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Advancements in Cancer Biomarkers
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Advancements in Cancer Biomarkers

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Oncology".

Deadline for manuscript submissions: 31 July 2025 | Viewed by 1796

Special Issue Editor

Dr. Christos Mikropoulos

E-Mail Website
Guest Editor
St Luke’s Cancer Centre, Royal Surrey Hospital, Guildford GU1 1EB, UK
Interests: cancer genetics; biomarkers; SABR; brachytherapy
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Following the discovery of the first tumor biomarker by Henry Bence-Jones in 1847, the study of new cancer biomarkers has accelerated, propelled onwards by advancements in molecular technology. The identification of novel cancer biomarkers now utilizes modified immunoassay, molecular hybridization, next-generation nucleic acid sequencing, gene amplification, gene editing and liquid biopsy technology.

Within the current era of innovation and development, recent publications have explored the use of circulating tumor DNA (ctDNA) and circulating micro-RNA (c-miRNA) for the diagnosis and prognosis of colorectal cancer, esophageal cancer and non-small cell lung cancer. The unique methylation profile of cancer cells identified from gene methylation can differentiate between several gastrointestinal cancers, which can be used to predict the origin of tumors in metastatic disease. Tumor-infiltrating lymphocytes (TILs) have prognostic potential in triple-negative breast cancer and are predictors of patients’ response in melanoma. TILs have even been studied for their therapeutic potential, leading to the FDA approval of Lifileucel for advanced melanoma, demonstrating the importance of molecular studies in transforming our understanding at the cellular level and driving precision medicine. Proteomics and metabolomics further represent emerging research, with attempts to identify cancer-specific biomarkers and predict drug sensitivity in ovarian and breast cancer through mass spectrometry.

Within the cornucopia of available literature on cancer biomarkers, the International Journal of Molecular Sciences (IJMS) has published over 500 articles on cancer biomarkers in the last two years alone and continues to pioneer experimental and theoretical progress. This Special Issue focuses on advancements in cancer biomarkers to update and orientate the scientific community on the continual expansive field of molecular oncology. We hope to unite specialists from various disciplines, including molecular biology, biochemistry, biophysics, biogenetics, computational biology and biotechnology, including artificial intelligence.

This Special Issue is led by Dr. Christos Mikropoulos and assisted by our GE's Assistant Editor, Dr. Michael Hannides (<michael.hannides@nhs.net>, Clinical Oncology, Royal Surrey NHS Foundation Trust, Egerton Road, Surrey, Guildford GU2 7XX, UK). Please note that this Special Issue is focused on molecular research, so pure clinical research will not be accepted, but we welcome clinical submissions with biomolecular experiments.

Dr. Christos Mikropoulos
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • biomarkers
  • ctDNA
  • mircroRNA
  • proteomics
  • gene methylation
  • TIL
  • transcriptomics
  • micro RNA
  • tumor microenvironment
  • gene methylation
  • proteomics

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Published Papers (3 papers)

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Research

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18 pages, 2384 KiB  
Article
Distinctive Features of Extracellular Vesicles Present in the Gastric Juice of Patients with Gastric Cancer and Healthy Subjects
by Gleb Skryabin, Adel Enikeev, Anastasiia Beliaeva, Sergey Galetsky, Dmitry Bagrov, Andrey Moiseenko, Anna Vnukova, Oiatiddin Imaraliev, Ivan Karasev and Elena Tchevkina
Int. J. Mol. Sci. 2025, 26(12), 5857; https://doi.org/10.3390/ijms26125857 - 18 Jun 2025
Viewed by 255
Abstract
Extracellular vesicles (EVs) are key mediators of intercellular communication and play a vital role in cancer progression. While EVs in the blood are well-studied, those in local body fluids, such as gastric juice (GJ), remain underinvestigated. Previously, we first characterized GJ-derived EVs and [...] Read more.
Extracellular vesicles (EVs) are key mediators of intercellular communication and play a vital role in cancer progression. While EVs in the blood are well-studied, those in local body fluids, such as gastric juice (GJ), remain underinvestigated. Previously, we first characterized GJ-derived EVs and demonstrated their potential for gastric cancer (GC) screening. Here, we conducted a detailed morphological analysis of GJ-EVs using cryo-electron microscopy, identifying both typical and atypical EV subtypes, and categorized their relative abundances. A subsequent comparison of the size distribution of GJ-derived EVs by nanoparticle tracking analysis revealed significant differences between samples obtained from GC patients (n = 40) and healthy subjects (n = 25). Additionally, the mean EV sizes differed significantly according to the presence of the tetraspanin protein CD9. Furthermore, the ratio of CD9-positive to CD9-negative EV samples differed between cancer patients and healthy donors. These data suggest that GJ contains distinct subpopulations of EVs that vary in size and CD9 expression, as well as EVs with certain types of atypical morphology. The identification of discrepancies in EV size and the presence of CD9 between GJ from cancer patients and healthy individuals offers potential avenues for the identification of new GC markers. Full article
(This article belongs to the Special Issue Advancements in Cancer Biomarkers)
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28 pages, 14266 KiB  
Article
Identification of CDK1 as a Biomarker for the Treatment of Liver Fibrosis and Hepatocellular Carcinoma Through Bioinformatics Analysis
by Jiayi Qin and Zhuan Li
Int. J. Mol. Sci. 2025, 26(8), 3816; https://doi.org/10.3390/ijms26083816 - 17 Apr 2025
Viewed by 1239
Abstract
Cyclin-dependent kinase 1 (CDK1) has emerged as a critical regulator of cell cycle progression, yet its role in liver fibrosis-associated hepatocellular carcinoma (LF-HCC) remains underexplored. This study aimed to systematically evaluate CDK1’s prognostic significance, immune regulatory functions, and therapeutic potential in LF-HCC pathogenesis. [...] Read more.
Cyclin-dependent kinase 1 (CDK1) has emerged as a critical regulator of cell cycle progression, yet its role in liver fibrosis-associated hepatocellular carcinoma (LF-HCC) remains underexplored. This study aimed to systematically evaluate CDK1’s prognostic significance, immune regulatory functions, and therapeutic potential in LF-HCC pathogenesis. Integrated bioinformatics approaches were applied to multi-omics datasets from GEO, TCGA, and TIMER databases. Differentially expressed genes were identified through enrichment analysis and protein–protein interaction networks. Survival outcomes were assessed via Kaplan–Meier analysis, while immune cell infiltration patterns were quantified using CIBERSORT. Molecular docking simulations evaluated CDK1’s binding affinity with pharmacologically active compounds (alvocidib, seliciclib, alsterpaullone) using AutoDock Vina. CDK1 demonstrated significant overexpression in LF-HCC tissues compared to normal controls (p < 0.001). Elevated CDK1 expression correlated with reduced overall survival (HR = 2.41, 95% CI:1.78–3.26, p = 0.003) and advanced tumor staging (p = 0.007). Immune profiling revealed strong associations between CDK1 levels and immunosuppressive cell infiltration, particularly regulatory T cells (r = 0.63, p = 0.001) and myeloid-derived suppressor cells (r = 0.58, p = 0.004). Molecular docking confirmed high-affinity binding of CDK1 to kinase inhibitors through conserved hydrogen-bond interactions (binding energy ≤ −8.5 kcal/mol), with alvocidib showing optimal binding stability. This multimodal analysis establishes CDK1 as both a prognostic biomarker and immunomodulatory regulator in LF-HCC pathogenesis. The enzyme’s dual role in driving tumor progression and reshaping the immune microenvironment positions it as a promising therapeutic target. Computational validation of CDK1 inhibitors provides a rational basis for developing precision therapies against LF-HCC, bridging translational gaps between biomarker discovery and clinical application. Full article
(This article belongs to the Special Issue Advancements in Cancer Biomarkers)
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Review

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28 pages, 939 KiB  
Review
Targets for CAR Therapy in Multiple Myeloma
by Olga A. Bezborodova, Galina V. Trunova, Elena R. Nemtsova, Varvara A. Khokhlova, Julia B. Venediktova, Natalia B. Morozova, Maria S. Vorontsova, Anna D. Plyutinskaya, Elena P. Zharova, Peter V. Shegai and Andrey D. Kaprin
Int. J. Mol. Sci. 2025, 26(13), 6051; https://doi.org/10.3390/ijms26136051 - 24 Jun 2025
Viewed by 62
Abstract
Multiple myeloma (MM or plasma cell myeloma) is a heterogenous B-cell malignant tumor that typically exhibits a high recurrence rate, resistance to drugs, and molecular diversity of tumor subclones. Given the limited efficacy of standard therapy options, cellular immunotherapy featuring a chimeric antigen [...] Read more.
Multiple myeloma (MM or plasma cell myeloma) is a heterogenous B-cell malignant tumor that typically exhibits a high recurrence rate, resistance to drugs, and molecular diversity of tumor subclones. Given the limited efficacy of standard therapy options, cellular immunotherapy featuring a chimeric antigen receptor (CAR) has proven tangible potential in treatment for relapsed and refractory forms of MM. The rational choice of a tumor target which shows high selectivity, stable expression, and biological significance is key to the successful implementation of CAR therapy. This review has summarized and analyzed data from the literature on biological properties, the features of expression, and the clinical development stages of CAR cell products for MM treatment which target BCMA, GPRC5D, FcRH5, SLAMF7, CD38, CD138, TACI, APRIL, CD19, TNFR2, CD44v6, CD70, NKG2D ligands, etc. Special focus is on strategic approaches to overcoming antigenic escape, such as multi-specific CAR constructs, logical activation sequences, and controlled safety systems. The analysis underscores the need for integrating the molecular selection of targets with cutting-edge bioengineering solutions as a key trend for raising the efficacy, stability, and safety of cellular therapy in the case of MM. Full article
(This article belongs to the Special Issue Advancements in Cancer Biomarkers)
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