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Epigenetic Biomarkers and Applications for Liquid Biopsy Based Diagnostics

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: closed (15 May 2023) | Viewed by 5875

Special Issue Editor


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Guest Editor
Molecular Diagnostics, Center for Health & Bioresources, AIT Austrian Institute of Technology Vienna, 1210 Vienna, Austria
Interests: DNA methylation; biomarkers; microarrays; protein arrays; molecular diagnostics; cancer research; diagnostics of syndromal and hereditary neoplastic disease

Special Issue Information

Dear Colleagues,

Epigenetic changes are associated with many clinical indications and health issues, such as aging and lifestyle; diabetes; cardio-, neurological and psychiatric diseases; and various cancers. Similar to clinical epigenetics, the liquid biopsy approach primarily emerged in the field of cancer diagnostics. In recent years, other common diseases have also been studied to further implement the concept of liquid biopsy for these clinical indications. The detection of tissue-specific and disease-related epigenetic modifications at the DNA, RNA and protein levels in peripheral blood or other sample types has the potential to provide molecular diagnostic methods to improve clinical decision-making in precision medicine in the near future. The detection of epigenetic changes is already being utilized in many clinical settings, so these approaches have the potential to complement or replace genetic mutation detection approaches. There have been dramatic improvements in early cancer diagnostics over the years. More than a decade ago, epigenomics began with a single DNA methylation marker; now, Grail currently uses more than 100,000 DNA methylation sites for the detection of cancer-specific epigenetics alterations in cell-free DNA from blood plasma. By building on these improvements, in the future, we expect that the combination of epigenetic markers and technical analytical developments will improve the liquid biopsy approach and pave the way for a wide range of innovative applications.

In line with the journal’s mission—IJMS is a journal of molecular science; therefore, pure clinical studies will not be suitable but clinical submissions with biomolecular experiments are welcomed—we aim to focus on the technical, methodological and molecular aspects of ongoing work in the field by linking together epigenetic biomarkers and liquid biopsy or other non- and minimal- invasive analytical concepts. The results of this endeavor will be presented in this Special Issue, entitled "Epigenetic Biomarkers and Applications of Liquid-Biopsy-based Diagnostics". Therefore, we invite colleagues from this field to present their approaches to epigenetics and biomarker research. This special issue is assisted by Topical Advisory Panel Member Dr. Christa Noehammer ([email protected]).

Dr. Andreas Weinhäusel
Guest Editor

Manuscript Submission Information

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Keywords

  • epigenetics
  • DNA methylation
  • miRNA
  • shRNA
  • histone modification
  • minimal-invasive
  • diagnostics
  • liquid biopsy
  • plasma
  • body fluids
  • cell free DNA
  • circulating tumor cell - CTC
  • multiplexing
  • biomarkers

Published Papers (2 papers)

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Research

16 pages, 5077 KiB  
Article
MicroRNA-155-5p, Reduced by Curcumin-Re-Expressed Hypermethylated BRCA1, Is a Molecular Biomarker for Cancer Risk in BRCA1-methylation Carriers
by Nisreen Al-Moghrabi, Maram Al-Showimi, Nujoud Al-Yousef and Lamya AlOtai
Int. J. Mol. Sci. 2023, 24(10), 9021; https://doi.org/10.3390/ijms24109021 - 19 May 2023
Cited by 2 | Viewed by 1528
Abstract
Constitutional BRCA1-methylation is a cancer risk factor for breast (BC) and ovarian (OC) cancer. MiR-155, regulated by BRCA1, is a multifunctional microRNA that plays a crucial role in the immune system. The present study assessed the modulation of miR-155-5p expression in [...] Read more.
Constitutional BRCA1-methylation is a cancer risk factor for breast (BC) and ovarian (OC) cancer. MiR-155, regulated by BRCA1, is a multifunctional microRNA that plays a crucial role in the immune system. The present study assessed the modulation of miR-155-5p expression in peripheral white blood cells (WBCs) of BC and OC patients and cancer-free (CF) BRCA1-methylation female carriers. Additionally, we investigated the potential of curcumin to suppress miR-155-5p in BRCA1-deficient breast cancer cell lines. MiR-155-5p expression was measured using a stem-loop RT-qPCR method. Gene expression levels were determined using qRT-PCR and immunoblotting. MiR-155-5p was more highly expressed in the BRCA1-hypermethylated HCC-38 and UACC-3199 BC cell lines than in the BRCA1-mutated (HCC-1937) and WT BRCA1 (MDA-MB-321) cell lines. Curcumin suppressed miR-155-5p in the HCC-38 cells but not in the HCC-1937 cells via the re-expression of BRCA1. Elevated levels of miR-155-5p were detected in patients with non-aggressive and localized breast tumors and in patients with late-stage aggressive ovarian tumors, as well as in CF BRCA1-methylation carriers. Notably, IL2RG levels were reduced in the OC and CF groups but not in the BC group. Together, our findings suggest opposing effects of WBC miR-155-5p, according to the cell and cancer type. In addition, the results point to miR-155-5p as a candidate biomarker of cancer risk among CF-BRCA1-methylation carriers. Full article
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13 pages, 6005 KiB  
Article
Establishment of an Absolute Quantitative Method to Detect a Plasma tRNA-Derived Fragment and Its Application in the Non-Invasive Diagnosis of Gastric Cancer
by Xiuchong Yu, Xuemei Song, Yaoyao Xie, Shuangshuang Zhang and Junming Guo
Int. J. Mol. Sci. 2023, 24(1), 322; https://doi.org/10.3390/ijms24010322 - 24 Dec 2022
Cited by 8 | Viewed by 1836
Abstract
(1) Transfer RNA (tRNA)-derived fragments (tRFs) are a new category of regulatory non-coding RNAs with distinct biological functions in cancer. They are produced from pre-tRNAs or mature tRNAs and their sequences are relatively short; thus, the amplification of tRFs, especially those in body [...] Read more.
(1) Transfer RNA (tRNA)-derived fragments (tRFs) are a new category of regulatory non-coding RNAs with distinct biological functions in cancer. They are produced from pre-tRNAs or mature tRNAs and their sequences are relatively short; thus, the amplification of tRFs, especially those in body fluids, is faced with certain technical difficulties. In this study, we established a quantitative method to detect plasma tRF-27-87R8WP9N1E5 (tRF-27) and used it to screen gastric cancer patients. (2) A specific stem-loop-structure reverse transcription primer, a TaqMan probe, and amplification primers for tRF-27 were prepared, and the absolute quantitative method was used to measure plasma tRF-27 levels. To determine the noninvasive diagnostic value of tRF-27 in gastric cancer, plasma tRF-27 levels in patients with benign and malignant lesions (120 healthy individuals, 48 patients with benign lesions, 48 patients with precancerous lesions, and 72 patients with early gastric cancer) were analyzed. Plasma tRF-27 levels were also analyzed in 106 preoperative gastric cancer patients, 106 postoperative gastric cancer patients, and 120 healthy individuals. Survival curves and Cox regression models were established and analyzed. (3) A new absolute quantitative method to determine the plasma tRF-27 copy number was established. Plasma tRF-27 levels were significantly increased in gastric cancer patients compared to healthy individuals, and the area under the receiver operating characteristic curve was 0.7767, when the cutoff value was 724,807 copies/mL, with sensitivity and specificity values of 0.6226 and 0.8917, respectively. The positive predictive and negative predictive values were 83.50% and 72.80%, respectively. Plasma tRF-27 levels in postoperative gastric cancer patients were significantly decreased compared to preoperative gastric cancer patients and tended to the levels of healthy individuals. Moreover, tRF-27 levels were closely related to tumor size and Ki67 expression in gastric cancer patients. Prognostic analysis showed that tRF-27 may be an independent predictor of overall survival. (4) This novel and non-invasive method of measuring plasma tRF-27 levels was valuable in the early diagnosis of gastric cancer. Full article
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