficult. As an important regulator of gene expression, DNA methylation can influence tumor heterogeneity. In this study, we explored the prognostic value of subtypes based on DNA methylation status in 424 colon adenocarcinoma samples from the Cancer Genome Atlas database. Differences in DNA methylation levels were associated with differences in T, N, and M category, age, stage, and prognosis. Seven subgroups were identified based on consensus clustering using 356 CpG sites that significantly influenced survival. Finally, a prognostic model was constructed and used to classify samples in a testing dataset into seven DNA methylation subgroups based on the classification results of a training dataset. These specific classifications based on DNA methylation may help account for heterogeneity within previously established molecular subgroups of colon adenocarcinoma and could potentially aid in the development of more effective personalized treatments.

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Genistein exerts anti-colorectal cancer actions: clinical reports, computational and validated findings

Liu

Lan

Zhang

et al. 2023

Aging

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Colorectal cancer (CRC) is presently a health challenge in China. Although clinical chemotherapy is prescribed availably, the negative effects and poor prognoses still occur. Genistein has antitumor properties in our previous studies. However, the molecular mechanisms underlying the anti-CRC effects of genistein remain unclear. Increasing evidences have indicated that the induction of autophagy, one of cell death models, is closely associated with the formation and development of human cancer. In the current study, a systematic bioinformatics approach using network pharmacology and molecular docking imitation was aimed at identifying the pharmacological targets and anti-CRC mechanisms of genistein, characterized by autophagy-related processes and pathways. Moreover, experimental validation was conducted by using clinical and cell culture samples. All 48 potential targets of genistein-anti-CRC-associated autophagy were screened accordingly. Further bioinformatics analyses identified 10 core genistein-anti-CRC targets related to autophagy, and enrichment-assayed results revealed that the biological processes of these core targets might regulate multiple molecular pathways, including the estrogen signaling pathway. Additionally, molecular docking data demonstrated that genistein has a high affinity for epidermal growth factor receptor (EGFR) and estrogen receptor 1 (ESR1). Both EGFR and ESR1 proteins were highly expressed in clinical CRC samples. Preliminary in vitro data showed that genistein effectively reduced cellular proliferation, activated apoptosis, and suppressed EGFR and ESR1 protein expressions in CRC cells. Our research findings uncovered the molecular mechanisms of genistein against CRC, and the potential drug targets associated with autophagy in genistein treatment of CRC were identified and validated experimentally, including EGFR and ESR1.

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GLAD-PCR Assay of DNA Methylation Markers Associated with Colorectal Cancer

Cited by 5 publications

References 0 publications

GLAD-PCR assay of R(5mC)GY sites in the regulatory region of tumor-suppressor genes associated with gastric cancer

GLAD-PCR assay of R(5mC)GY sites in the regulatory region of tumor-suppressor genes associated with gastric cancer

Molecular subtypes based on DNA methylation predict prognosis in colon adenocarcinoma patients

Genistein exerts anti-colorectal cancer actions: clinical reports, computational and validated findings

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