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Molecular Diagnostic and Prognostic Markers of Human Cancers
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Molecular Diagnostic and Prognostic Markers of Human Cancers

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Human Genomics and Genetic Diseases".

Deadline for manuscript submissions: closed (25 January 2025) | Viewed by 7547

Special Issue Editor

Dr. Hilal Arnouk

E-Mail Website
Guest Editor
Department of Pathology, Chicago College of Osteopathic Medicine, Precision Medicine Program, College of Graduate Studies, Midwestern University, Downers Grove, IL 60515, USA
Interests: molecular pathology; molecular diagnostics; precision medicine oncology; cancer immunotherapy

Special Issue Information

Dear Colleagues,

Cancer is a collection of several diseases that contribute significantly to morbidity and mortality worldwide. An accurate diagnosis is critical for detecting malignancies in their initial stages before they metastasize and become resistant to treatment. Precision medicine describes the ability to customize personalized medical care to individual patients through the incorporation of molecular profiles and clinical characteristics in treatment determination utilizing molecular diagnostics and targeted therapies.

Diagnostic and prognostic biomarkers are a valuable tool for cancer screening and for monitoring disease progression and recurrence. Moreover, molecular biomarkers can predict the response or resistance to a certain therapeutic modality along with potential adverse events, thus enabling individualized oncology treatments. Indeed, personalized oncology practices incorporate the clinicopathological parameters and molecular signature of each type of cancer when determining the best option for individual patients' targeted therapies.

Molecular targeted treatments for cancer rely on developing small molecule drugs and monoclonal antibodies that disrupt the cancer cell’s signaling pathways responsible for sustaining proliferative activities, evading growth suppressors, resisting apoptosis, enabling replicative immortality, inducing angiogenesis, and activating invasion and metastasis.

We aim to highlight recent discoveries in the field of molecular diagnostics and the identification of novel molecular targets that fuel the development of innovative targeted therapies for cancer.

Dr. Hilal Arnouk
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. Genes 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 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

  • molecular diagnostics
  • molecular pathology
  • precision medicine oncology
  • diagnostic biomarkers
  • prognostic biomarkers
  • therapeutic targets
  • genomics
  • proteomics

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Published Papers (4 papers)

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Research

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32 pages, 4595 KiB  
Article
Integrative In Silico Analysis to Identify Functional and Structural Impacts of nsSNPs on Programmed Cell Death Protein 1 (PD-1) Protein and UTRs: Potential Biomarkers for Cancer Susceptibility
by Hakeemah Al-Nakhle, Retaj Al-Shahrani, Jawanah Al-Ahmadi, Wesal Al-Madani and Rufayda Al-Juhani
Genes 2025, 16(3), 307; https://doi.org/10.3390/genes16030307 - 4 Mar 2025
Viewed by 1062
Abstract
Background: Programmed cell death protein 1 (PD-1), encoded by the PDCD1 gene, is critical in immune checkpoint regulation and cancer immune evasion. Variants in PDCD1 may alter its function, impacting cancer susceptibility and disease progression. Objectives: This study evaluates the structural, functional, and [...] Read more.
Background: Programmed cell death protein 1 (PD-1), encoded by the PDCD1 gene, is critical in immune checkpoint regulation and cancer immune evasion. Variants in PDCD1 may alter its function, impacting cancer susceptibility and disease progression. Objectives: This study evaluates the structural, functional, and regulatory impacts of non-synonymous single-nucleotide polymorphisms (nsSNPs) in the PDCD1 gene, focusing on their pathogenic and oncogenic roles. Methods: Computational tools, including PredictSNP1.0, I-Mutant2.0, MUpro, HOPE, MutPred2, Cscape, Cscape-Somatic, GEPIA2, cBioPortal, and STRING, were used to analyze 695 nsSNPs in the PD1 protein. The analysis covered structural impacts, stability changes, regulatory effects, and oncogenic potential, focusing on conserved domains and protein–ligand interactions. Results: The analysis identified 84 deleterious variants, with 45 mapped to conserved regions like the Ig V-set domain essential for ligand-binding interactions. Stability analyses identified 78 destabilizing variants with significant protein instability (ΔΔG values). Ten nsSNPs were identified as potential cancer drivers. Expression profiling showed differential PDCD1 expression in tumor versus normal tissues, correlating with improved survival in skin melanoma but limited value in ovarian cancer. Regulatory SNPs disrupted miRNA-binding sites and transcriptional regulation, affecting PDCD1 expression. STRING analysis revealed key PD-1 protein partners within immune pathways, including PD-L1 and PD-L2. Conclusions: This study highlights the significance of PDCD1 nsSNPs as potential biomarkers for cancer susceptibility, advancing the understanding of PD-1 regulation. Experimental validation and multi-omics integration are crucial to refine these findings and enhance theraputic strategies. Full article
(This article belongs to the Special Issue Molecular Diagnostic and Prognostic Markers of Human Cancers)
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14 pages, 2404 KiB  
Article
Prognostic Relevance of Copy Number Losses in Ovarian Cancer
by Andrea Jemma, Alessandra Ardizzoia, Serena Redaelli, Angela Bentivegna, Marialuisa Lavitrano and Donatella Conconi
Genes 2024, 15(11), 1487; https://doi.org/10.3390/genes15111487 - 19 Nov 2024
Viewed by 1364
Abstract
Background/Objectives: Aneuploidy is a prevalent cancer feature that occurs in many solid tumors. For example, high-grade serous ovarian cancer shows a high level of copy number alterations and genomic rearrangements. This makes genomic variants appealing as diagnostic or prognostic biomarkers, as well as [...] Read more.
Background/Objectives: Aneuploidy is a prevalent cancer feature that occurs in many solid tumors. For example, high-grade serous ovarian cancer shows a high level of copy number alterations and genomic rearrangements. This makes genomic variants appealing as diagnostic or prognostic biomarkers, as well as for their easy detection. In this study, we focused on copy number (CN) losses shared by ovarian cancer stem cells (CSCs) to identify chromosomal regions that may be important for CSC features and, in turn, for patients’ prognosis. Methods: Array-CGH and bioinformatic analyses on three CSCs subpopulations were performed. Results: Pathway and gene ontology analyses on genes involved in copy number loss in all CSCs revealed a significant decrease in mRNA surveillance pathway, as well as miRNA-mediated gene silencing. Then, starting from these CN losses, we validated their potential prognostic relevance by analyzing the TCGA cohort. Notably, losses of 4q34.3-q35.2, 8p21.2-p21.1, and 18q12.2-q23 were linked to increased genomic instability. Loss of 18q12.2-q23 was also related to a higher tumor stage and poor prognosis. Finally, specific genes mapping in these regions, such as PPP2R2A and TPGS2A, emerged as potential biomarkers. Conclusions: Our findings highlight the importance of genomic alterations in ovarian cancer and their impact on tumor progression and patients’ prognosis, offering advance in understanding of the application of numerical aberrations as prognostic ovarian cancer biomarkers. Full article
(This article belongs to the Special Issue Molecular Diagnostic and Prognostic Markers of Human Cancers)
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14 pages, 1052 KiB  
Article
Associations between Radiomics and Genomics in Non-Small Cell Lung Cancer Utilizing Computed Tomography and Next-Generation Sequencing: An Exploratory Study
by Alessandro Ottaiano, Francesca Grassi, Roberto Sirica, Emanuela Genito, Giovanni Ciani, Vittorio Patanè, Riccardo Monti, Maria Paola Belfiore, Fabrizio Urraro, Mariachiara Santorsola, Alfonso Maria Ponsiglione, Marco Montella, Salvatore Cappabianca, Alfonso Reginelli, Mario Sansone, Giovanni Savarese and Roberta Grassi
Genes 2024, 15(6), 803; https://doi.org/10.3390/genes15060803 - 18 Jun 2024
Cited by 2 | Viewed by 2143
Abstract
Background: Radiomics, an evolving paradigm in medical imaging, involves the quantitative analysis of tumor features and demonstrates promise in predicting treatment responses and outcomes. This study aims to investigate the predictive capacity of radiomics for genetic alterations in non-small cell lung cancer (NSCLC). [...] Read more.
Background: Radiomics, an evolving paradigm in medical imaging, involves the quantitative analysis of tumor features and demonstrates promise in predicting treatment responses and outcomes. This study aims to investigate the predictive capacity of radiomics for genetic alterations in non-small cell lung cancer (NSCLC). Methods: This exploratory, observational study integrated radiomic perspectives using computed tomography (CT) and genomic perspectives through next-generation sequencing (NGS) applied to liquid biopsies. Associations between radiomic features and genetic mutations were established using the Area Under the Receiver Operating Characteristic curve (AUC-ROC). Machine learning techniques, including Support Vector Machine (SVM) classification, aim to predict genetic mutations based on radiomic features. The prognostic impact of selected gene variants was assessed using Kaplan–Meier curves and Log-rank tests. Results: Sixty-six patients underwent screening, with fifty-seven being comprehensively characterized radiomically and genomically. Predominantly males (68.4%), adenocarcinoma was the prevalent histological type (73.7%). Disease staging is distributed across I/II (38.6%), III (31.6%), and IV (29.8%). Significant correlations were identified with mutations of ROS1 p.Thr145Pro (shape_Sphericity), ROS1 p.Arg167Gln (glszm_ZoneEntropy, firstorder_TotalEnergy), ROS1 p.Asp2213Asn (glszm_GrayLevelVariance, firstorder_RootMeanSquared), and ALK p.Asp1529Glu (glcm_Imc1). Patients with the ROS1 p.Thr145Pro variant demonstrated markedly shorter median survival compared to the wild-type group (9.7 months vs. not reached, p = 0.0143; HR: 5.35; 95% CI: 1.39–20.48). Conclusions: The exploration of the intersection between radiomics and cancer genetics in NSCLC is not only feasible but also holds the potential to improve genetic predictions and enhance prognostic accuracy. Full article
(This article belongs to the Special Issue Molecular Diagnostic and Prognostic Markers of Human Cancers)
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Review

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13 pages, 3573 KiB  
Review
Cornulin as a Key Diagnostic and Prognostic Biomarker in Cancers of the Squamous Epithelium
by Varun Shankavaram, Dean Shah, Aseel Alashqar, Jackson Sweeney and Hilal Arnouk
Genes 2024, 15(9), 1122; https://doi.org/10.3390/genes15091122 - 26 Aug 2024
Cited by 1 | Viewed by 2022
Abstract
The prevalence of squamous cell carcinoma is increasing, and efforts that aid in an early and accurate diagnosis are crucial to improve clinical outcomes for patients. Cornulin, a squamous epithelium-specific protein, has recently garnered attention due to its implications in the progression of [...] Read more.
The prevalence of squamous cell carcinoma is increasing, and efforts that aid in an early and accurate diagnosis are crucial to improve clinical outcomes for patients. Cornulin, a squamous epithelium-specific protein, has recently garnered attention due to its implications in the progression of squamous cell carcinoma developed in several tissues. As an epidermal differentiation marker, it is involved in skin anchoring, regulating cellular proliferation, and is a putative tumor suppressor. The physiologically healthy squamous epithelium displays a considerable level of Cornulin, whereas squamous cell carcinomas have marked downregulation, suggesting that Cornulin expression levels can be utilized for the early detection and follow-up on the progression of these types of cancer. Cornulin’s expression patterns in cervical cancer have been examined, and findings support the stepwise downregulation of Cornulin levels that accompanies the progression to neoplasia in the cervix. Additional studies documented a similar trend in expression in other types of cancer, such as cutaneous, esophageal, and oropharyngeal squamous cell carcinomas. The consistent and predictable pattern of Cornulin expression across several squamous cell carcinomas and its correlation with key clinicopathological parameters make it a reliable biomarker for assessing the transformation and progression events in the squamous epithelium, thus potentially contributing to the early detection, definitive diagnosis, and more favorable prognosis for these cancer patients. Full article
(This article belongs to the Special Issue Molecular Diagnostic and Prognostic Markers of Human Cancers)
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