Methylation Status of Immune Response Genes Promoters in Cell-Free DNA Differs in Hemodialyzed Patients with Diabetic Nephropathy According to the Intensity of Anemia Therapy

2013 ◽  
Vol 36 (3-4) ◽  
pp. 280-286 ◽  
Author(s):  
Marie Korabecna ◽  
Eva Pazourkova ◽  
Ales Horinek ◽  
Magdalena Mokrejsova ◽  
Vladimir Tesar
Keyword(s):  
Immune Response ◽  
Diabetic Nephropathy ◽  
Methylation Status ◽  
Cell Free Dna ◽  
Immune Response Genes ◽  
Free Dna

Alterations in methylation status of immune response genes promoters in cell-free DNA during a hemodialysis procedure

2012 ◽  
Vol 12 (sup1) ◽  
pp. S27-S33 ◽  
Author(s):  
Marie Korabecna ◽  
Eva Pazourkova ◽  
Ales Horinek ◽  
Magdalena Mokrejsova ◽  
Vladimir Tesar
Keyword(s):  
Immune Response ◽  
Methylation Status ◽  
Cell Free Dna ◽  
Immune Response Genes ◽  
Free Dna

304-OR: 5-Hydroxymethylcytosines in Circulating Cell-Free DNA Reveal Diabetic Nephropathy

Diabetes ◽  
2020 ◽  
Vol 69 (Supplement 1) ◽  
pp. 304-OR
Author(s):  
CHANG ZENG ◽  
YING YANG ◽  
ZHOU ZHANG ◽  
CHUAN HE ◽  
WEI ZHANG ◽  
...  
Keyword(s):  
Diabetic Nephropathy ◽  
Cell Free Dna ◽  
Free Dna ◽  
Circulating Cell Free Dna

Methylation of FBN1, SPG20, ITF2, RUNX3, SNCA, MLH1, and SEPT9 genes in circulating cell-free DNA as biomarkers of colorectal cancer

2021 ◽  
pp. 1-30
Author(s):  
Maryam Alizadeh-Sedigh ◽  
Mohammad Sadegh Fazeli ◽  
Habibollah Mahmoodzadeh ◽  
Shahin Behrouz Sharif ◽  
Ladan Teimoori-Toolabi
Keyword(s):  
Colorectal Cancer ◽  
Early Detection ◽  
Diagnostic Performance ◽  
Methylation Status ◽  
Melting Curve ◽  
Melting Curve Analysis ◽  
Promoter Regions ◽  
Cell Free Dna ◽  
Free Dna ◽  
Tumor Tissues

BACKGROUND: Investigating aberrant tumor-specific methylation in plasma cell-free DNA provides a promising and noninvasive biomarker for cancer detection. OBJECTIVE: We aimed to investigate methylation status of some promoter regions in the plasma and tumor tissues to find biomarkers for early detection of colorectal cancer. METHODS: This case-control study on seventy colorectal cancer patients and fifty matched healthy controls used Methylation-Specific High-Resolution Melting Curve analysis to evaluate the methylation of the selected promoter regions in converted genomic tissue DNA and plasma cfDNA. RESULTS: The methylation levels in selected regions of SPG20 (+24375 to +24680, +24209 to +24399, and +23625 to +23883), SNCA (+807 to +1013, +7 to +162, and -180 to +7), FBN1 (+223 to +429, +1 to +245, and -18 to -175), ITF2 (+296 to +436 and -180 to +55), SEPT9 (-914412 to -91590 and -99083 to -92264), and MLH1 (-13 to +22) were significantly higher in tumor tissues compared with normal adjacent tissues. The methylation levels of FBN1, ITF2, SNCA, and SPG20 promoters were significantly higher in the patient’s plasma compared to patient’s normal tissue and plasma of healthy control subjects. FBN1, SPG20, and SEPT9 promoter methylation had a good diagnostic performance for discriminating CRC tissues from normal adjacent tissues (AUC > 0.8). A panel of SPG20, FBN1, and SEPT9 methylation had a higher diagnostic value than that of any single biomarker and other panels in tissue-based assay (AUC > 0.9). The methylation of FBN1(a) and SPG20(a) regions, as the closest region to the first coding sequence (CDS), had a good diagnostic performance in plasma cfDNA (AUC > 0.8) while a panel consisted of FBN1(a) and SPG20(a) regions showed excellent diagnostic performance for CRC detection in plasma cfDNA (AUC > 0.9). CONCLUSION: Methylation of FBN1(a) and SPG20(a) promoter regions in the plasma cfDNA can be an excellent simple, non-invasive blood-based test for early detection of CRC.

scholarly journals Methylation status and long‐fragment cell‐free DNA are prognostic biomarkers for gastric cancer

2021 ◽  
Author(s):  
Kazuhide Ko ◽  
Yoshikazu Kananazawa ◽  
Takeshi Yamada ◽  
Daisuke Kakinuma ◽  
Kunihiko Matsuno ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Methylation Status ◽  
Prognostic Biomarkers ◽  
Cell Free Dna ◽  
Free Dna

scholarly journals Exploration of Euchromatin Cell-Free DNA Methylation in Breast Cancer

2020 ◽  
pp. 1-3
Author(s):  
Chen-Hsiung Yeh ◽  
Keyword(s):  
Breast Cancer ◽  
Dna Methylation ◽  
Genomic Dna ◽  
Methylation Status ◽  
Active Regions ◽  
Breast Cancer Patients ◽  
Plasma Dna ◽  
Cell Free Dna ◽  
Cancer Management ◽  
Free Dna

Circulating cell-Free DNA (cfDNA) is emerging as a non-invasive liquid biopsy biomarker for personalized and precision cancer management. While extensive tissue-based DNA methylation profiling at global and gene levels have been documented, studies regarding methylation status of cfDNA at the sub-genome scale as well as correlation with that of tissue-derived genomic DNA have yet to be explored. The ability to specifically interrogate DNA methylation status of the transcriptionally active regions within chromosomes, i.e., euchromatin, not only fulfills the knowledge gap but also provides a much needed longitudinal and real-time insight for early cancer detection and intervention. We have developed a proprietary technology for selective enrichment of euchromatin cfDNA and analyzed the 5-methylcytosine (5-mC) content in these circulating nucleocomplexes. Paired tissue and plasma DNA (n=28) were obtained from breast cancer patients at various stages with ages and genders matched to the control arm (n=21). Quantitative measurement of DNA methylation was determined by ELISA-based assays. Our results revealed significant lower methylation levels from breast cancer cohort as compared to the cancer-free group (P<0.01). Most importantly, the methylation quantification dataset from euchromatin cfDNA strongly correlated with that of tissue genomic DNA (R²=0.72). This is the first report on euchromatin cfDNA methylation and provides promising outcomes for its future clinical application

scholarly journals Association of plasma cell-free DNA with survival in patients with IDH wild-type glioblastoma

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Stephen J Bagley ◽  
Jacob Till ◽  
Aseel Abdalla ◽  
Hareena K Sangha ◽  
Stephanie S Yee ◽  
...  
Keyword(s):  
Plasma Cell ◽  
Dna Methyltransferase ◽  
Methylation Status ◽  
Progression Free Survival ◽  
Wild Type ◽  
Cell Free Dna ◽  
Free Survival ◽  
Methylguanine Dna Methyltransferase ◽  
Free Dna ◽  
Post Hoc

Abstract Background We aimed to determine whether plasma cell-free DNA (cfDNA) concentration is associated with survival in patients with isocitrate dehydrogenase (IDH) wild-type glioblastoma (GBM). Methods Pre-operative and post-chemoradiotherapy blood samples were prospectively collected from patients with newly diagnosed IDH wild-type GBM. Patients underwent surgical resection or biopsy and received adjuvant radiotherapy with concomitant temozolomide. Cell-free DNA (cfDNA) was isolated from plasma and quantified using SYBR Green-based q polymerase chain reaction (qPCR). Results Sixty-two patients were enrolled and categorized into high vs. low cfDNA groups relative to the pre-operative median value (25.2 ng/mL, range 5.7–153.0 ng/mL). High pre-operative cfDNA concentration was associated with inferior PFS (median progression-free survival (PFS), 3.4 vs. 7.7 months; log-rank P = .004; hazard ratio [HR], 2.19; 95% CI, 1.26–3.81) and overall survival (OS) (median OS, 8.0 vs. 13.9 months; log-rank P = .01; HR, 2.43; 95% CI, 1.19–4.95). After adjusting for risk factors, including O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation status, pre-operative cfDNA remained independently associated with PFS (HR, 2.70; 95% CI, 1.50–4.83; P = .001) and OS (HR, 2.65; 95% CI, 1.25–5.59; P = .01). Post-hoc analysis of change in cfDNA post-chemoradiotherapy compared to pre-surgery (n = 24) showed increasing cfDNA concentration was associated with worse PFS (median, 2.7 vs. 6.0 months; log-rank P = .003; HR, 4.92; 95% CI, 1.53–15.84) and OS (median, 3.9 vs. 19.4 months; log-rank P &lt; .001; HR, 7.77; 95% CI, 2.17–27.76). Conclusions cfDNA concentration is a promising prognostic biomarker for patients with IDH wild-type GBM. Plasma cfDNA can be obtained noninvasively and may enable more accurate estimates of survival and effective clinical trial stratification.

scholarly journals A serum-based DNA methylation assay provides accurate detection of glioma

2021 ◽  
Author(s):  
Thais Sabedot ◽  
Tathiane Malta ◽  
James Snyder ◽  
Kevin Nelson ◽  
Michael Wells ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Liquid Biopsy ◽  
Somatic Mutations ◽  
Methylation Status ◽  
Experimental Treatment ◽  
Cell Free Dna ◽  
Invasive Approach ◽  
Non Invasive ◽  
Free Dna

Abstract Background The detection of somatic mutations in cell-free DNA (cfDNA) from liquid biopsy has emerged as a non-invasive tool to monitor the follow-up of cancer patients. However, the significance of cfDNA clinical utility remains uncertain in patients with brain tumors, primarily because of the limited sensitivity cfDNA has to detect real tumor-specific somatic mutations. This unresolved challenge has prevented accurate follow-up of glioma patients with non-invasive approaches. Methods Genome-wide DNA methylation profiling of tumor tissue and serum cell-free DNA of glioma patients. Results Here, we developed a non-invasive approach to profile the DNA methylation status in the serum of patients with gliomas and identified a cfDNA-derived methylation signature that is associated with the presence of gliomas and related immune features. By testing the signature in an independent discovery and validation cohorts, we developed and verified a score metric (the “glioma epigenetic liquid biopsy score” or GeLB) that optimally distinguished patients with or without glioma (sensitivity: 100%, specificity: 97.78%). Furthermore, we found that changes in GeLB score reflected clinicopathological changes during surveillance (e.g., progression, pseudoprogression or response to standard or experimental treatment). Conclusions Our results suggest that the GeLB score can be used as a complementary approach to diagnose and follow up patients with glioma.

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