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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 672

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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

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Keywords

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

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Published Papers (1 paper)

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Research

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 516
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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