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Molecular Diagnostics and Genomics of Tumors, 2nd Edition
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Molecular Diagnostics and Genomics of Tumors, 2nd Edition

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: 20 November 2026 | Viewed by 6936

Special Issue Editor

Prof. Dr. Petra Korać

E-Mail Website
Guest Editor
Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
Interests: tumor biology; molecular pathology; medical genetics; cell biology; genomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

As you are aware, in the last few decades, tumor genomics, transcriptomics, and proteomics have become requisite information for precise diagnostics that lead to precise and effective therapy. With the development of molecular methods and accumulation of knowledge about tumor biology, behavior, and progression, new biomarkers arise almost daily. In this Special Issue, we aim to collect recent advances in the field—both basic research-oriented papers from the field of tumor genomics and papers about the development of new approaches in applied genomics. We hope that this issue will cover one of many subjects in this promising field, such as

  • Genomics as a basis for molecular diagnostics;
  • Description of new cancer biomarkers;
  • Cancer genomics insights;
  • Development of precision medicine;
  • Prediction methods in cancer biology;
  • Clinical relevance of tumor genomics data.

Prof. Dr. Petra Korać
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 250 words) can be sent to the Editorial Office for assessment.

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

  • tumor biology
  • cancer genomics
  • molecular diagnostics
  • biomarkers
  • precision medicine

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Published Papers (7 papers)

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Research

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16 pages, 9624 KB  
Article
Modeled Aqueous Humor Protein Concentrations to Enable Biomarker Development in Uveal Melanoma
by Elaine Huang, Yilin Chen, Chen-Ching Peng, Donny Liang, Mark Reid, Atrey Khoche, Peter Kuhn, Jeremy Mason, Xuejuan Jiang, Jesse L. Berry and Liya Xu
Int. J. Mol. Sci. 2026, 27(7), 3124; https://doi.org/10.3390/ijms27073124 - 30 Mar 2026
Viewed by 353
Abstract
Uveal melanoma (UM) lacks minimally invasive and reproducible biomarkers to support clinical risk stratification, motivating the need for molecular profiling of aqueous humor (AH) as an alternative to fine-needle tumor aspiration (FNAB). This study aimed to generate a calibrated AH protein concentration map [...] Read more.
Uveal melanoma (UM) lacks minimally invasive and reproducible biomarkers to support clinical risk stratification, motivating the need for molecular profiling of aqueous humor (AH) as an alternative to fine-needle tumor aspiration (FNAB). This study aimed to generate a calibrated AH protein concentration map to identify tumor-associated signals present at clinically measurable levels and assess their associations with established molecular and clinical features. AH samples from 70 UM eyes were analyzed using next-generation sequencing-based proximity extension assays (PEAs), and leftover AH from 27 samples was further assessed using qPCR-based PEA to obtain reference concentration values. Regression models derived from overlapping proteins enabled extrapolation of calibrated pg/mL-level concentrations across the full cohort. Twenty-three proteins had median modeled concentrations above 5 pg/mL and were examined for clinical relevance and translational feasibility. Several proteins, including CXCL8, CXCL10, VEGFA, HGF, PDCD1, FLT1, FLT3LG, and CCL2, showed progressive increases from GEP1/PRAME− to GEP2/PRAME+ tumors and from AJCC Stage I/II to Stage III/IV, with Stage IV tumors demonstrating significant elevations in CXCL8, VEGFA, and PDCD1. Pathway analysis revealed activation of inflammatory and tumor microenvironment pathways, and upstream regulator analysis identified VEGFA and CCL2 as potential drivers. These findings demonstrate that calibrated AH proteomic profiling can identify clinically measurable protein changes associated with UM risk and stage, supporting its potential utility for biomarker development. Full article
(This article belongs to the Special Issue Molecular Diagnostics and Genomics of Tumors, 2nd Edition)
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12 pages, 3484 KB  
Article
ESCO2 Interacts with TRF1/2 and Facilitates Telomere Maintenance
by Jiahui Guo, Jingjing Ji, Jinfeng Liu and Mengfan Tang
Int. J. Mol. Sci. 2026, 27(6), 2635; https://doi.org/10.3390/ijms27062635 - 13 Mar 2026
Viewed by 375
Abstract
Establishment of sister chromatid cohesion N-acetyltransferase 2 (ESCO2) is an acetyltransferase involved in sister chromatid cohesion. Here we demonstrated that ESCO2 has a new role in telomere maintenance through its binding with telomeric repeat-binding factor TRF1 and TRF2. Loss of ESCO2 induces aberrant [...] Read more.
Establishment of sister chromatid cohesion N-acetyltransferase 2 (ESCO2) is an acetyltransferase involved in sister chromatid cohesion. Here we demonstrated that ESCO2 has a new role in telomere maintenance through its binding with telomeric repeat-binding factor TRF1 and TRF2. Loss of ESCO2 induces aberrant DNA damage at telomeres and leads to dramatic telomere shortening. ESCO2 associates with several proteins involved in DNA replication and repair, including BLM, WRN, TopBP1, BRIP1, BRCA1, and MUS81. Moreover, we show that ESCO2 acts in epistasis with BLM in promoting telomere stability. Taken together, our data suggest that ESCO2 is required for the maintenance of telomere stability, presumably by coordinating multiple replication and repair factors to facilitate telomere replication and protection. Full article
(This article belongs to the Special Issue Molecular Diagnostics and Genomics of Tumors, 2nd Edition)
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27 pages, 8014 KB  
Article
Molecular Context of ADAR-Mediated Editing of Coding RNA in Colorectal and Lung Cancers
by Alexander Modestov, Daniil Luppov, Ivan Gaziev, Nikita Golushko, Galina Zakharova, Marianna Zolotovskaia, Elena Poddubskaya, Alexander Seryakov, Vladimir Prassolov, Marina Sekacheva and Anton Buzdin
Int. J. Mol. Sci. 2026, 27(6), 2625; https://doi.org/10.3390/ijms27062625 - 13 Mar 2026
Viewed by 470
Abstract
RNA editing is a critical post-transcriptional modification that contributes to transcriptomic and proteomic diversity. The most common A-to-I (recognized as G) RNA editing enzymes are adenosine deaminases acting on RNA 1 and 2 (ADAR1 and ADAR2, respectively), which mediate alterations across all regions [...] Read more.
RNA editing is a critical post-transcriptional modification that contributes to transcriptomic and proteomic diversity. The most common A-to-I (recognized as G) RNA editing enzymes are adenosine deaminases acting on RNA 1 and 2 (ADAR1 and ADAR2, respectively), which mediate alterations across all regions of mRNA molecules. However, a systematic cross-tissue view of RNA editing and its molecular correlates is still lacking. Here, we developed a rapid method for ADAR editing assessment based on 24 frequently edited positions in coding regions, which enables faster estimation of RNA editing levels than previous methods. We applied this metric to assess RNA editing in normal and cancerous lung and colorectal tissues. We analyzed RNA and whole exome sequencing profiles of experimental 172 colorectal and 144 lung cancer samples, and literature 646 colorectal and 1037 lung cancer samples. We also examined two types of control tissues: tumor-matched normal tissues (51 colorectal and 108 lung samples) and healthy tissues (6 colorectal and 7 lung samples). Overall ADAR-mediated RNA editing levels were ~2.9- and ~4.7-fold higher in healthy controls than in colorectal and lung cancers, respectively. In addition to their well-known association with immune cells, we identified positive correlations of ADAR editing with 740 molecular pathways including those responsible for extracellular matrix organization, RAS-MAPK axis and G2/M phase cell cycle arrest, and negative—with 139 pathways responsible for DNA repair, apoptosis, expression of transposable elements, and other factors. Full article
(This article belongs to the Special Issue Molecular Diagnostics and Genomics of Tumors, 2nd Edition)
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21 pages, 2597 KB  
Article
Accurate RET Fusion Detection in Solid Tumors Using RNA Sequencing Coverage Imbalance Analysis
by Ivan Gaziev, Anna Khristichenko, Daniil Luppov, Maria Suntsova, Ekaterina Bondarenko, Maria Reinberg, Alina Matrosova, Nadezhda Khilal, Maksim Sorokin, Marina Sekacheva, Elena Poddubskaya, Anton Buzdin and Galina Zakharova
Int. J. Mol. Sci. 2025, 26(23), 11300; https://doi.org/10.3390/ijms262311300 - 22 Nov 2025
Viewed by 1212
Abstract
Accurate detection of oncogenic gene fusions is becoming increasingly important given the availability of highly effective targeted therapies. However, their identification in clinical practice remains challenging due to the rarity of individual events, diversity of partner genes, and variability of breakpoint locations. Conventional [...] Read more.
Accurate detection of oncogenic gene fusions is becoming increasingly important given the availability of highly effective targeted therapies. However, their identification in clinical practice remains challenging due to the rarity of individual events, diversity of partner genes, and variability of breakpoint locations. Conventional approaches such as immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) lack multiplexing capacity and demonstrate variable sensitivity and specificity, while direct identification of fusion transcripts in whole-transcriptome sequencing (RNA-seq) profiles provides broader applicability but limited sensitivity, as fusion junctions are frequently supported by a minimal number of reads or even no reads at all. In this study, a novel approach was employed to accurately detect clinically actionable RET (REarranged during Transfection) fusions. This approach entailed the measurement of the imbalance in RNA-seq read coverage of potential fusion oncogenes at their 3′ and 5′ exons. A total of 1327 experimental solid tumor RNA-seq profiles were screened, including 154 non-small cell lung cancer and 221 thyroid cancer samples. The RET status was validated in 78 selected cases by targeted NGS and Sanger sequencing. An analysis of the coverage imbalance was conducted, which enabled the accurate discrimination between true and false positive RET fusions. This approach outperformed other methods and yielded 100% sensitivity and specificity with optimized thresholds. The findings were validated using an independent cohort of 79 thyroid cancer cases, confirming the reliability of the results. Among the 18 RET fusion-positive samples, one was identified as an extremely rare case (RUFY3::RET), and two were determined to be novel fusions (FN1::RET, PPP1R21::RET). The findings of this study demonstrate that exon coverage imbalance analysis serves as a robust complement to computational RNA-seq analysis pipelines for the detection of clinically relevant RET fusions. Full article
(This article belongs to the Special Issue Molecular Diagnostics and Genomics of Tumors, 2nd Edition)
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13 pages, 1818 KB  
Article
During the Formation of Vasculogenic Mimicry by Melanoma Cells, the Silencing of Two Sets of Developmental Genes Is Coupled Either with an Increase or a Decrease in Contacts with the Nucleoli
by Nickolai A. Tchurikov, Elena S. Klushevskaya, Viktoriya N. Lukicheva, Antonina N. Kretova, Elizaveta N. Poperekova, Vladimir R. Chechetkin, Galina I. Kravatskaya, Amalia A. Vartanian, Ildar R. Alembekov and Yuri V. Kravatsky
Int. J. Mol. Sci. 2025, 26(23), 11289; https://doi.org/10.3390/ijms262311289 - 22 Nov 2025
Viewed by 617
Abstract
Vasculogenic mimicry is the capacity of growing cancer cells to overcome the lack of normal capillaries and hypoxia by forming networks of sinuses lacking endothelial cells. The formation of vasculogenic mimicry by melanoma cells is coupled with the upregulation of the genes involved [...] Read more.
Vasculogenic mimicry is the capacity of growing cancer cells to overcome the lack of normal capillaries and hypoxia by forming networks of sinuses lacking endothelial cells. The formation of vasculogenic mimicry by melanoma cells is coupled with the upregulation of the genes involved in ribosome biogenesis, the downregulation of hundreds of developmental genes, and strong changes in the inter-chromosomal contacts of developmental genes with rDNA clusters. The epigenetic mechanism driving the regulatory role of inter-chromosomal contacts of genes with nucleoli is not yet known. This study aimed to determine whether these contacts are associated with either the silencing or the activation of the expression of developmental genes. Here, two different sets of developmental genes are subjected to silencing either by increasing or decreasing their contacts with nucleoli. Our data indicate that one set of developmental genes mainly associated with system development is silenced by the contacts, while another set of genes involved mainly in the generation of neurons is silenced by the loss of contacts with the nucleoli. We conclude that mechanisms of silencing of these sets of developmental genes lead to the loss of the established differentiated state of melanoma cells and to the formation of more aggressive cancer cells. The data also indicate the important role of the nucleoli in the global regulation of gene expression during differentiation and cancer. Full article
(This article belongs to the Special Issue Molecular Diagnostics and Genomics of Tumors, 2nd Edition)
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Review

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29 pages, 3250 KB  
Review
Machine Learning Models for Cancer Research: A Narrative Review of Bulk RNA-Seq Applications
by Elena A. Pudova, Vladislav S. Pavlov, Zulfiya G. Guvatova, Maria S. Fedorova, Petr V. Shegai, Anna V. Kudryavtseva and Anastasiya V. Snezhkina
Int. J. Mol. Sci. 2025, 26(24), 12081; https://doi.org/10.3390/ijms262412081 - 16 Dec 2025
Cited by 1 | Viewed by 1898
Abstract
Integrating the advantages of machine learning with the rapidly accumulating high-throughput sequencing data facilitates our capacity for biological discovery and the advancement of molecular medicine. In recent years, bulk RNA-seq technology has established itself as a cost-effective and widely used method for obtaining [...] Read more.
Integrating the advantages of machine learning with the rapidly accumulating high-throughput sequencing data facilitates our capacity for biological discovery and the advancement of molecular medicine. In recent years, bulk RNA-seq technology has established itself as a cost-effective and widely used method for obtaining complete transcriptome profiles of test samples, enabling the identification of key cancer-associated expression patterns. Various machine learning algorithms, in turn, enable the development of informative diagnostic and prognostic models, ensuring the efficient processing of high-dimensional RNA-Seq data. The convergence of these methods shows great promise for oncology. In this narrative review, we describe bulk RNA-Seq-based ML models in oncology as a complete workflow from data preprocessing to model validation. We provide practical recommendations for algorithm selection and study design, and discuss bulk RNA-Seq deconvolution as a cost-effective alternative to single-cell RNA-Seq for analyzing tumor cellular composition. These insights offer a practical guide for developing reproducible diagnostic and prognostic models with translational potential. Full article
(This article belongs to the Special Issue Molecular Diagnostics and Genomics of Tumors, 2nd Edition)
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20 pages, 2285 KB  
Review
Regulatory Mechanisms and Functional Roles of Readthrough Transcripts in Tumorigenesis
by Alexander Modestov, Galina Zakharova, Elena Poddubskaya and Anton Buzdin
Int. J. Mol. Sci. 2025, 26(20), 9975; https://doi.org/10.3390/ijms26209975 - 14 Oct 2025
Cited by 1 | Viewed by 1416
Abstract
The search for novel tumor-specific markers and therapeutic targets is driving the development of more effective and personalized treatment strategies for cancer patients. This article focuses on investigating a promising new source of biomarkers—readthrough transcripts, or downstream-of-gene (DoG) transcripts. These transcripts are extended [...] Read more.
The search for novel tumor-specific markers and therapeutic targets is driving the development of more effective and personalized treatment strategies for cancer patients. This article focuses on investigating a promising new source of biomarkers—readthrough transcripts, or downstream-of-gene (DoG) transcripts. These transcripts are extended products of gene transcription that continue into intergenic regions and can overlap neighboring genes, sometimes giving rise to cis-splicing of adjacent gene (cis-SAGe) transcripts. Recent studies suggest that besides frequently being a “transcriptional noise”, DoG transcripts can perform regulatory functions, serve as a source of novel protein products, and act as prognostic markers of patient survival across various cancers. This article aims to investigate the regulatory mechanisms and functional significance of readthrough transcripts in tumors, to identify currently known tumor-specific variants with potential utility as cancer biomarkers or therapeutic targets, and to evaluate the most suitable approaches for their detection. The knowledge gained through this research may provide a foundation for the development of diagnostic test systems and the design of new anticancer drugs. Full article
(This article belongs to the Special Issue Molecular Diagnostics and Genomics of Tumors, 2nd Edition)
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