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Linking Genomic Changes with Cancer in the NGS Era, 2nd Edition

A special issue of Current Issues in Molecular Biology (ISSN 1467-3045). This special issue belongs to the section "Bioinformatics and Systems Biology".

Deadline for manuscript submissions: 31 August 2025 | Viewed by 3393

Special Issue Editors

Prof. Dr. Javier Azúa-Romeo

E-Mail Website
Guest Editor
Department of Human Anatomy and Histology, Faculty of Medicine, University of Zaragoza, 50009 Zaragoza, Spain
Interests: pathology; histology; cancer; biomakers; molecular biology; cytology
Dr. Paula Paulo

E-Mail Website
Guest Editor
Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal
Interests: prostate cancer; inherited cancer predisposition; DNA-repair; molecular tumor subtypes; targeted cancer therapeutics; CRISPR/Cas9 gene editing; functional assays
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The arrival and evolution of next-generation sequencing (NGS) technology has enlarged our capacity to read genetic code in-depth, beginning a new era in the identification of disease-causing genetic changes. While our ability to “read” individual genetic changes has dramatically increased, the “translationability” of the identified changes is complex, and the establishment of a new driver gene/variant constitutes a NGS-based genetic screening bottleneck. This is particularly true in cancer, where only a very small fraction of the 10–20% of the cancers associated with familial aggregation have a known underlying genetic cause. Moreover, the profile of genomic changes in the 80–90% of the cancers arising sporadically is highly heterogeneous, making it difficult to distinguish driving, secondary and progression-associated genomic variation.     

In this Special Issue, we invite researchers to submit their work highlighting or discarding the identification of new genes/variants as a cause of cancer development or progression. Evidence may include case–control studies, segregation analysis, gene/variant specific gene editing (CRISPR/Cas9 or other), protein structure analysis, functional studies, or other approaches considered relevant for validation of a gene–disease association.

You can read the publications in the first volume of our Special Issue here:
https://www.mdpi.com/journal/cimb/special_issues/genomic_cancer_

Prof. Dr. Javier Azúa-Romeo
Dr. Paula Paulo
Guest Editors

Manuscript Submission Information

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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. Current Issues in Molecular Biology 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 2200 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

  • next-generation sequencing (NGS)
  • genetic variation
  • driver gene
  • functional validation
  • gene editing
  • cancer

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Published Papers (4 papers)

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Research

16 pages, 10927 KiB  
Article
Oncogene-Induced Senescence Transcriptomes Signify Premalignant Colorectal Adenomas
by Sofian Al Shboul, Heyam Awad, Anas Abu-Humaidan, Nidaa A. Ababneh, Ashraf I. Khasawneh and Tareq Saleh
Curr. Issues Mol. Biol. 2025, 47(4), 221; https://doi.org/10.3390/cimb47040221 - 25 Mar 2025
Viewed by 197
Abstract
Background: Oncogene-induced senescence (OIS) is a tumor-suppressive mechanism that halts uncontrolled cell proliferation in premalignant lesions. Further investigation into its role in colorectal tumorigenesis is essential. We investigated the expression of OIS transcriptomic landscapes in premalignant colorectal adenomas and whether their resolution is [...] Read more.
Background: Oncogene-induced senescence (OIS) is a tumor-suppressive mechanism that halts uncontrolled cell proliferation in premalignant lesions. Further investigation into its role in colorectal tumorigenesis is essential. We investigated the expression of OIS transcriptomic landscapes in premalignant colorectal adenomas and whether their resolution is part to adenoma-to-carcinoma progression. Methods: Using a publicly available gene expression dataset (GSE117606), we analyzed 66 paired (matched) adenoma–adenocarcinoma samples. Single-sample gene set enrichment analysis (ssGSEA) was performed to assess OIS and senescence-associated secretory phenotype (SASP) signatures, and differential gene expression analysis was conducted to examine key senescence-related genes. Results: OIS and SASP signatures were significantly enriched in adenomas compared to adenocarcinomas (p < 0.05). Pairwise comparisons confirmed that 65% of patients exhibited higher OIS scores in adenomas, while SASP enrichment declined in 59–61% of cases. Several senescence regulators (CDKN1A, CDKN2B, and E2F3), ECM remodeling genes (MMP10 and TIMP2), and NF-κB-driven SASP factors (CCL2, CXCL2, NFKB1, and NFKB2) were significantly downregulated in adenocarcinomas, indicating the resolution of senescence-associated inflammatory signaling during tumor progression. Conclusions: These findings support the predominance of OIS phenotypes in colorectal adenomas, suggesting their potential role as a temporary barrier to tumorigenesis in colorectal cancer. Full article
(This article belongs to the Special Issue Linking Genomic Changes with Cancer in the NGS Era, 2nd Edition)
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23 pages, 8865 KiB  
Article
A Novel Ferroptosis-Related Gene Prognosis Signature and Identifying Atorvastatin as a Potential Therapeutic Agent for Hepatocellular Carcinoma
by Ling Wang, Xiaoqin He, Yang Shen, Jiayu Chen, Yukai Chen, Zhuolin Zhou and Ximing Xu
Curr. Issues Mol. Biol. 2025, 47(3), 201; https://doi.org/10.3390/cimb47030201 - 18 Mar 2025
Viewed by 307
Abstract
Among the most common malignant tumors, hepatocellular carcinoma (HCC) is a primary liver cancer type that has a high mortality rate. HCC often presents insidiously, is prone to recurrence, and has limited treatment efficacy. Ferroptosis regulates tumorigenesis, progression, and metastasis, which is a [...] Read more.
Among the most common malignant tumors, hepatocellular carcinoma (HCC) is a primary liver cancer type that has a high mortality rate. HCC often presents insidiously, is prone to recurrence, and has limited treatment efficacy. Ferroptosis regulates tumorigenesis, progression, and metastasis, which is a novel form of iron-dependent cell death. Numerous studies suggest that HCC is sensitive to ferroptosis, indicating that targeted therapies aimed at inducing ferroptosis may represent a promising new approach to cancer treatment. This study aims to find genes associated with HCC and ferroptosis, as well as to screen for potential agents that may cause ferroptosis in HCC. Transcriptome and clinical sample data were obtained from the TCGA database to identify differentially expressed genes related to ferroptosis. Using various regression and survival analysis techniques, we developed a prognostic model based on four core genes and evaluated its predictive potential. Subsequently, we screened for potential therapeutic agents in the Connective Map (CMap) database, designated as compound Atorvastatin, based on differential genes from two risk groups and related to ferroptosis. Through experiments conducted in vivo and in vitro, we demonstrated that Atorvastatin can induce ferroptosis in HCC cells while inhibiting their growth and migration. In conclusion, this research targets ferroptosis therapy and provides new insights for improving the prediction and prevention of HCC. Full article
(This article belongs to the Special Issue Linking Genomic Changes with Cancer in the NGS Era, 2nd Edition)
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18 pages, 5456 KiB  
Article
SJB2-043, a USP1 Inhibitor, Suppresses A549 Cell Proliferation, Migration, and EMT via Modulation of PI3K/AKT/mTOR, MAPK, and Wnt Signaling Pathways
by Lipeng Wu, Meng Yu, Huosheng Liang, Long Lin, Huajian Li, Guangyang Chen, Halimulati Muhetaer, Jingjing Li, Bo Wu, Xuejing Jia, Yuanye Dang, Guodong Zheng and Chuwen Li
Curr. Issues Mol. Biol. 2025, 47(3), 155; https://doi.org/10.3390/cimb47030155 - 27 Feb 2025
Viewed by 600
Abstract
Objective: Non-small cell lung cancer (NSCLC) remains one of the most significant contributors to cancer-related mortality. This investigation explores the influence and underlying mechanisms of the USP1 inhibitor SJB2-043 on A549 cells, with the aim of advancing the development of anti-NSCLC therapeutics. Methods: [...] Read more.
Objective: Non-small cell lung cancer (NSCLC) remains one of the most significant contributors to cancer-related mortality. This investigation explores the influence and underlying mechanisms of the USP1 inhibitor SJB2-043 on A549 cells, with the aim of advancing the development of anti-NSCLC therapeutics. Methods: Publicly available databases were utilized to assess USP1 expression and its association with the progression of NSCLC. Gene expression variations were ascertained through RNA sequencing, followed by the Kyoto Encyclopedia of Genes and Genomes and Gene Ontology pathway enrichment evaluations. Various doses of SJB2-043 were administered to A549 cells to evaluate its impact on cell multiplication, motility, apoptosis, and the cell cycle using CCK-8 assays, colony formation, wound healing, flow cytometry, and Western blotting (WB). Results: USP1 was found to be overexpressed in NSCLC specimens and linked to adverse prognosis. Treatment with SJB2-043 markedly inhibited A549 cell proliferation and migration, diminished clonogenic potential, and triggered apoptosis in a dose-dependent manner. Modifications in the cell cycle were observed, showing an elevated percentage of cells in the G2 phase while exhibiting a parallel decline in the G1 phase. WB examination demonstrated diminished protein levels of N-cadherin, CyclinB1, CDK1, C-myc, Bcl-2, p-ERK/ERK, p-p38/p38, p-JNK/JNK, p-AKT/AKT, and p-mTOR/mTOR, alongside an upregulation of E-cadherin, ZO-1, occludin, p53, Bax, p-β-catenin/β-catenin, and GSK3β. Conclusions: SJB2-043 exerts a suppressive effect on A549 cell proliferation, migration, and epithelial–mesenchymal transition while enhancing apoptosis. These cellular effects appear to be mediated through the inhibition of the MAPK, Wnt/β-catenin, and PI3K/AKT/mTOR signaling cascades, in addition to modulation of the cell cycle. Full article
(This article belongs to the Special Issue Linking Genomic Changes with Cancer in the NGS Era, 2nd Edition)
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11 pages, 751 KiB  
Article
Novel Mutations in AKT1 Gene in Prostate Cancer Patients in Jordan
by Ala’a Alasmar, Zina Al-Alami, Sima Zein, Asmaa Al-Smadi, Samir Al Bashir, Mohammed S. Alorjani, Raed M. Al-Zoubi and Mazhar Al Zoubi
Curr. Issues Mol. Biol. 2024, 46(9), 9856-9866; https://doi.org/10.3390/cimb46090586 - 4 Sep 2024
Cited by 1 | Viewed by 1922
Abstract
The AKT1 oncogene is related to various cancers due to its critical role in the PIC3CA/AKT1 pathway; however, most of the studies screened the hotspot mutation AKT1 (E17K) with various incidences. Low frequency or lack of AKT1 (E17K) mutation was reported in prostate [...] Read more.
The AKT1 oncogene is related to various cancers due to its critical role in the PIC3CA/AKT1 pathway; however, most of the studies screened the hotspot mutation AKT1 (E17K) with various incidences. Low frequency or lack of AKT1 (E17K) mutation was reported in prostate cancer (PC) patients. This study aims to explore genetic alterations in the AKT1 PH domain by extending the sequencing to include AKT1 gene exons 3 and 4. Genomic DNA was extracted from 84 Formalin-Fixed Paraffin-Embedded samples of PC patients in Jordan, and then subjected to PCR and sequencing for the targeted exons. This study revealed the presence of two novel mutations (N53Y and Q59K) and a high frequency of mutations in exon 4, with a lack of mutations in the E17K hotspot. Nine missense and two synonymous mutations were detected in exon 4 (Phe27Tyr, Phe27Leu, Ala58Thr, Ser56Phe, Arg41Trp, Phe35Leu, Asp32Glu, Phe35Tyr, and Gln43Lys) and (Ser56 and Glu40), respectively. Two synonymous mutations were detected in exon 3 (Leu12 and Ser2). It is concluded that there is a high frequency of AKT1 mutation in PC patients in Jordan with two novel missense mutations in the Pleckstrin homology (PH) domain. E17K hotspot mutation was not detected in any tested samples, which underlined the significant role of mutations in other AKT1 exons in PC development. Full article
(This article belongs to the Special Issue Linking Genomic Changes with Cancer in the NGS Era, 2nd Edition)
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