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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: 20 August 2026 | Viewed by 10086

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Dr. Yoshihito Kano

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Guest Editor

Department of Clinical Oncology, Graduate School of Medical and Dental Sciences, Institute of Science Tokyo, 1-5-45 Yushima, Bunkyo-Ku, Tokyo 113-8510, Japan
Interests: medical oncology; cancer genomic medicine; targeted therapy

Special Issue Information

Dear Colleagues,

This Special Issue will focus on recent advances in cancer genomics, covering a wide range of topics such as genomic and structural variations, biomarker discovery, and novel methodologies for understanding cancer biology. With the rapid development of emerging technologies, we also welcome studies that explore computational approaches, artificial intelligence, and their potential to enhance the interpretation of complex genomic data. These technologies hold promise for improving patient outcomes and accelerating precision oncology.

Contributions addressing the integration of genomics into clinical practice, highlighting translational research, or proposing innovative solutions to current challenges in cancer genomics are particularly encouraged. Furthermore, we are interested in research targeting "undruggable" oncogenes, such as KRAS, focusing on drug discovery and development strategies that overcome previous limitations. Studies exploring novel therapeutic approaches and molecular mechanisms to address these challenging targets are highly welcomed.

This Special Issue aims to provide a platform for cutting-edge and multidisciplinary research that pushes the boundaries of cancer genomics and fosters collaboration across different scientific domains.

Topics of interest include, but are not limited to:

Genomic and structural variations in cancer
Biomarker discovery for precision oncology
The integration of multi-omics data with AI for personalized cancer care
AI-driven diagnostics and treatment planning in oncology
Drug discovery for undruggable targets, including KRAS

Dr. Yoshihito Kano
Guest Editor

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Keywords

cancer genomics
biomarker discovery
precision oncology
KRAS and undruggable targets
artificial intelligence in oncology
multi-omics data integration
drug discovery

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Published Papers (7 papers)

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12 pages, 1107 KB

Open AccessArticle

Evaluation of NTRK Fusions Detection Method in Esophageal Squamous Cell Carcinoma and Gastric Adenocarcinoma

by Tomoyuki Momma, Motonobu Saito, Shotaro Nakajima, Katsuharu Saito, Erika Machida, Ken Miyabe, Yusuke Sato, Hiroyuki Hanayama, Hirokazu Okayama, Zenichiro Saze, Kosaku Mimura, Naoto Tsuchiya, Akiteru Goto, Kouya Shiraishi and Koji Kono

Int. J. Mol. Sci. 2026, 27(1), 336; https://doi.org/10.3390/ijms27010336 - 28 Dec 2025

Viewed by 912

Abstract

Neurotrophic tyrosine receptor kinase (NTRK) fusions function as oncogenes and have been targeted by TRK inhibitors with excellent clinical outcomes. The international expert consensus recommends immunohistochemical (IHC) screening for TRK protein followed by next generation sequencing (NGS) to measure expression of NTRK fusions for tumors with low NTRK fusion expression. To confirm the clinical utility of this recommendation in esophageal and gastric cancers, total TRK protein expression was measured by IHC using anti-pan-TRK antibody in 254 esophageal squamous cell carcinoma (ESCC) and 401 gastric adenocarcinoma (GA) samples. Subsequently, DNA-based NGS and fluorescence in situ hybridization (FISH) were performed for tumors expressing TRK to measure NTRK fusion expression. Further, expression of NTRK fusions was evaluated in esophageal and gastric cancers using public databases. IHC staining revealed TRK was expressed in 10 out of 254 ESCC and 0 out of 401 GC cases. NGS and FISH analyses were performed for 10 TRK positive ESCC cases, identifying that none of these cases harbored NTRK fusions. In silico analyses further confirmed that NTRK fusions are rarely present in esophageal and gastric cancers. IHC screening for TRK protein is recommended to detect NTRK fusions, but this method may include many false-positives cases based on the sequencing analysis. Full article

(This article belongs to the Special Issue New Advances in Cancer Genomics)

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15 pages, 2843 KB

Open AccessArticle

Nucleotide Substitution Biases in Related Cancer Driver Genes

by Adam Khadre, Yifan Dou, Golrokh C. Mirzaei and Ruben C. Petreaca

Int. J. Mol. Sci. 2025, 26(24), 11903; https://doi.org/10.3390/ijms262411903 - 10 Dec 2025

Viewed by 798

Abstract

Nucleotide substitutions are common in cancer cells, and they occur in both protein coding regions and non-coding regions (5′ and 3′ UTRs and introns). Although substitutions in non-coding regions have the potential to alter gene expression, it is the alteration of coding regions that affects protein function and has the most drastic effect on cellular transformation. Mutations in certain genes (e.g., TP53, KRAS) are common to nearly all cancers, but most cancers are characterized by specific gene mutation signatures. In this report, we investigated nucleotide substitution signatures in coding regions of the top 25 most frequently mutated genes in multiple human cancers. The goal was to examine whether unique nucleotide substitution biases are associated with various cancers. A pan-cancer analysis showed that the most altered nucleotide is guanine, which is biased towards G->A transitions. A per-cancer analysis identified ten cancers with biased substitutions in certain genes. Some of these biases were expected (e.g., KRAS in gastrointestinal cancers or JAK2 in blood cancers). Our analysis revealed biased signature substitutions in 17 genes, of which 14 were characterized as drivers and constituted a closely related set of cell cycle regulators. We conclude that nucleotide substitution biases contribute to specific alterations in cancer genes that produce cellular transformation. Principle component analysis of nucleotide substitutions shows that most cancers cluster together, meaning that they have similar nucleotide changes. However, certain cancers, most notably lung, pancreas, and blood cancers, can be differentiated from each other based on specific nucleotide signatures. Thus, nucleotide substitution patterns can be used to differentiate between some cancers. Full article

(This article belongs to the Special Issue New Advances in Cancer Genomics)

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25 pages, 10302 KB

Open AccessArticle

Deciphering the Role of ADAMTS6 in the Epithelial–Mesenchymal Transition of Lung Adenocarcinoma Cells

by Kirill V. Odarenko, Anastasiya M. Matveeva, Grigory A. Stepanov, Marina A. Zenkova and Andrey V. Markov

Int. J. Mol. Sci. 2025, 26(24), 11850; https://doi.org/10.3390/ijms262411850 - 8 Dec 2025

Viewed by 773

Abstract

A disintegrin and metalloproteinase with thrombospondin motifs 6 (ADAMTS6) is an extracellular matrix (ECM) protease that promotes the invasion of lung adenocarcinoma (LUAD) cells. Herein, we investigate its role in epithelial-mesenchymal transition (EMT), a process that drives metastasis and drug resistance in LUAD. Re-analysis of microarray and RNA sequencing data from LUAD cells revealed that during EMT, TGF-β1 increased ADAMTS6 expression, presumably through the SMAD pathway, as SMAD2 loss completely blocked this effect. Moreover, ADAMTS6 was shown to occupy hub positions within TGF-β1-associated gene networks. Using additional datasets, we found that ADAMTS6 expression increased under other EMT-inducing conditions, including IL-1β induction and acquired gefitinib resistance, but decreased upon knockdown of Twist1, a master regulator of EMT. Knockout of ADAMTS6 repressed colony formation, migration, invasion, and doxorubicin resistance but enhanced cell–ECM adhesion in A549 cells. This effect was mediated by EMT inhibition, evidenced by upregulation of E-cadherin and downregulation of N-cadherin, vimentin, and Twist1, and was accompanied by suppressed nuclear translocation of the NF-κB p65 subunit. Re-analysis of transcriptomic data from patient tumors demonstrated that high ADAMTS6 expression correlated with the expression of EMT markers, further supporting the ADAMTS6–EMT link. Moreover, high ADAMTS6 expression was associated with worse survival prognosis. Overall, ADAMTS6 promotes EMT in LUAD cells and may be considered a marker of this process, as well as a potential therapeutic target for its inhibition. Full article

(This article belongs to the Special Issue New Advances in Cancer Genomics)

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18 pages, 1337 KB

Open AccessArticle

Dysregulated Alternative Splicing in Breast Cancer Subtypes of RIF1 and Other Transcripts

by Emma Parker, Laura Akintche, Alexandra Pyatnitskaya, Shin-ichiro Hiraga and Anne D. Donaldson

Int. J. Mol. Sci. 2025, 26(15), 7308; https://doi.org/10.3390/ijms26157308 - 29 Jul 2025

Viewed by 1671

Abstract

Genome instability is a hallmark of cancer, often driven by mutations and altered expression of genome maintenance factors involved in DNA replication and repair. Rap1 Interacting Factor 1 (RIF1) plays a crucial role in genome stability and is implicated in cancer pathogenesis. Cells express two RIF1 splice variants, RIF1-Long and RIF1-Short, which differ in their ability to protect cells from DNA replication stress. Here, we investigate differential expression and splicing of RIF1 in cancer cell lines following replication stress and in patients using matched normal and tumour data from The Cancer Genome Atlas (TCGA). Overall RIF1 expression is altered in several cancer types, with increased transcript levels in colon and lung cancers. RIF1 also exhibits distinct splicing patterns, particularly in specific breast cancer subtypes. In Luminal A (LumA), Luminal B (LumB), and HER2-enriched breast cancers (HER2E), RIF1 Exon 31 tends to be excluded, favouring RIF1-Short expression and correlating with poorer clinical outcomes. These breast cancer subtypes also tend to exclude other short exons, suggesting length-dependent splicing dysregulation. Basal breast cancer also shows exon exclusion, but unlike other subtypes, it shows no short-exon bias. Surprisingly, however, in basal breast cancer, RIF1 Exon 31 is not consistently excluded, which may impact prognosis since RIF1-Long protects against replication stress. Full article

(This article belongs to the Special Issue New Advances in Cancer Genomics)

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25 pages, 3180 KB

Open AccessArticle

CCR4-NOT Transcription Complex Subunit 7 (CNOT7) Protein and Leukocyte-Associated Immunoglobulin-like Receptor-1 in Breast Cancer Progression: Clinical Mechanistic Insights and In Silico Therapeutic Potential

by Mona M. Elanany, Dina Mostafa, Ahmad A. Hady, Mona Y. Y. Abd Allah, Nermin S. Ahmed, Nehal H. Elghazawy, Wolfgang Sippl, Tadashi Yamamoto and Nadia M. Hamdy

Int. J. Mol. Sci. 2025, 26(15), 7141; https://doi.org/10.3390/ijms26157141 - 24 Jul 2025

Viewed by 1927

Abstract

Metastatic breast cancer (BC) spread underscores the need for novel prognostic biomarkers. This study investigated CCR4-NOT Transcription Complex Subunit 7 (CNOT7) and leukocyte-associated immunoglobulin-like receptor-1 (LAIR-1) in BC progression and natural killer (NK) cell resistance. In the current study, 90 female BC patients (46 non-metastatic, 44 metastatic) were analyzed. CNOT7 and LAIR-1 protein levels were measured in serum via ELISA and CNOT7 expression in tissue by immunohistochemistry (IHC). In silico tools explored related pathways. Computational analyses, including in silico bioinformatics and molecular docking, explored gene functions, interactions, and ligand binding to CNOT7 and LAIR-1. CNOT7 serum levels were significantly elevated in metastatic patients (mean 4.710) versus non-metastatic patients (mean 3.229, p < 0.0001). Conversely, LAIR-1 serum levels were significantly lower in metastatic (mean 56.779) versus non-metastatic patients (mean 67.544, p < 0.0001). High CNOT7 was found in 50% (45/90) of cases, correlating with higher tumor grade, hormone receptor negativity, and increased lymph node involvement. Elevated CNOT7 and lower LAIR-1 levels were associated with worse overall survival. Pathway analysis linked CNOT7 to the PI3K/AKT/mTOR pathway. Computational findings elucidated CNOT7′s cellular roles, gene/protein interaction networks for LAIR-1/CNOT7, and distinct ligand binding profiles. High CNOT7 levels are associated with advanced BC stages and poor clinical outcomes, which suggests its utility as a prognostic biomarker. The inverse relationship between CNOT7 and LAIR-1 provides mechanistic insights into BC progression and immune evasion, further supported by in silico investigations. Full article

(This article belongs to the Special Issue New Advances in Cancer Genomics)

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26 pages, 6652 KB

Open AccessArticle

Platelet-Rich Plasma (PRP) Mitigates Silver Nanoparticle (AgNP)-Induced Pulmonary Fibrosis via iNOS/CD68/CASP3/TWIST1 Regulation: An Experimental Study and Bioinformatics Analysis

by Shaimaa R. Abdelmohsen, Ranya M. Abdelgalil, Asmaa M. Elmaghraby, Amira M. Negm, Reham Hammad, Eleni K. Efthimiadou, Sara Seriah, Hekmat M. El Magdoub, Hemat Elariny, Islam Farrag, Nahla El Shenawy, Doaa Abdelrahaman, Hussain Almalki, Ahmed A. Askar, Marwa M. El-Mosely, Fatma El Zahraa Abd El Hakam and Nadia M. Hamdy

Int. J. Mol. Sci. 2025, 26(14), 6782; https://doi.org/10.3390/ijms26146782 - 15 Jul 2025

Viewed by 2210

Abstract

Platelet-rich plasma (PRP) has become an increasingly valuable biologic approach for personalized regenerative medicine because of its potent anti-inflammatory/healing effects. It is thought to be an excellent source of growth factors that can promote tissue healing and lessen fibrosis. Although this treatment has demonstrated effectiveness in numerous disease areas, its impact on pulmonary fibrosis (PF) caused by silver nanoparticles (AgNPs) via its antiapoptotic effects remains to be explored. AgNPs were synthesized biologically by Bacillus megaterium ATCC 55000. AgNP characterization was carried out via UV–Vis spectroscopy, X-ray diffraction (XRD), dynamic light scattering (DLS), transmission electron microscopy (TEM), and scanning electron microscopy (SEM) imaging to reveal monodispersed spheres with a mean diameter of 45.17 nm. A total of 48 male Wistar rats divided into six groups, with 8 rats per group, were used in the current study on the basis of sample size and power. The groups used were the PRP donor, control, AgNP, AgNP + PRP, AgNP + dexamethasone (Dexa) rat groups, and a recovery group. Body weights, hydroxyproline (HP) levels, and CASP3 and TWIST1 gene expression levels were assessed. H&E and Sirius Red staining were performed. Immunohistochemical studies for inducible nitric oxide synthase (iNOS) and cluster of differentiation 68 (CD68) with histomorphometry were conducted. A significant reduction in body weight (BWt) was noted in the AgNP group compared with the AgNP + PRP group (p < 0.001). HP, CASP3, and TWIST1 expression levels were significantly increased by AgNPs but decreased upon PRP (p < 0.001) treatment. Compared with those in the control group, the adverse effects of AgNPs included PF, lung alveolar collapse, thickening of the interalveolar septa, widespread lymphocytic infiltration, increased alveolar macrophage CD68 expression, and iNOS positivity in the cells lining the alveoli. This work revealed that PRP treatment markedly improved the histopathological and immunohistochemical findings observed in the AgNP group in a manner comparable to that of the Dexa. In conclusion, these results demonstrated the therapeutic potential of PRP in a PF rat model induced via AgNPs. This study revealed that PRP treatment significantly improved the histopathological and immunohistochemical alterations observed in the AgNP-induced group, with effects comparable to those of the Dexa. In conclusion, these findings highlight the therapeutic potential of PRP in a rat model of AgNP-induced PF. Full article

(This article belongs to the Special Issue New Advances in Cancer Genomics)

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15 pages, 1285 KB

Open AccessCase Report

Longitudinal Whole-Exome Sequencing of Cell-Free DNA Reveals Molecular Evolution and Heterogeneous Clinical Outcomes in PD-L1 Stratified Advanced NSCLC Adenocarcinoma Patients Treated with Atezolizumab

by Viola Bianca Serio, Tommaso Regoli, Debora Maffeo, Ignazio Martellucci, Diletta Rosati, Marco Ghisalberti, Alberto Balistreri, Gianluca Santamaria, Niccolò Vono, Francesca Mari, Francesca Colombo, Elisa Frullanti and Maria Palmieri

Int. J. Mol. Sci. 2026, 27(7), 2947; https://doi.org/10.3390/ijms27072947 - 24 Mar 2026

Viewed by 913

Abstract

Programmed death-ligand 1 (PD-L1) expression is routinely used to guide immune checkpoint inhibitor (ICI) therapy in advanced non-small cell lung cancer (NSCLC), yet clinical benefit remains heterogeneous even among PD-L1–high tumors. Liquid biopsy based on cell-free DNA (cfDNA) enables minimally invasive, real-time monitoring of tumor evolution. We report four cases of metastatic lung adenocarcinoma treated with atezolizumab, integrating longitudinal whole-exome sequencing (WES) of cfDNA with radiological assessment. Four patients with PD-L1–positive (≥60%) metastatic NSCLC received atezolizumab monotherapy. Serial cfDNA samples (1–3 per patient) were analyzed by high-depth WES. Distinct molecular trajectories paralleled divergent clinical outcomes. One patient achieved a complete molecular response, characterized by progressive clearance of KRAS, ATM, and NF1 mutant clones, which was concordant with radiological remission. A second patient showed an initial molecular response, followed by clonal rebound of TP53, NF1, and NOTCH2 mutant populations and the emergence of PTEN and KIF1A variants, suggesting clinical progression. Two patients exhibited primary resistance despite high PD-L1 expression, with persistent or expanding clones and early subclonal diversification; in one case, new EGFR and BRAF alterations emerged under treatment pressure. Notably, switching to platinum-based chemotherapy in a non-responder induced a measurable molecular response, highlighting discordance between PD-L1 status and immunotherapy efficacy. Longitudinal cfDNA WES captured dynamic clonal remodeling under immunotherapy and anticipated radiological outcomes. These findings underscore the clinical necessity of integrating dynamic molecular monitoring by liquid biopsy to overcome the limitations of static PD-L1 assessment, refine therapeutic stratification, and identify early resistance mechanisms in advanced NSCLC. Full article

(This article belongs to the Special Issue New Advances in Cancer Genomics)

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