Correction to: Current status of development of methylation biomarkers for in vitro diagnostic IVD applications

Taryma-Leśniak, Olga; Sokołowska, K; Wojdacz, Tomasz K.

doi:10.1186/s13148-020-00902-9

Cited by 8 publications

(4 citation statements)

References 1 publication

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“…Since some genes seem to acquire a tissue-specific DNA methylation pattern [41], and aberrant DNA methylation is a common and early event in tumourigenesis [42,43], this epigenetic alteration is deemed as a promising biomarker for cancer diagnosis [44]. As DNA methylation is a stable modification, it can be profiled using small amounts of routinely collected DNA samples from biopsies, or even DNA released by tumour cells into biological fluids, such as peripheral blood, which can be detected through non-invasive methods [45,46]. All these features make DNA methylation an easily and readily applicable tool useful for the clinical practice.…”

Section: Discussionmentioning

confidence: 99%

A DNA Methylation-Based Gene Signature Can Predict Triple-Negative Breast Cancer Diagnosis

et al. 2021

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Triple-negative breast cancer (TNBC) is the most aggressive breast cancer (BC) subtype and lacks targeted treatment. It is diagnosed by the absence of immunohistochemical expression of several biomarkers, but this method still displays some interlaboratory variability. DNA methylome aberrations are common in BC, thereby methylation profiling could provide the identification of accurate TNBC diagnosis biomarkers. Here, we generated a signature of differentially methylated probes with class prediction ability between 5 non-neoplastic breast and 7 TNBC tissues (error rate = 0.083). The robustness of this signature was corroborated in larger cohorts of additional 58 non-neoplastic breast, 93 TNBC, and 150 BC samples from the Gene Expression Omnibus repository, where it yielded an error rate of 0.006. Furthermore, we validated by pyrosequencing the hypomethylation of three out of 34 selected probes (FLJ43663, PBX Homeobox 1 (PBX1), and RAS P21 protein activator 3 (RASA3) in 51 TNBC, even at early stages of the disease. Finally, we found significantly lower methylation levels of FLJ43663 in cell free-DNA from the plasma of six TNBC patients than in 15 healthy donors. In conclusion, we report a novel DNA methylation signature with potential predictive value for TNBC diagnosis.

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Section: Discussionmentioning

confidence: 99%

A DNA Methylation-Based Gene Signature Can Predict Triple-Negative Breast Cancer Diagnosis

et al. 2021

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“…The DNA regions whose methylation changes can be detected in damaged organs or tissues, blood genomic DNA, DNA from various body fluids, and circulating-free DNA are selected as markers of disease progression. Markers making it possible to quite accurately predict oncological diseases at their early stages, evaluate the effect of therapy, detect recurrent cases, and even identify tumor types in some cases, have been selected [ 112 , 113 , 114 ].…”

Section: Dna Methylation and Pathogenetic Conditionsmentioning

confidence: 99%

DNA Methylation: Genomewide Distribution, Regulatory Mechanism and Therapy Target

et al. 2023

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DNA methylation is the most important epigenetic modification involved in the regulation of transcription, imprinting, establishment of X-inactivation, and the formation of a chromatin structure. DNA methylation in the genome is often associated with transcriptional repression and the formation of closed heterochromatin. However, the results of genome-wide studies of the DNA methylation pattern and transcriptional activity of genes have nudged us toward reconsidering this paradigm, since the promoters of many genes remain active despite their methylation. The differences in the DNA methylation distribution in normal and pathological conditions allow us to consider methylation as a diagnostic marker or a therapy target. In this regard, the need to investigate the factors affecting DNA methylation and those involved in its interpretation becomes pressing. Recently, a large number of protein factors have been uncovered, whose ability to bind to DNA depends on their methylation. Many of these proteins act not only as transcriptional activators or repressors, but also affect the level of DNA methylation. These factors are considered potential therapeutic targets for the treatment of diseases resulting from either a change in DNA methylation or a change in the interpretation of its methylation level. In addition to protein factors, a secondary DNA structure can also affect its methylation and can be considered as a therapy target. In this review, the latest research into the DNA methylation landscape in the genome has been summarized to discuss why some DNA regions avoid methylation and what factors can affect its level or interpretation and, therefore, can be considered a therapy target.

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“…The potential outlined above of clinical epigenetics for early disease detection has resulted in a flurry of in-vitro diagnostic (IVD) tests based on DNA methylation analysis of ctDNA, with the majority of these tests targeting panels of hypermethylated CpGs associated with specific oncogenic genes, typically for the detection of a single specific cancer type [ 52 , 53 , 54 ]. For example, the UroMark test is one promising assay to detect bladder cancer (BC) from residual DNA in voided urine.…”

Section: The Potential Value Of Methylated-cfdna For Developing Stmcedmentioning

confidence: 99%

Opportunities for Early Cancer Detection: The Rise of ctDNA Methylation-Based Pan-Cancer Screening Technologies

et al. 2022

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The efficiency of conventional screening programs to identify early-stage malignancies can be limited by the low number of cancers recommended for screening as well as the high cumulative false-positive rate, and associated iatrogenic burden, resulting from repeated multimodal testing. The opportunity to use minimally invasive liquid biopsy testing to screen asymptomatic individuals at-risk for multiple cancers simultaneously could benefit from the aggregated diseases prevalence and a fixed specificity. Increasing both latter parameters is paramount to mediate high positive predictive value—a useful metric to evaluate a screening test accuracy and its potential harm-benefit. Thus, the use of a single test for multi-cancer early detection (stMCED) has emerged as an appealing strategy for increasing early cancer detection rate efficiency and benefit population health. A recent flurry of these stMCED technologies have been reported for clinical potential; however, their development is facing unique challenges to effectively improve clinical cost–benefit. One promising avenue is the analysis of circulating tumour DNA (ctDNA) for detecting DNA methylation biomarker fingerprints of malignancies—a hallmark of disease aetiology and progression holding the potential to be tissue- and cancer-type specific. Utilizing panels of epigenetic biomarkers could potentially help to detect earlier stages of malignancies as well as identify a tumour of origin from blood testing, useful information for follow-up clinical decision making and subsequent patient care improvement. Overall, this review collates the latest and most promising stMCED methodologies, summarizes their clinical performances, and discusses the specific requirements multi-cancer tests should meet to be successfully implemented into screening guidelines.

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Correction to: Current status of development of methylation biomarkers for in vitro diagnostic IVD applications

Abstract: An amendment to this paper has been published and can be accessed via the original article.

Cited by 8 publications

References 1 publication

A DNA Methylation-Based Gene Signature Can Predict Triple-Negative Breast Cancer Diagnosis

A DNA Methylation-Based Gene Signature Can Predict Triple-Negative Breast Cancer Diagnosis

DNA Methylation: Genomewide Distribution, Regulatory Mechanism and Therapy Target

Opportunities for Early Cancer Detection: The Rise of ctDNA Methylation-Based Pan-Cancer Screening Technologies

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