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Cancer Genomics

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: closed (20 April 2025) | Viewed by 14456

Special Issue Editors

Dr. Ricardo Armisén

E-Mail Website
Guest Editor
Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Concepcin, Chile
Interests: RNA biology; cancer functional genomics; precision medicine; molecular diagnostics
Special Issues, Collections and Topics in MDPI journals
Dr. Hector R. Contreras

E-Mail Website1 Website2
Guest Editor
Laboratory of Cellular and Molecular Oncology, Department of Basic and Clinical Oncology, Faculty of Medicine, University de Chile, Santiago 8380453, Chile
Interests: epithelial–mesenchymal transition; cancer stem cell; prostate cancer; colon cancer; breast cancer
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

During the development and progression of cancer, neoplastic cells acquire a series of genetic changes that result in drastic modifications both in how the cell responds to its environment and in the cell dynamics itself. Advancements in genomic technologies and next-generation sequencing have produced a wealth of information and provided substantial insights into the pathogenesis of diseases. Especially in cancer, these tools have been exceptionally useful for identifying novel signal transduction pathways, with a great potential for the discovery of new biomarkers and therapeutic targets. However, the translation of these findings into a breakthrough in the understanding of cancer biology and the care of cancer patients remains a major challenge.

This Special Issue highlights novel findings in cancer genomics arising from the combined use of computational tools, high-throughput sequencing technology, bioinformatics, cell biology and translational research to understand cancer biology, from genomics to cell signaling and from disease models to actual patients. Translational efforts to make the knowledge of cellular and molecular biology of cancer useful for patients with cancer, and research performed in understudied specific cancer patients, are of special interest.

Dr. Ricardo Armisén
Dr. Hector R. Contreras
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

  • precision oncology
  • cancer genomics
  • personalized medicine
  • mutagenesis
  • molecular epidemiology

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Related Special Issue

Published Papers (7 papers)

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Research

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23 pages, 8662 KiB  
Article
Identification of the EBF1/ETS2/KLF2-miR-126-Gene Feed-Forward Loop in Breast Carcinogenesis and Stemness
by Alessandra Gambacurta, Valentina Tullio, Isabella Savini, Alessandro Mauriello, Maria Valeria Catani and Valeria Gasperi
Int. J. Mol. Sci. 2025, 26(1), 328; https://doi.org/10.3390/ijms26010328 - 2 Jan 2025
Cited by 2 | Viewed by 1371
Abstract
MicroRNA (miR)-126 is frequently downregulated in malignancies, including breast cancer (BC). Despite its tumor-suppressive role, the mechanisms underlying miR-126 deregulation in BC remain elusive. Through silencing experiments, we identified Early B Cell Factor 1 (EBF1), ETS Proto-Oncogene 2 (ETS2), and Krüppel-Like Factor 2 [...] Read more.
MicroRNA (miR)-126 is frequently downregulated in malignancies, including breast cancer (BC). Despite its tumor-suppressive role, the mechanisms underlying miR-126 deregulation in BC remain elusive. Through silencing experiments, we identified Early B Cell Factor 1 (EBF1), ETS Proto-Oncogene 2 (ETS2), and Krüppel-Like Factor 2 (KLF2) as pivotal regulators of miR-126 expression. These transcription factors were found to be downregulated in BC due to epigenetic silencing or a “poised but not transcribed” promoter state, impairing miR-126 expression. Gene Ontology analysis of differentially expressed miR-126 target genes in the Cancer Genome Atlas: Breast Invasive Carcinoma (TCGA-BRCA) cohort revealed their involvement in cancer-related pathways, primarily signal transduction, chromatin remodeling/transcription, and differentiation/development. Furthermore, we defined interconnections among transcription factors, miR-126, and target genes, identifying a potential feed-forward loop (FFL) crucial in maintaining cellular identity and preventing the acquisition of stemness properties associated with cancer progression. Our findings propose that the dysregulation of the EBF1/ETS2/KLF2/miR-126 axis disrupts this FFL, promoting oncogenic transformation and progression in BC. This study provides new insights into the molecular mechanisms of miR-126 downregulation in BC and highlights potential targets for therapeutic intervention. Further research is warranted to clarify the role of this FFL in BC, and to identify novel therapeutic strategies aimed at modulating this network as a whole, rather than targeting individual signals, for cancer management. Full article
(This article belongs to the Special Issue Cancer Genomics)
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19 pages, 4175 KiB  
Article
Long-Read MDM4 Sequencing Reveals Aberrant Isoform Landscape in Metastatic Melanomas
by Nehaal Patrick and Michael Markey
Int. J. Mol. Sci. 2024, 25(17), 9415; https://doi.org/10.3390/ijms25179415 - 30 Aug 2024
Viewed by 1373
Abstract
MDM4 is upregulated in the majority of melanoma cases and has been described as a “key therapeutic target in cutaneous melanoma”. Numerous isoforms of MDM4 exist, with few studies examining their specific expression in human tissues. The changes in splicing of MDM4 during [...] Read more.
MDM4 is upregulated in the majority of melanoma cases and has been described as a “key therapeutic target in cutaneous melanoma”. Numerous isoforms of MDM4 exist, with few studies examining their specific expression in human tissues. The changes in splicing of MDM4 during human melanomagenesis are critical to p53 activity and represent potential therapeutic targets. Compounding this, studies relying on short reads lose “connectivity” data, so full transcripts are frequently only inferred from the presence of splice junction reads. To address this problem, long-read nanopore sequencing was utilized to read the entire length of transcripts. Here, MDM4 transcripts, both alternative and canonical, are characterized in a pilot cohort of human melanoma specimens. RT-PCR was first used to identify the presence of novel splice junctions in these specimens. RT-qPCR then quantified the expression of major MDM4 isoforms observed during sequencing. The current study both identifies and quantifies MDM4 isoforms present in melanoma tumor samples. In the current study, we observed high expression levels of MDM4-S, MDM4-FL, MDM4-A, and the previously undescribed Ensembl transcript MDM4-209. A novel transcript lacking both exons 6 and 9 is observed and named MDM4-A/S for its resemblance to both MDM4-A and MDM4-S isoforms. Full article
(This article belongs to the Special Issue Cancer Genomics)
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18 pages, 8512 KiB  
Article
Stratification of Colorectal Patients Based on Survival Analysis Shows the Value of Consensus Molecular Subtypes and Reveals the CBLL1 Gene as a Biomarker of CMS2 Tumours
by Gloria Alfonsín, Alberto Berral-González, Andrea Rodríguez-Alonso, Macarena Quiroga, Javier De Las Rivas and Angélica Figueroa
Int. J. Mol. Sci. 2024, 25(3), 1919; https://doi.org/10.3390/ijms25031919 - 5 Feb 2024
Cited by 2 | Viewed by 2396
Abstract
The consensus molecular subtypes (CMSs) classification of colorectal cancer (CRC) is a system for patient stratification that can be potentially applied to therapeutic decisions. Hakai (CBLL1) is an E3 ubiquitin–ligase that induces the ubiquitination and degradation of E-cadherin, inducing epithelial-to-mesenchymal transition (EMT), tumour [...] Read more.
The consensus molecular subtypes (CMSs) classification of colorectal cancer (CRC) is a system for patient stratification that can be potentially applied to therapeutic decisions. Hakai (CBLL1) is an E3 ubiquitin–ligase that induces the ubiquitination and degradation of E-cadherin, inducing epithelial-to-mesenchymal transition (EMT), tumour progression and metastasis. Using bioinformatic methods, we have analysed CBLL1 expression on a large integrated cohort of primary tumour samples from CRC patients. The cohort included survival data and was divided into consensus molecular subtypes. Colon cancer tumourspheres were used to analyse the expression of stem cancer cells markers via RT-PCR and Western blotting. We show that CBLL1 gene expression is specifically associated with canonical subtype CMS2. WNT target genes LGR5 and c-MYC show a similar association with CMS2 as CBLL1. These mRNA levels are highly upregulated in cancer tumourspheres, while CBLL1 silencing shows a clear reduction in tumoursphere size and in stem cell biomarkers. Importantly, CMS2 patients with high CBLL1 expression displayed worse overall survival (OS), which is similar to that associated with CMS4 tumours. Our findings reveal CBLL1 as a specific biomarker for CMS2 and the potential of using CMS2 with high CBLL1 expression to stratify patients with poor OS. Full article
(This article belongs to the Special Issue Cancer Genomics)
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15 pages, 3011 KiB  
Article
miR-195-5p as Regulator of γ-Catenin and Desmosome Junctions in Colorectal Cancer
by Emanuele Piccinno, Viviana Scalavino, Raffaele Armentano, Gianluigi Giannelli and Grazia Serino
Int. J. Mol. Sci. 2023, 24(23), 17084; https://doi.org/10.3390/ijms242317084 - 3 Dec 2023
Cited by 11 | Viewed by 2078
Abstract
Desmosomes play a key role in the regulation of cell adhesion and signaling. Dysregulation of the desmosome complex is associated with the loss of epithelial cell polarity and disorganized tissue architecture typical of colorectal cancer (CRC). The aim of this study was to [...] Read more.
Desmosomes play a key role in the regulation of cell adhesion and signaling. Dysregulation of the desmosome complex is associated with the loss of epithelial cell polarity and disorganized tissue architecture typical of colorectal cancer (CRC). The aim of this study was to investigate and characterize the effect of miR-195-5p on desmosomal junction regulation in CRC. In detail, we proposed to investigate the deregulation of miR-195-5p and JUP, a gene target that encodes a desmosome component in CRC patients. JUP closely interacts with desmosomal cadherins, and downstream, it regulates several intracellular transduction factors. We restored the miR-195-5p levels by transient transfection in colonic epithelial cells to examine the effects of miR-195-5p on JUP mRNA and protein expression. The JUP regulation by miR-195-5p, in turn, determined a modulation of desmosome cadherins (Desmoglein 2 and Desmocollin 2). Furthermore, we focused on whether the miR-195-5p gain of function was also able to modulate the expression of key components of Wnt signaling, such as NLK, LEF1 and Cyclin D1. In conclusion, we have identified a novel mechanism controlled by miR-195-5p in the regulation of adhesive junctions, suggesting its potential clinical relevance for future miRNA-based therapy in CRC. Full article
(This article belongs to the Special Issue Cancer Genomics)
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17 pages, 5378 KiB  
Article
Firing of Replication Origins Is Disturbed by a CDK4/6 Inhibitor in a pRb-Independent Manner
by Su-Jung Kim, Chrystelle Maric, Lina-Marie Briu, Fabien Fauchereau, Giuseppe Baldacci, Michelle Debatisse, Stéphane Koundrioukoff and Jean-Charles Cadoret
Int. J. Mol. Sci. 2023, 24(13), 10629; https://doi.org/10.3390/ijms241310629 - 25 Jun 2023
Viewed by 2473
Abstract
Over the last decade, CDK4/6 inhibitors (palbociclib, ribociclib and abemaciclib) have emerged as promising anticancer drugs. Numerous studies have demonstrated that CDK4/6 inhibitors efficiently block the pRb-E2F pathway and induce cell cycle arrest in pRb-proficient cells. Based on these studies, the inhibitors have [...] Read more.
Over the last decade, CDK4/6 inhibitors (palbociclib, ribociclib and abemaciclib) have emerged as promising anticancer drugs. Numerous studies have demonstrated that CDK4/6 inhibitors efficiently block the pRb-E2F pathway and induce cell cycle arrest in pRb-proficient cells. Based on these studies, the inhibitors have been approved by the FDA for treatment of advanced hormonal receptor (HR) positive breast cancers in combination with hormonal therapy. However, some evidence has recently shown unexpected effects of the inhibitors, underlining a need to characterize the effects of CDK4/6 inhibitors beyond pRb. Our study demonstrates how palbociclib impairs origin firing in the DNA replication process in pRb-deficient cell lines. Strikingly, despite the absence of pRb, cells treated with palbociclib synthesize less DNA while showing no cell cycle arrest. Furthermore, this CDK4/6 inhibitor treatment disturbs the temporal program of DNA replication and reduces the density of replication forks. Cells treated with palbociclib show a defect in the loading of the Pre-initiation complex (Pre-IC) proteins on chromatin, indicating a reduced initiation of DNA replication. Our findings highlight hidden effects of palbociclib on the dynamics of DNA replication and of its cytotoxic consequences on cell viability in the absence of pRb. This study provides a potential therapeutic application of palbociclib in combination with other drugs to target genomic instability in pRB-deficient cancers. Full article
(This article belongs to the Special Issue Cancer Genomics)
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Review

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21 pages, 385 KiB  
Review
Targeting Pathways in Neuroblastoma: Advances in Treatment Strategies and Clinical Outcomes
by Diana Benchia, Ovidiu Daniel Bîcă, Ioan Sârbu, Bogdan Savu, Diana Farcaș, Ingrith Miron, Anca Lavinia Postolache, Elena Cojocaru, Olivier Abbo and Carmen Iulia Ciongradi
Int. J. Mol. Sci. 2025, 26(10), 4722; https://doi.org/10.3390/ijms26104722 - 15 May 2025
Viewed by 627
Abstract
Neuroblastoma (NB) is a childhood cancer originating from neural crest cells of the sympathetic nervous system. Despite the advances in multimodal therapy, the treatment of high-risk NB remains challenging. The present review outlines several evidence-related insights into the molecular mechanisms of NB pathogenesis, [...] Read more.
Neuroblastoma (NB) is a childhood cancer originating from neural crest cells of the sympathetic nervous system. Despite the advances in multimodal therapy, the treatment of high-risk NB remains challenging. The present review outlines several evidence-related insights into the molecular mechanisms of NB pathogenesis, focusing on genetic drivers (e.g., MYCN amplification) and disrupted signaling pathways (PI3K/Akt/mTOR; Notch; Jak2/STAT3), as well as on the tumor microenvironment’s role in progression and resistance. The authors highlight current and emerging therapeutic strategies, including molecularly targeted agents; immunotherapies; and differentiation approaches under investigation. The complexity and heterogeneity of NB underscores the need for continued translational research and for combined strategies aimed at improving outcomes for affected children, highlighting the need for integration of molecular profiling and precision medicine to guide treatment. Full article
(This article belongs to the Special Issue Cancer Genomics)
20 pages, 1520 KiB  
Review
ADAR-Mediated A>I(G) RNA Editing in the Genotoxic Drug Response of Breast Cancer
by Yanara A. Bernal, Eduardo Durán, Isidora Solar, Eduardo A. Sagredo and Ricardo Armisén
Int. J. Mol. Sci. 2024, 25(13), 7424; https://doi.org/10.3390/ijms25137424 - 6 Jul 2024
Cited by 1 | Viewed by 2536
Abstract
Epitranscriptomics is a field that delves into post-transcriptional changes. Among these modifications, the conversion of adenosine to inosine, traduced as guanosine (A>I(G)), is one of the known RNA-editing mechanisms, catalyzed by ADARs. This type of RNA editing is the most common type of [...] Read more.
Epitranscriptomics is a field that delves into post-transcriptional changes. Among these modifications, the conversion of adenosine to inosine, traduced as guanosine (A>I(G)), is one of the known RNA-editing mechanisms, catalyzed by ADARs. This type of RNA editing is the most common type of editing in mammals and contributes to biological diversity. Disruption in the A>I(G) RNA-editing balance has been linked to diseases, including several types of cancer. Drug resistance in patients with cancer represents a significant public health concern, contributing to increased mortality rates resulting from therapy non-responsiveness and disease progression, representing the greatest challenge for researchers in this field. The A>I(G) RNA editing is involved in several mechanisms over the immunotherapy and genotoxic drug response and drug resistance. This review investigates the relationship between ADAR1 and specific A>I(G) RNA-edited sites, focusing particularly on breast cancer, and the impact of these sites on DNA damage repair and the immune response over anti-cancer therapy. We address the underlying mechanisms, bioinformatics, and in vitro strategies for the identification and validation of A>I(G) RNA-edited sites. We gathered databases related to A>I(G) RNA editing and cancer and discussed the potential clinical and research implications of understanding A>I(G) RNA-editing patterns. Understanding the intricate role of ADAR1-mediated A>I(G) RNA editing in breast cancer holds significant promise for the development of personalized treatment approaches tailored to individual patients’ A>I(G) RNA-editing profiles. Full article
(This article belongs to the Special Issue Cancer Genomics)
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