International Journal of Molecular Sciences

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Dr. Christa Nöhammer

AIT Austrian Institute of Technology GmbH, 1210 Vienna, Austria
Interests: DNA methylation; microRNAs; multi-omics biomarkers; liquid biopsy (blood, saliva, and CSF); extracellular vesicles; microarrays; next-generation sequencing; biomarkers for cancer-, cardiovascular-, and immune-mediated disease diagnostics
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Dr. Walter Pulverer

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Guest Editor

Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, 1210 Vienna, Austria
Interests: tumor

Special Issue Information

Dear Colleagues,

In recent years, there have evolved several diagnostic techniques and procedures used to diagnose cancer. Nevertheless they often produce undesired high levels of false positives, and they're also expensive, have accessibility issues, and involve exposure to ionizing radiation.

Now, a number of assays have been developed for microRNA, circulating DNA, measuring protein, and methylated DNA biomarkers in the blood for the detection of cancer. In addition, biopsies for molecular and biomarker diagnosis have also been utilized but are uncomfortable for patients. Moreover, while these approaches are of clinical value that is more specific to late-stage cancer, they have limited value for the early detection of cancer. So, the identification of highly specific and highly selective novel molecular biomarkers for cancer diagnosis is warranted. In this Special Issue, we describe the pros and cons of current molecular approaches used in the diagnosis of cancer, as well as the technical advances and challenges for establishing molecular biomarkers for determining the risk, detection, and progression of cancer.

Dr. Christa Nöhammer
Dr. Walter Pulverer
Guest Editors

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Keywords

cancer
cancer biomarkers
cancer staging
diagnostic tools
novel biomarkers
proteomics
molecular markers
metabolic profiling
prognostic value

Published Papers (2 papers)

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Research

19 pages, 8283 KiB

Open AccessArticle

Temperature-Wise Calibration Increases the Accuracy of DNA Methylation Levels Determined by High-Resolution Melting (HRM)

by Katja Zappe and Margit Cichna-Markl

Int. J. Mol. Sci. 2024, 25(10), 5082; https://doi.org/10.3390/ijms25105082 - 7 May 2024

Viewed by 305

Abstract

High-resolution melting (HRM) is a cost-efficient tool for targeted DNA methylation analysis. HRM yields the average methylation status across all CpGs in PCR products. Moreover, it provides information on the methylation pattern, e.g., the occurrence of monoallelic methylation. HRM assays have to be calibrated by analyzing DNA methylation standards of known methylation status and mixtures thereof. In general, DNA methylation levels determined by the classical calibration approach, including the whole temperature range in between normalization intervals, are in good agreement with the mean of the DNA methylation status of individual CpGs determined by pyrosequencing (PSQ), the gold standard of targeted DNA methylation analysis. However, the classical calibration approach leads to highly inaccurate results for samples with heterogeneous DNA methylation since they result in more complex melt curves, differing in their shape compared to those of DNA standards and mixtures thereof. Here, we present a novel calibration approach, i.e., temperature-wise calibration. By temperature-wise calibration, methylation profiles over temperature are obtained, which help in finding the optimal calibration range and thus increase the accuracy of HRM data, particularly for heterogeneous DNA methylation. For explaining the principle and demonstrating the potential of the novel calibration approach, we selected the promoter and two enhancers of MGMT, a gene encoding the repair protein MGMT. Full article

(This article belongs to the Special Issue Biomarkers in Cancers: New Advances)

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17 pages, 4143 KiB

Open AccessArticle

Use of Enzymatically Converted Cell-Free DNA (cfDNA) Data for Copy Number Variation-Linked Fragmentation Analysis Allows for Early Colorectal Cancer Detection

by Iva Černoša, Fernando Trincado-Alonso, Pol Canal-Noguer, Kristi Kruusmaa and Alexandre Perera-Lluna

Int. J. Mol. Sci. 2024, 25(6), 3502; https://doi.org/10.3390/ijms25063502 - 20 Mar 2024

Viewed by 1025

Abstract

The use of non-invasive liquid biopsy-based cell-free DNA (cfDNA) analysis is an emerging method of cancer detection and intervention. Different analytical methodologies are used to investigate cfDNA characteristics, resulting in costly and long analysis processes needed for combining different data. This study investigates the possibility of using cfDNA data converted for methylation analysis for combining the cfDNA fragment size with copy number variation (CNV) in the context of early colorectal cancer detection. Specifically, we focused on comparing enzymatically and bisulfite-converted data for evaluating cfDNA fragments belonging to chromosome 18. Chromosome 18 is often reported to be deleted in colorectal cancer. We used counts of short and medium cfDNA fragments of chromosome 18 and trained a linear model (LDA) on a set of 2959 regions to predict early-stage (I–IIA) colorectal cancer on an independent test set. In total, 87.5% sensitivity and 92% specificity were obtained on the enzymatically converted libraries. Repeating the same workflow on bisulfite-converted data yielded lower accuracy results with 58.3% sensitivity, implying that enzymatic conversion preserves the cancer fragmentation footprint in whole genome data better than bisulfite conversion. These results could serve as a promising new avenue for the early detection of colorectal cancer using fragmentation and methylation approaches on the same datasets. Full article

(This article belongs to the Special Issue Biomarkers in Cancers: New Advances)

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