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Genetic Alterations in Tumors
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Genetic Alterations in Tumors

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

Deadline for manuscript submissions: closed (25 April 2023) | Viewed by 10855

Special Issue Editors

Prof. Dr. Giuseppe Damante

E-Mail Website
Guest Editor
1. Department of Medicine, University of Udine, Udine, Italy
2. Institute of Medical Genetics, Academic Hospital of Udine, Udine, Italy
Interests: medical genetics; genetic diseases; cancer genetics
Dr. Rebecca Chin

E-Mail Website
Guest Editor
Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
Interests: signaling pathways; solid tumors
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

With advances in high-throughput technologies like next-generation sequencing, remarkable progress has been made in understanding genetic events that define the identity of tumors and characterize cancer development and metastasis. Integrative analysis of genomic alterations, signaling, and other molecular changes in tumor cells have allowed not only biomarker discovery, but also the identification of novel therapeutic targets. Personalized cancer therapy based on genetic status has shown great promise for the improvement of patient outcomes. However, many challenges remain, including tumor heterogeneity and therapeutic resistance arising from genetic mutations as compensatory mechanisms. It is also now clear that there are interplays between the genome and epigenome of tumor cells, adding another layer of complexity in our understanding of cancer.

In this Special Issue, we welcome reviews, original research articles, and short communications that focus on advances related to identifying genetic events that improve cancer diagnosis, the development of targeted therapy, combating resistance, as well as genetic events changing the epigenomic landscape of tumor cells.

Prof. Dr. Giuseppe Damante
Dr. Rebecca Chin
Guest Editors

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. 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

  • Genetic
  • Genomic
  • Gene fusion
  • Breast cancer
  • Metastasis
  • Epigenome
  • Signaling
  • Precision medicine
  • Resistance
  • Patient tailoring

Published Papers (4 papers)

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Research

21 pages, 3424 KiB  
Article
2.4 GHz Electromagnetic Field Influences the Response of the Circadian Oscillator in the Colorectal Cancer Cell Line DLD1 to miR-34a-Mediated Regulation
by Soňa Olejárová, Roman Moravčík and Iveta Herichová
Int. J. Mol. Sci. 2022, 23(21), 13210; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232113210 - 30 Oct 2022
Cited by 4 | Viewed by 2723
Abstract
Radiofrequency electromagnetic fields (RF-EMF) exert pleiotropic effects on biological processes including circadian rhythms. miR-34a is a small non-coding RNA whose expression is modulated by RF-EMF and has the capacity to regulate clock gene expression. However, interference between RF-EMF and miR-34a-mediated regulation of the [...] Read more.
Radiofrequency electromagnetic fields (RF-EMF) exert pleiotropic effects on biological processes including circadian rhythms. miR-34a is a small non-coding RNA whose expression is modulated by RF-EMF and has the capacity to regulate clock gene expression. However, interference between RF-EMF and miR-34a-mediated regulation of the circadian oscillator has not yet been elucidated. Therefore, the present study was designed to reveal if 24 h exposure to 2.4 GHz RF-EMF influences miR-34a-induced changes in clock gene expression, migration and proliferation in colorectal cancer cell line DLD1. The effect of up- or downregulation of miR-34a on DLD1 cells was evaluated using real-time PCR, the scratch assay test and the MTS test. Administration of miR-34a decreased the expression of per2, bmal1, sirtuin1 and survivin and inhibited proliferation and migration of DLD1 cells. When miR-34a-transfected DLD1 cells were exposed to 2.4 GHz RF-EMF, an increase in cry1 mRNA expression was observed. The inhibitory effect of miR-34a on per2 and survivin was weakened and abolished, respectively. The effect of miR-34a on proliferation and migration was eliminated by RF-EMF exposure. In conclusion, RF-EMF strongly influenced regulation mediated by the tumour suppressor miR-34a on the peripheral circadian oscillator in DLD1 cells. Full article
(This article belongs to the Special Issue Genetic Alterations in Tumors)
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17 pages, 2663 KiB  
Article
Role of m6A RNA Methylation in Thyroid Cancer Cell Lines
by Lorenzo Allegri, Federica Baldan, Elisabetta Molteni, Catia Mio and Giuseppe Damante
Int. J. Mol. Sci. 2022, 23(19), 11516; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231911516 - 29 Sep 2022
Cited by 7 | Viewed by 1702
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification of RNA in eukaryotic cells, and, in recent years, it has gained increasing attention. A good amount of data support the involvement of m6A modification in tumorigenesis, tumor progression, and metastatic dissemination. However, the role [...] Read more.
N6-methyladenosine (m6A) is the most abundant internal modification of RNA in eukaryotic cells, and, in recent years, it has gained increasing attention. A good amount of data support the involvement of m6A modification in tumorigenesis, tumor progression, and metastatic dissemination. However, the role of this RNA modification in thyroid cancer still remains poorly investigated. In this study, m6A-related RNA methylation profiles are compared between a normal thyroid cell line and different thyroid cancer cell lines. With this approach, it was possible to identify the different patterns of m6A modification in different thyroid cancer models. Furthermore, by silencing METTL3, which is the main player in the RNA methylation machinery, it was possible to evaluate the impact of m6A modification on gene expression in an anaplastic thyroid cancer model. This experimental approach allowed us to identify DDI2 as a gene specifically controlled by the m6A modification in anaplastic thyroid cancer cell lines. Altogether, these data are a proof of concept that RNA methylation widely occurs in thyroid cancer cell models and open a way forward in the search for new molecular patterns for diagnostic discrimination between benign and malignant lesions. Full article
(This article belongs to the Special Issue Genetic Alterations in Tumors)
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14 pages, 3643 KiB  
Article
Targeted Next-Generation Sequencing-Based Multiple Gene Mutation Profiling of Patients with Rectal Adenocarcinoma Receiving or Not Receiving Neoadjuvant Chemoradiotherapy
by You-Kang Chang, Hui-Hwa Tseng, Chung-Man Leung, Kuo-Cheng Lu and Kuo-Wang Tsai
Int. J. Mol. Sci. 2022, 23(18), 10353; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231810353 - 08 Sep 2022
Cited by 2 | Viewed by 1509
Abstract
This study investigated whether oncogenic and tumor-suppressive gene mutations are involved in the differential outcomes of patients with rectal carcinoma receiving neoadjuvant chemoradiotherapy (nCRT). Genomic DNA was obtained from formalin-fixed paraffin-embedded (FFPE) specimens of patients with rectal carcinoma who received a complete nCRT [...] Read more.
This study investigated whether oncogenic and tumor-suppressive gene mutations are involved in the differential outcomes of patients with rectal carcinoma receiving neoadjuvant chemoradiotherapy (nCRT). Genomic DNA was obtained from formalin-fixed paraffin-embedded (FFPE) specimens of patients with rectal carcinoma who received a complete nCRT course. Gene mutation status was examined in specimens from patients before and after nCRT by using the AmpliSeq platform. Our data revealed that the nonsynonymous p53, APC, KRAS, CDKN2A, and EGFR mutations were observed in 93.1%, 65.5%, 48.6%, and 31% of the patients with rectal adenocarcinoma, respectively. BRAF, FBXW7, PTEN, and SMAD4 mutations were observed in 20.7% of patients with rectal carcinoma. The following 12 gene mutations were observed more frequently in the patients exhibiting a complete response than in those demonstrating a poor response before nCRT: ATM, BRAF, CDKN2A, EGFR, FLT3, GNA11, KDR, KIT, PIK3CA, PTEN, PTPN11, SMAD4, and TP53. In addition, APC, BRAF, FBXW7, KRAS, SMAD4, and TP53 mutations were retained after nCRT. Our results indicate a complex mutational profile in rectal carcinoma, suggesting the involvement of BRAF, SMAD4, and TP53 genetic variants in the outcomes of patients with nCRT. Full article
(This article belongs to the Special Issue Genetic Alterations in Tumors)
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20 pages, 4883 KiB  
Article
In-Silico Evaluation of Genetic Alterations in Ovarian Carcinoma and Therapeutic Efficacy of NSC777201, as a Novel Multi-Target Agent for TTK, NEK2, and CDK1
by Harshita Nivrutti Khedkar, Yu-Chi Wang, Vijesh Kumar Yadav, Prateeti Srivastava, Bashir Lawal, Ntlotlang Mokgautsi, Maryam Rachmawati Sumitra, Alexander T. H. Wu and Hsu-Shan Huang
Int. J. Mol. Sci. 2021, 22(11), 5895; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22115895 - 31 May 2021
Cited by 8 | Viewed by 3661
Abstract
Ovarian cancer is often detected at the advanced stages at the time of initial diagnosis. Early-stage diagnosis is difficult due to its asymptomatic nature, where less than 30% of 5-year survival has been noticed. The underlying molecular events associated with the disease’s pathogenesis [...] Read more.
Ovarian cancer is often detected at the advanced stages at the time of initial diagnosis. Early-stage diagnosis is difficult due to its asymptomatic nature, where less than 30% of 5-year survival has been noticed. The underlying molecular events associated with the disease’s pathogenesis have yet to be fully elucidated. Thus, the identification of prognostic biomarkers as well as developing novel therapeutic agents for targeting these markers become relevant. Herein, we identified 264 differentially expressed genes (DEGs) common in four ovarian cancer datasets (GSE14407, GSE18520, GSE26712, GSE54388), respectively. We constructed a protein-protein interaction (PPI) interaction network with the overexpressed genes (72 genes) and performed gene enrichment analysis. In the PPI networks, three proteins; TTK Protein Kinase (TTK), NIMA Related Kinase 2 (NEK2), and cyclin-dependent kinase (CDK1) with higher node degrees were further evaluated as therapeutic targets for our novel multi-target small molecule NSC777201. We found that the upregulated DEGs were enriched in KEGG and gene ontologies associated with ovarian cancer progression, female gamete association, otic vesicle development, regulation of chromosome segregation, and therapeutic failure. In addition to the PPI network, ingenuity pathway analysis also implicate TTK, NEK2, and CDK1 in the elevated salvage pyrimidine and pyridoxal pathways in ovarian cancer. The TTK, NEK2, and CDK1 are over-expressed, demonstrating a high frequency of genetic alterations, and are associated with poor prognosis of ovarian cancer cohorts. Interestingly, NSC777201 demonstrated anti-proliferative and cytotoxic activities (GI50 = 1.6 µM~1.82 µM and TGI50 = 3.5 µM~3.63 µM) against the NCI panels of ovarian cancer cell lines and exhibited a robust interaction with stronger affinities for TTK, NEK2, and CDK1, than do the standard drug, paclitaxel. NSC777201 displayed desirable properties of a drug-like candidate and thus could be considered as a novel small molecule for treating ovarian carcinoma. Full article
(This article belongs to the Special Issue Genetic Alterations in Tumors)
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