Genomic and Transcriptomic Research in the Discovery and Application of Colorectal Cancer Circulating Markers

Sep 24, 2026

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Colorectal cancer (CRC) is a leading malignancy worldwide, where outcomes depend strongly on early detection, appropriate therapy selection, monitoring of treatment success, and timely diagnosis of recurrences. This review emphasizes the need for integrated genomic and epigenetic characterization to refine diagnostic, therapeutic, and preventive strategies and support informed clinical decision-making. It highlights liquid biopsy methods using circulating DNA and RNA markers, including cancer-associated mutations, DNA methylation changes, and non-coding RNA expression shifts, and discusses marker discovery, verification, clinical applicability, and future improvements.

LanguageEnglish

CategoryHealthcare

FormatPDF

Pages34

Reading Time1 h 26 min

AccessFree to download

Introduction

Background on CRC burden and survival

Molecular heterogeneity and subtype classification

Abstracted review focus

Circulating DNA/RNA markers and liquid biopsy approach

Cancer-associated mutations, methylation, and non-coding RNAs

Marker discovery, verification, clinical use, and future directions

Review Genomic and Transcriptomic Research in the Discovery and Application of Colorectal Cancer Circulating Markers Anastasia A. Ponomaryova 1, Elena Yu. Rykova 2,3,*, Anastasia I. Solovyova 4, Anna S. Tarasova 1, Dmitry N. Kostromitsky 1, Alexey Yu. Dobrodeev 1, Sergey A. Afanasiev 1 and Nadezhda V. Cherdyntseva 1,5 Citation: Ponomaryova, A.A.; Rykova, E.Y.; Solovyova, A.I.; Tarasova, A.S.; Kostromitsky, D.N.; Dobrodeev, A.Y.; Afanasiev, S.A.; Cherdyntseva, N.V. Genomic and Transcriptomic Research in the Discovery and Application of Colorectal Cancer Circulating Markers. Int. J. Mol. Sci. 2023, 24, 12407. [https://doi.org/](https://doi.org/)[ ](https://doi.org/)[10.3390/ijms241512407](10.3390/ijms241512407) Academic Editors: David Alexander Forsyth Gillespie and Enrico Gaffo Received: 15 May 2023 Revised: 24 July 2023 Accepted: 2 August 2023 Published: 3 August 2023 Copyright: © 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ([https://](https://)[ ](https://)[creativecommons.org/licenses/by/](creativecommons.org/licenses/by/)[ ](creativecommons.org/licenses/by/)[4.0/](4.0/)) . 1 Cancer Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009 Tomsk, Russia 2 Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia 3 Department of Engineering Problems of Ecology, Novosibirsk State Technical University, 630087 Novosibirsk, Russia 4 Department of Biochemistry, Medico-Biological Faculty, Siberian State Medical University, 634050 Tomsk, Russia 5 Faculty of Chemistry, National Research Tomsk State University, 634050 Tomsk, Russia * Correspondence: [rykova.elena.2014@gmail.com](rykova.elena.2014@gmail.com); Tel.: +7-(383)-363-49-80 Abstract: Colorectal cancer (CRC) is the most frequently occurring malignancy in the world. However, the mortality from CRC can be reduced through early diagnostics, selection of the most effective treatment, observation of the therapy success, and the earliest possible diagnosis of recurrences. A comprehensive analysis of genetic and epigenetic factors contributing to the CRC development is needed to reﬁne diagnostic, therapeutic, and preventive strategies and to ensure appropriate decision making in managing speciﬁc CRC cases. The liquid biopsy approach utilizing circulating markers has demonstrated its good performance as a tool to detect the changes in the molecular pathways associated with various cancers. In this review, we attempted to brief the main tendencies in the development of circulating DNA and RNA-based markers in CRC such as cancer-associated DNA mutations, DNA methylation changes, and non-coding RNA expression shifts. Attention is devoted to the existing circulating nucleic acid-based CRC markers, the possibility of their application in clinical practice today, and their future improvement. Approaches to the discovery and veriﬁcation of new markers are described, and the existing problems and potential solutions for them are highlighted. Keywords: colorectal cancer; diagnosis; prognosis; prediction of therapy response; circulating DNAs; circulating RNAs; detection of circulating markers 1. Introduction Colorectal cancer (CRC) is a dangerous disorder, which is characterized by a very high frequency and mortality [1] . Currently, the only workable approach to reduce the CRC-related mortality is the earliest possible diagnosis providing a higher probability for the illness to be treated. The 5-year survival rates directly correlate with the stage when the disease is diagnosed; in particular, the survival rate is considerably higher for the subjects diagnosed at I–IIa CRC stages as compared with later course [2] . The adequate care and screening are most important for the survival rate of CRC subjec

FAQs

Why is early diagnosis crucial for colorectal cancer outcomes?

CRC mortality can be reduced through the earliest possible diagnosis, which increases the chance of effective treatment. Survival rates correlate with the stage at diagnosis, with higher survival for earlier stages (I–IIa).

What is the role of liquid biopsy in this review?

The review highlights liquid biopsy as a tool to detect molecular pathway changes in cancers using circulating markers. It focuses on circulating DNA and RNA-based markers for CRC.

Which types of circulating markers are discussed for CRC?

The review covers circulating nucleic acid markers, including cancer-associated DNA mutations, DNA methylation changes, and shifts in non-coding RNA expression. It also addresses existing markers, their clinical application, and future improvements.

Sep 24, 2026

Uploaded by Fahsai