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Genes
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Genetic and Genomic Abnormalities in Cancer
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Genetic and Genomic Abnormalities in Cancer

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (20 March 2024) | Viewed by 3418

Special Issue Editors

Dr. Clelia Tiziana Storlazzi

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Guest Editor
Department of Biology, University of Bari Aldo Moro, Bari, Italy
Interests: cancer; cytogenetics; amplification; chimeric transcript; circular RNA
Dr. Doron Tolomeo

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Guest Editor
Department of Biology, University of Bari Aldo Moro, Bari, Italy
Interests: cancer; hematological malignancies; solid tumors; chimeric transcript; circular RNA; neocentromeres
Dr. Giorgia Simonetti

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Guest Editor
IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, FC, Italy
Interests: acute myeloid leukemia; genomics; cell metabolism; targeted therapies
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Background: Genetic and genomic alterations are at the basis of the mechanisms behind the somatic cell phenotype modification from normal to tumoral. Such DNA aberrations range from simple point mutations (resulting in coding gene misexpression) to chromosomal aberrations, considering alterations in the ploidy number and chromosome structure. The latter have a strong impact on oncogene and tumor suppressor gene transcription.

Aim and scope: The present Special Issue aims to collect the most interesting insights into the genetics and genomics of tumor cells in order to provide new evidence to identify new genetic biomarkers that can possibly be used in non-invasive diagnostic assays.

History: In recent decades, the development of next-generation sequencing technologies has revolutionized the perspectives of cancer research, leading to an exponential amplification of our knowledge on cancer genetics and genomics. This huge amount of information is now being refined via more sophisticated approaches (such as single-cell sequencing) and integrations with a number of disease features.

Cutting-Edge Research

  • Identification of novel genetic mutations, fusion genes, chromosomal alterations, and copy number variations associated with a specific tumor type.
  • Functional impact of genetic/genomic alterations on tumor onset and progression.
  • Epigenetic alterations accompanying specific genetic/genomic alterations in cancer.
  • Novel bioinformatics applied to next-generation sequencing approaches in cancer research. 
  • Genetic/genomics alterations in the diagnosis (mainly in non-invasive approaches), prognosis, and treatment of cancer patients.
  • Single-cell sequencing discoveries and bioinformatic tools in cancer research.

The kinds of papers that we are soliciting: We request researchers, clinicians, and experts in the fields of genetics and genomics to contribute research articles, reviews, and short communications on the Special Issue’s topic.

Dr. Clelia Tiziana Storlazzi
Dr. Doron Tolomeo
Dr. Giorgia Simonetti
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. Genes 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 2600 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

  • point mutation
  • amplification
  • translocation
  • deletion
  • inversion
  • duplication
  • aneuploidy
  • polyploidy
  • chromothripsis
  • single cell

Published Papers (2 papers)

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22 pages, 3357 KiB  
Review
Advancements in Focal Amplification Detection in Tumor/Liquid Biopsies and Emerging Clinical Applications
by Aram Arshadi, Doron Tolomeo, Santina Venuto and Clelia Tiziana Storlazzi
Genes 2023, 14(6), 1304; https://doi.org/10.3390/genes14061304 - 20 Jun 2023
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Abstract
Focal amplifications (FAs) are crucial in cancer research due to their significant diagnostic, prognostic, and therapeutic implications. FAs manifest in various forms, such as episomes, double minute chromosomes, and homogeneously staining regions, arising through different mechanisms and mainly contributing to cancer cell heterogeneity, [...] Read more.
Focal amplifications (FAs) are crucial in cancer research due to their significant diagnostic, prognostic, and therapeutic implications. FAs manifest in various forms, such as episomes, double minute chromosomes, and homogeneously staining regions, arising through different mechanisms and mainly contributing to cancer cell heterogeneity, the leading cause of drug resistance in therapy. Numerous wet-lab, mainly FISH, PCR-based assays, next-generation sequencing, and bioinformatics approaches have been set up to detect FAs, unravel the internal structure of amplicons, assess their chromatin compaction status, and investigate the transcriptional landscape associated with their occurrence in cancer cells. Most of them are tailored for tumor samples, even at the single-cell level. Conversely, very limited approaches have been set up to detect FAs in liquid biopsies. This evidence suggests the need to improve these non-invasive investigations for early tumor detection, monitoring disease progression, and evaluating treatment response. Despite the potential therapeutic implications of FAs, such as, for example, the use of HER2-specific compounds for patients with ERBB2 amplification, challenges remain, including developing selective and effective FA-targeting agents and understanding the molecular mechanisms underlying FA maintenance and replication. This review details a state-of-the-art of FA investigation, with a particular focus on liquid biopsies and single-cell approaches in tumor samples, emphasizing their potential to revolutionize the future diagnosis, prognosis, and treatment of cancer patients. Full article
(This article belongs to the Special Issue Genetic and Genomic Abnormalities in Cancer)
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9 pages, 1018 KiB  
Case Report
Detection of a Novel MSI2-C17orf64 Transcript in a Patient with Aggressive Adenocarcinoma of the Gastroesophageal Junction: A Case Report
by Anna Ferrari, Roberto Fiocca, Elena Bonora, Chiara Domizio, Eugenio Fonzi, Davide Angeli, Gian Domenico Raulli, Sandro Mattioli, Giovanni Martinelli and Chiara Molinari
Genes 2023, 14(4), 918; https://doi.org/10.3390/genes14040918 - 15 Apr 2023
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Abstract
Adenocarcinoma of the esophagus (EAC) and gastroesophageal junction (GEJ-AC) is associated with poor prognosis, treatment resistance and limited systemic therapeutic options. To deeply understand the genomic landscape of this cancer type, and potentially identify a therapeutic target in a neoadjuvant chemotherapy non-responder 48-year-old [...] Read more.
Adenocarcinoma of the esophagus (EAC) and gastroesophageal junction (GEJ-AC) is associated with poor prognosis, treatment resistance and limited systemic therapeutic options. To deeply understand the genomic landscape of this cancer type, and potentially identify a therapeutic target in a neoadjuvant chemotherapy non-responder 48-year-old man, we adopted a multi-omic approach. We simultaneously evaluated gene rearrangements, mutations, copy number status, microsatellite instability and tumor mutation burden. The patient displayed pathogenic mutations of the TP53 and ATM genes and variants of uncertain significance of three kinases genes (ERBB3, CSNK1A1 and RPS6KB2), along with FGFR2 and KRAS high copy number amplification. Interestingly, transcriptomic analysis revealed the Musashi-2 (MSI2)-C17orf64 fusion that has never been reported before. Rearrangements of the RNA-binding protein MSI2 with a number of partner genes have been described across solid and hematological tumors. MSI2 regulates several biological processes involved in cancer initiation, development and resistance to treatment, and deserves further investigation as a potential therapeutic target. In conclusion, our extensive genomic characterization of a gastroesophageal tumor refractory to all therapeutic approaches led to the discovery of the MSI2-C17orf64 fusion. The results underlie the importance of deep molecular analyses enabling the identification of novel patient-specific markers to be monitored during therapy or even targeted at disease evolution. Full article
(This article belongs to the Special Issue Genetic and Genomic Abnormalities in Cancer)
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