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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 Diagnostics (ISSN 2075-4418). This special issue belongs to the section "Pathology and Molecular Diagnostics".

Deadline for manuscript submissions: 31 December 2025 | Viewed by 4272

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 clinical applications: diagnostic, prognostic, and predictive.

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, a single genetic or genomic test may serve multiple purposes depending on the clinical context. The role of these tests in clinical management is expected to grow continuously. 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.

You may choose our Joint Special Issue in Biomolecules.

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. Diagnostics is an international peer-reviewed open access semimonthly 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 2600 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

  • cancer genetics and genomics
  • diagnostic tests
  • prognostic tests
  • predictive tests
  • nucleic acid
  • companion diagnostics
  • targeted therapy

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Published Papers (5 papers)

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29 pages, 3277 KB  
Article
A Pilot Study of Exploring miRNA–Protein Interaction Networks in Pancreatic Ductal Adenocarcinoma Patients: Implications for Diagnosis and Prognosis
by Sena Şen, Merve Çiğdem Özgel, Şeref Buğra Tunçer, Hamza Uğur Bozbey, Senem Karabulut and Didem Taştekin
Diagnostics 2025, 15(19), 2479; https://doi.org/10.3390/diagnostics15192479 (registering DOI) - 27 Sep 2025
Abstract
Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies for which there are few effective biomarkers for diagnosis, prognosis, and treatment monitoring. Given the paucity of data in the literature, this study aimed to evaluate the biomarker potential of selected [...] Read more.
Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies for which there are few effective biomarkers for diagnosis, prognosis, and treatment monitoring. Given the paucity of data in the literature, this study aimed to evaluate the biomarker potential of selected miRNAs (miR-222-3p, miR-3154, miR-3945, miR-4534, and miR-4742) and their protein targets in the context of PDAC. Methods: The expression levels of miRNA candidates were quantified by real-time quantitative PCR in lymphocyte samples from 46 PDAC patients and 50 healthy controls. In silico analyses were performed to identify potential target genes and proteins. ELISA was used to measure protein expression in both groups. Statistical analyses included ROC curve analysis, linear regression, and correlation analyses. In addition, correlations between miRNA/protein expression and clinicopathologic characteristics, including survival, were investigated. Results: miR-222-3p and miR-3154 were significantly downregulated in PDAC patients compared to controls (p < 0.001). Among the dual miRNA combinations, miR-222-3p and miR-4534 showed the highest discriminatory power (AUC = 0.629, p = 0.022). The miR-222-3p expression was significantly increased in patients with a history of alcohol consumption (p = 0.02). Significant correlations were observed between miR-3154 expression and T-stage (p = 0.01) and between perineural invasion and miR-222-3p levels (p = 0.02). Survival analysis showed that high miR-3945 expression was significantly associated with shorter overall survival (p = 0.001). Elevated levels of ESR1, HCFC1, and EPC1 were significantly associated with lymphatic invasion (p < 0.05), while high KCNA1 expression correlated with shorter survival (p = 0.006), indicating its potential as a negative prognostic biomarker. Linear regression analysis revealed a significant positive correlation between miR-3945 and KCNA1 expression (β = 0.259, p = 0.038), indicating a possible regulatory interaction. A borderline correlation was also found between miR-4742 and EPC1 expression (p = 0.055). Conclusions: This study identifies several miRNAs and associated proteins with diagnostic and prognostic significance in PDAC. The results emphasize the clinical relevance of integrating multi-layered analyses of miRNA–protein interactions. The observed associations highlight the role of these molecular markers in tumor progression and patient survival and offer promising opportunities for future research and clinical application in precision oncology. Full article
(This article belongs to the Special Issue Genetic and Genomic Biomarkers in Cancer Diagnosis, Prognosis, and Treatment Prediction)
25 pages, 1455 KB  
Article
Expression Analysis of miR-519a-3p and miR-379-5p in Colorectal Cancer Patients: A Combined Experimental and Bioinformatic Approach
by Turkan Gurer, Mehmet Emin Kizakoglu, Alper Aytekin and Rusen Avsar
Diagnostics 2025, 15(16), 2023; https://doi.org/10.3390/diagnostics15162023 - 13 Aug 2025
Viewed by 531
Abstract
Background/Objectives: Colorectal cancer (CRC) is one of the most common malignancies worldwide. microRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression post-transcriptionally and have emerged as important regulators in cancer biology. This study aimed to investigate the roles of miR-379-5p and [...] Read more.
Background/Objectives: Colorectal cancer (CRC) is one of the most common malignancies worldwide. microRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression post-transcriptionally and have emerged as important regulators in cancer biology. This study aimed to investigate the roles of miR-379-5p and miR-519a-3p in CRC using Quantitative Real-Time PCR (RT-qPCR) and comprehensive bioinformatic analyses. Methods: Tumor tissues and matched adjacent normal tissues were collected from 54 patients with CRC. The expression levels of miR-379-5p and miR-519a-3p in these tissues were determined using the RT-qPCR method. To investigate the functional roles of differently expressed miRNAs, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to construct miRNA–transcription factor (TF)–target gene–disease interaction networks. Results: It was found that the expression level of miR-379-5p was statistically significantly increased in tumor tissues compared to normal tissues, while miR-519a-3p was decreased (p < 0.05). GO analysis revealed enrichment in several important biological processes, including cellular protein metabolic processes, biosynthetic processes, response to stress, and nucleic acid binding TF activity. KEGG analysis exhibited that dysregulated miRNAs were associated with important pathways related to carcinogenesis, such as p53 signaling, TGF-beta signaling, and FoxO signaling pathways. Additionally, the miRNAs-TFs-Genes-Diseases Networks analysis identified ESR1 and FOXA1 as common target TFs of dysregulated miRNAs. Network analyses showed that dysregulated miRNAs interact with CRC-associated genes (Caspase 3 (CASP3), Adenomatous polyposis coli (APC), and AKT serine/threonine kinase 3 (AKT3)). Conclusions: The present study indicates that miR-379-5p and miR-519a-3p may be involved in CRC progression, with miR-379-5p being upregulated and miR-519a-3p being downregulated in tumor tissues. However, further functional studies are required to clarify their potential roles in tumor biology. The findings of the study suggest that miR-379-5p and miR-519a-3p may be associated with regulatory pathways related to CRC. These miRNAs have the potential to serve as diagnostic biomarkers or therapeutic targets in CRC. Full article
(This article belongs to the Special Issue Genetic and Genomic Biomarkers in Cancer Diagnosis, Prognosis, and Treatment Prediction)
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19 pages, 2601 KB  
Article
Mortality Outcome Associated with Specific KRAS, NRAS, and BRAF Hot-Spot Mutations in Metastatic Colorectal Cancer Patients: A Retrospective Cohort Study
by Omer Abdelgadir, Yong-Fang Kuo, M. Firoze Khan, Anthony O. Okorodudu, Yu-Wei Cheng and Jianli Dong
Diagnostics 2025, 15(5), 590; https://doi.org/10.3390/diagnostics15050590 - 28 Feb 2025
Cited by 2 | Viewed by 1946
Abstract
Background/Objective: The prognostic value of specific hot-spot mutations within KRAS, NRAS, and BRAF genes in metastatic colorectal cancer (mCRC) genes remains debatable. This study explores whether certain KRAS, NRAS, and BRAF mutations are associated with the risk of all-cause [...] Read more.
Background/Objective: The prognostic value of specific hot-spot mutations within KRAS, NRAS, and BRAF genes in metastatic colorectal cancer (mCRC) genes remains debatable. This study explores whether certain KRAS, NRAS, and BRAF mutations are associated with the risk of all-cause mortality in mCRC. Methods: We retrospectively analyzed records of 494 patients with mCRC treated at the University of Texas Medical Branch between January 2016 and July 2023. Data on genetic mutations and clinicopathological features were collected for this analysis. We estimated survival probabilities and conducted multivariable Cox proportional hazards regression to evaluate the impact of specific mutations on all-cause mortality risk. Results: KRAS c.35G>T (p.Gly12Val) and c.34G>T (p.Gly12Cys) mutations were significantly associated with an increased risk of all-cause mortality in the overall mCRC population and the treated mCRC subgroup. KRAS c.38G>A (p.Gly13Asp) was significantly associated with an increased risk of all-cause mortality in the treated mCRC subgroup but BRAF c.1799T>A (p.Val600Glu) was significantly associated with an increased risk of all-cause mortality in the overall mCRC population. No significant association was observed between NRAS mutations and mortality risk in mCRC, possibly due to their lower frequency or different biological effects compared to KRAS and BRAF mutations. Conclusions: These findings suggest that specific KRAS [c.35G>T (p.Gly12Val), c.34G>T (p.Gly12Cys), and c.38G>A (p.Gly13Asp)] and BRAF c.1799T>A (p.Val600Glu) mutations may have prognostic value in mCRC. However, given the single-center study design and lack of direct therapeutic implications, larger multicenter studies are needed to substantiate these results and better define the clinical relevance of these mutations. Full article
(This article belongs to the Special Issue Genetic and Genomic Biomarkers in Cancer Diagnosis, Prognosis, and Treatment Prediction)
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11 pages, 3371 KB  
Case Report
A Relapsed AML Case Featuring MYC and MECOM Rearrangements
by Kevin A. Murgas, Pons Materum III, Luke Z. Li, Jacob Rocha, Michael Schuster, Tahmeena Ahmed and Carlos A. Tirado
Diagnostics 2025, 15(18), 2410; https://doi.org/10.3390/diagnostics15182410 - 22 Sep 2025
Viewed by 182
Abstract
Background/Objectives: Relapsed acute myeloid leukemia (AML) is often characterized by clonal evolution and acquired genomic abnormalities, which can inform prognosis and direct therapeutic decisions. The emergence of high-risk chromosomal rearrangements during relapse is of particular significance, yet the impact of rare and complex [...] Read more.
Background/Objectives: Relapsed acute myeloid leukemia (AML) is often characterized by clonal evolution and acquired genomic abnormalities, which can inform prognosis and direct therapeutic decisions. The emergence of high-risk chromosomal rearrangements during relapse is of particular significance, yet the impact of rare and complex events remains poorly understood. This report details a case of relapsed AML that demonstrated rare MYC and MECOM rearrangements and additional features that were not observed at initial diagnosis, emphasizing the clinical relevance of serial cytogenetic assessments. Case Description: A 70-year-old man was initially diagnosed with AML, exhibiting monocytic differentiation, an 11q23 deletion involving KMT2A loss, and a U2AF1 mutation. After achieving remission with azacitidine and venetoclax, the patient relapsed within ten months, necessitating reevaluation and modification of therapy. Repeat cytogenetic analysis at relapse revealed a distinct t(3;8)(q26.2;q24.3) exhibiting MYC and MECOM rearrangements, features that were absent at initial diagnosis. Conclusions: This case underscores the importance of serial cytogenetic and molecular profiling in relapsed AML. The emergence of new abnormalities upon relapse suggested underlying genomic instability and clonal evolution. MYC rearrangements are notably rare in AML, especially with concurrent MECOM rearrangements, highlighting a unique feature of this case. The identification of novel abnormalities at relapse may carry prognostic and therapeutic significance and may be used to refine risk stratification. Thus, ongoing cytogenetic monitoring is essential to adapt management approaches in evolving disease contexts. Full article
(This article belongs to the Special Issue Genetic and Genomic Biomarkers in Cancer Diagnosis, Prognosis, and Treatment Prediction)
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10 pages, 3476 KB  
Case Report
An Incidental Finding of Gain of a Diminished Chromosome 12 Centromere in an Individual with Lymphocytosis: A Case Report and Clinical Implications in Cytogenetic Testing
by Changqing Xia, Jeffrey J. Cannatella, Scott C. Smith, Pamela A. Althof, Haley Koerselman, Thomas Hempel, Erin E. Jaworski, Lisa M. Winkler, Joanna R. Spaulding, Diane Pickering, Joseph D. Khoury and Zhenya Tang
Diagnostics 2025, 15(5), 618; https://doi.org/10.3390/diagnostics15050618 - 4 Mar 2025
Viewed by 984
Abstract
Background: Fluorescence in situ hybridization (FISH) testing against chromosome 12 centromere (CEN12) is routinely included in the work-up of patients with suspected chronic lymphocytic leukemia (CLL) or monoclonal B-cell lymphocytosis (MBL). However, incidental findings can occur and be challenging. Methods: Interphase and [...] Read more.
Background: Fluorescence in situ hybridization (FISH) testing against chromosome 12 centromere (CEN12) is routinely included in the work-up of patients with suspected chronic lymphocytic leukemia (CLL) or monoclonal B-cell lymphocytosis (MBL). However, incidental findings can occur and be challenging. Methods: Interphase and metaphase FISH analyses with various probes, including CEN12 probes from different vendors, and conventional cytogenetics were applied. Results: A CLL FISH panel was performed at the clinician’s request on a peripheral blood specimen from a 55-year-old female with fluctuating leukocytosis and lymphocytosis for over six years. An additional diminished CEN12 FISH signal was observed in approximately 70% of the nucleated cells analyzed. Concurrent flow cytometry excluded a diagnosis of CLL or MBL, and karyotyping exhibited a normal female karyotype. Further studies excluded potential cross-hybridization due to limited specificity of the CEN12 probes and revealed the location of the additional diminished CEN12 signal on the centromere of one chromosome 16 homolog (CEN16), without other material from the short arm (12p) or long arm (12q) of chromosome 12 being involved. Conclusions: This is the first case with an “uncertain” trisomy 12 status, presenting a challenge to clinical cytogenetic diagnosis. Although the mechanism for this mosaic “partial trisomy 12” and its clinical impact remain unknown, this case highlights the importance of further investigation using orthogonal methods to clarify incidental findings during diagnostic practice. Full article
(This article belongs to the Special Issue Genetic and Genomic Biomarkers in Cancer Diagnosis, Prognosis, and Treatment Prediction)
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