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Genetic and Genomic Biomarkers in Cancer Diagnosis, Prognosis, and Treatment...
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Genetic and Genomic Biomarkers in Cancer Diagnosis, Prognosis, and Treatment Prediction

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Biomarkers".

Deadline for manuscript submissions: 31 July 2025 | Viewed by 1722

Special Issue Editor

Prof. Dr. Jianli Dong

E-Mail Website
Guest Editor
Department of Pathology, Sealy Center for Cancer Cell Biology, University of Texas Medical Branch, 5.202 John Sealy Annex, 301 University Boulevard, Galveston, TX 77555, USA
Interests: laboratory genetics and genomics; genetic and genomic biomarkers; cancer biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Advances in cancer genetics and genomics are expanding the opportunities for utilizing genetic and genomic biomarkers in cancer diagnosis, prognosis, and treatment prediction. Cancer genetic and genomic tests typically analyze nucleic acid-based biomarkers and can be categorized based on their medical applications: diagnostic, prognostic, and predictive.

Cancer diagnostic tests are used for cancer screening, diagnosis, subtyping, and staging. Prognostic tests provide insights into the natural progression of cancer and potential outcomes. In contrast, predictive tests offer information about how likely a patient is to respond to a specific drug or therapy.

Importantly, genetic and genomic test is expected to have an ever-increasing impact on oncology. For instance, biomarkers can help select patients who are likely to benefit from targeted therapies, monitor treatment resistance, assess recurrence risk, adjust therapeutic dosages, and identify pharmacogenetic risks for adverse drug reactions.

This approach enhances the accuracy of diagnoses, spares patients from ineffective treatments, and minimizes side effects, ultimately leading to more personalized and precise cancer management.

This Special Issue aims to highlight recent advances made in the development and utility of genetic and genomic assays in oncology. I encourage basic and pre-clinical researchers to present original research articles and reviews, emphasizing the current mechanisms and preclinical advancement of laboratory genetics and genomics in oncology.

I look forward to receiving your contributions.

You may choose our Joint Special Issue in Diagnostics.

Prof. Dr. Jianli Dong
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. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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

  • laboratory genetics and genomics
  • genetic and genomic biomarkers
  • diagnostic
  • prognostic
  • predictive
  • companion diagnosis
  • targeted therapy
  • nucleic acid

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Published Papers (2 papers)

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14 pages, 2188 KiB  
Article
The Prognostic, Predictive and Clinicopathological Implications of KRT81/HNF1A- and GATA6-Based Transcriptional Subtyping in Pancreatic Cancer
by Michael Guenther, Sai Agash Surendran, Lea Margareta Steinke, Iduna Liou, Melanie Alexandra Palm, Volker Heinemann, Michael Haas, Stefan Boeck and Steffen Ormanns
Biomolecules 2025, 15(3), 426; https://doi.org/10.3390/biom15030426 - 17 Mar 2025
Viewed by 647
Abstract
Background: Transcriptional subtypes of pancreatic ductal adenocarcinoma (PDAC) based on the expression of hallmark genes may have prognostic implications and potential predictive functions. The two most employed subtyping markers assess the combined expression of KRT81 and HNF1A or of GATA6 alone, which can [...] Read more.
Background: Transcriptional subtypes of pancreatic ductal adenocarcinoma (PDAC) based on the expression of hallmark genes may have prognostic implications and potential predictive functions. The two most employed subtyping markers assess the combined expression of KRT81 and HNF1A or of GATA6 alone, which can be detected by immunohistochemistry (IHC). This study aimed to determine the prognostic or predictive impact of both subtyping marker panels in two large cohorts of advanced and resected pancreatic ductal adenocarcinoma (PDAC) patients. Methods: Transcriptional subtypes were determined by combining the expression of KRT81/HNF1A or assessing GATA6 expression alone by IHC in samples of two independent PDAC patient cohorts (advanced PDAC n = 139 and resected PDAC n = 411) as well as in 57 matched primary tumors and their corresponding metastases. RNAseq-based expression data of 316 resected PDAC patients was analyzed for validation. Results: Transcriptional subtypes widely overlapped in both marker panels (χ2 p < 0.001) but switched during disease progression in up to 31.6% of patients. They had a modest impact on the patients’ prognosis in both cohorts, with longer overall survival (OS) for patients with KRT81−/HNF1A+ or GATA6+ tumors but better progression-free survival (PFS) and disease-free survival (DFS) in patients with KRT81+/GATA6− tumors treated with palliative or adjuvant gemcitabine-based chemotherapy. RNAseq expression data confirmed the findings. Conclusions: Transcriptional subtypes have differential responses to palliative and adjuvant gemcitabine-based chemotherapy and may change during disease progression. Both employed subtyping marker panels are equivalent and may be used to inform clinical therapy decisions. Full article
(This article belongs to the Special Issue Genetic and Genomic Biomarkers in Cancer Diagnosis, Prognosis, and Treatment Prediction)
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17 pages, 3254 KiB  
Article
Multi-Omics Characterization of Genome-Wide Abnormal DNA Methylation Reveals FGF5 as a Diagnosis of Nasopharyngeal Carcinoma Recurrence After Radiotherapy
by Zhi-Qing Long, Ran Ding, Ting-Qiu Quan, Rui Xu, Zhuo-Hui Huang, Denghui Wei, Wei-Hong Zheng and Ying Sun
Biomolecules 2025, 15(2), 283; https://doi.org/10.3390/biom15020283 - 14 Feb 2025
Viewed by 823
Abstract
Background: Aberrant expression and mutations in the fibroblast growth factor (FGF) family play crucial roles in cell differentiation, growth, and migration, contributing to tumor progression across various cancers. Nasopharyngeal carcinoma (NPC), a malignancy prevalent in East Asia, is primarily treated with radiotherapy; however, [...] Read more.
Background: Aberrant expression and mutations in the fibroblast growth factor (FGF) family play crucial roles in cell differentiation, growth, and migration, contributing to tumor progression across various cancers. Nasopharyngeal carcinoma (NPC), a malignancy prevalent in East Asia, is primarily treated with radiotherapy; however, radioresistance remains a major challenge, leading to recurrence and poor outcomes. While FGFs are known to activate signaling pathways such as MAPK, PI3K/AKT, and JAK/STAT to promote cancer progression, the specific role of individual FGFs in NPC radioresistance remains unclear. Emerging evidence highlights FGF5 as a key player in NPC progression, metastasis, and radioresistance, underscoring its potential as a therapeutic target to overcome treatment resistance and improve clinical outcomes. Methods: We analyzed single nucleotide variation (SNV) data, gene expression, and DNA methylation patterns using cancer datasets, including TCGA and GTEx, to investigate FGF5 expression. Differentially expressed genes (DEGs) were identified and interpreted using functional enrichment analysis, while survival analysis and gene set enrichment analysis (GSEA) were conducted to identify clinical correlations. DNA methylation patterns were specifically assessed using the HumanMethylation850 BeadChips on tissue samples from nine recurrent and nine non-recurrent NPC patients. Functional assays, including cell viability, migration, invasion, and clonogenic survival assays, were performed to evaluate the effects of FGF5 on NPC cell behavior in vitro and in vivo. Results: FGF5 showed elevated SNV frequencies across multiple cancers, particularly in HNSC and NPC. DNA methylation analysis revealed an inverse relationship between FGF5 expression and methylation levels in recurrent NPC tumors. Functional assays demonstrated that FGF5 enhances migration, invasion, and radioresistance in NPC cells. High FGF5 expression was associated with reduced distant metastasis-free survival (DMFS) and increased radioresistance, highlighting its role in metastatic progression and recurrence. Conclusions: FGF5 plays a significant role in the progression and recurrence of nasopharyngeal carcinoma. Its elevated expression correlates with increased migration, invasion, and radioresistance as well as reduced distant metastasis-free survival. These findings suggest that FGF5 contributes to the metastatic and recurrence potential of NPC, making it a potential target for therapeutic intervention in treating these cancers. Full article
(This article belongs to the Special Issue Genetic and Genomic Biomarkers in Cancer Diagnosis, Prognosis, and Treatment Prediction)
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