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Cancer Risk and Gene Variations
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Cancer Risk and Gene Variations

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

Deadline for manuscript submissions: closed (25 January 2024) | Viewed by 3896

Special Issue Editors

Dr. Emilio J. Córdova

E-Mail Website
Guest Editor
Clinic Research, National Institute of Genomic Medicine, Mexico City, Mexico
Interests: cancer risk; gene variation; next-generation sequencing; translational medicine
Dr. Leticia Rocha-Zavaleta

E-Mail Website
Guest Editor
Departamento de Biología Molecular y Biotecnología, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
Interests: cancer risk; gene variation; next-generation sequencing; translational medicine

Special Issue Information

Dear Colleagues,

The advancing of genomic technologies has allowed the identification of a great number of genetic variations associated with cancer development and has thus allowed us to deepen our knowledge of the genetic architecture of cancer risk. This knowledge has helped in the establishment of public health strategies to reduce cancer prevalence and to improve early molecular diagnostics.

This Special Issue aims to describe the state of the art of the current research performed in genetic and genomic risk in cancer. Contributions are expected to highlight genomic variations that underly genetic risk for specific types of cancers, explore genetic modifying factors in people exposed to known environmental carcinogens, characterize the functional effects of genetic variants on cellular models, evaluate the impact of genetic variation in pathophysiology mechanisms, and describe genomic variants as biomarkers of prognosis and treatment response.

Contributions in the form of research papers and critical reviews are all welcome.

Dr. Emilio J. Córdova
Dr. Leticia Rocha-Zavaleta
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

  • cancer risk
  • human variation
  • genetic modifying factor
  • environmental carcinogens and gene variants
  • functional variants

Published Papers (3 papers)

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Research

21 pages, 4215 KiB  
Article
Epigenetic and Genomic Hallmarks of PARP-Inhibitor Resistance in Ovarian Cancer Patients
by Tugce Senturk Kirmizitas, Caroline van den Berg, Ruben Boers, Jean Helmijr, Stavros Makrodimitris, Hamit Harun Dag, Marijn Kerkhofs, Corine Beaufort, Jaco Kraan, Wilfred F. J. van IJcken, Joost Gribnau, Pakriti Garkhail, Gatske Nieuwenhuyzen-de Boer, Eva-Maria Roes, Heleen van Beekhuizen, Tuba Gunel, Saskia Wilting, John Martens, Maurice Jansen and Ingrid Boere
Genes 2024, 15(6), 750; https://doi.org/10.3390/genes15060750 - 7 Jun 2024
Viewed by 762
Abstract
Background: Patients with advanced-stage epithelial ovarian cancer (EOC) receive treatment with a poly-ADP ribose-polymerase (PARP) inhibitor (PARPi) as maintenance therapy after surgery and chemotherapy. Unfortunately, many patients experience disease progression because of acquired therapy resistance. This study aims to characterize epigenetic and genomic [...] Read more.
Background: Patients with advanced-stage epithelial ovarian cancer (EOC) receive treatment with a poly-ADP ribose-polymerase (PARP) inhibitor (PARPi) as maintenance therapy after surgery and chemotherapy. Unfortunately, many patients experience disease progression because of acquired therapy resistance. This study aims to characterize epigenetic and genomic changes in cell-free DNA (cfDNA) associated with PARPi resistance. Materials and Methods: Blood was taken from 31 EOC patients receiving PARPi therapy before treatment and at disease progression during/after treatment. Resistance was defined as disease progression within 6 months after starting PARPi and was seen in fifteen patients, while sixteen patients responded for 6 to 42 months. Blood cfDNA was evaluated via Modified Fast Aneuploidy Screening Test-Sequencing System (mFast-SeqS to detect aneuploidy, via Methylated DNA Sequencing (MeD-seq) to find differentially methylated regions (DMRs), and via shallow whole-genome and -exome sequencing (shWGS, exome-seq) to define tumor fractions and mutational signatures. Results: Aneuploid cfDNA was undetectable pre-treatment but observed in six patients post-treatment, in five resistant and one responding patient. Post-treatment ichorCNA analyses demonstrated in shWGS and exome-seq higher median tumor fractions in resistant (7% and 9%) than in sensitive patients (7% and 5%). SigMiner analyses detected predominantly mutational signatures linked to mismatch repair and chemotherapy. DeSeq2 analyses of MeD-seq data revealed three methylation signatures and more tumor-specific DMRs in resistant than in responding patients in both pre- and post-treatment samples (274 vs. 30 DMRs, 190 vs. 57 DMRs, Χ2-test p < 0.001). Conclusion: Our genome-wide Next-Generation Sequencing (NGS) analyses in PARPi-resistant patients identified epigenetic differences in blood before treatment, whereas genomic alterations were more frequently observed after progression. The epigenetic differences at baseline are especially interesting for further exploration as putative predictive biomarkers for PARPi resistance. Full article
(This article belongs to the Special Issue Cancer Risk and Gene Variations)
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14 pages, 1967 KiB  
Article
Exploring the Relationship between CLPTM1L-MS2 Variants and Susceptibility to Bladder Cancer
by Mi-So Jeong, Jeong-Yeon Mun, Gi-Eun Yang, Min-Hye Kim, Sang-Yeop Lee, Yung Hyun Choi, Heui Soo Kim, Jong-Kil Nam, Tae Nam Kim and Sun-Hee Leem
Genes 2024, 15(1), 50; https://doi.org/10.3390/genes15010050 - 28 Dec 2023
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Abstract
CLPTM1L (Cleft Lip and Palate Transmembrane Protein 1-Like) has previously been implicated in tumorigenesis and drug resistance in cancer. However, the genetic link between CLPTM1L and bladder cancer remains uncertain. In this study, we investigated the genetic association of variable number of tandem [...] Read more.
CLPTM1L (Cleft Lip and Palate Transmembrane Protein 1-Like) has previously been implicated in tumorigenesis and drug resistance in cancer. However, the genetic link between CLPTM1L and bladder cancer remains uncertain. In this study, we investigated the genetic association of variable number of tandem repeats (VNTR; minisatellites, MS) regions within CLPTM1L with bladder cancer. We identified four CLPTM1L-MS regions (MS1~MS4) located in intron regions. To evaluate the VNTR polymorphic alleles, we analyzed 441 cancer-free controls and 181 bladder cancer patients. Our analysis revealed a higher frequency of specific repeat sizes within the MS2 region in bladder cancer cases compared to controls. Notably, 25 and 27 repeats were exclusively present in the bladder cancer group. Moreover, rare alleles within the medium-length repeat range (25–29 repeats) were associated with an elevated bladder cancer risk (odds ratio [OR] = 5.78, 95% confidence interval [CI]: 1.49–22.47, p = 0.004). We confirmed that all MS regions followed Mendelian inheritance, and demonstrated that MS2 alleles increased CLPTM1L promoter activity in the UM-UC3 bladder cancer cells through a luciferase assay. Our findings propose the utility of CLPTM1L-MS regions as DNA typing markers, particularly highlighting the potential of middle-length rare alleles within CLPTM1L-MS2 as predictive markers for bladder cancer risk. Full article
(This article belongs to the Special Issue Cancer Risk and Gene Variations)
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16 pages, 3384 KiB  
Article
Heterozygous Knockout of ARID4B Using CRISPR/Cas9 Attenuates Some Aggressive Phenotypes in a Breast Cancer Cell Line
by Fernando Gonzalez-Salinas, Jessica Herrera-Gamboa, Rocio Rojo and Victor Trevino
Genes 2023, 14(12), 2184; https://doi.org/10.3390/genes14122184 - 6 Dec 2023
Viewed by 1482
Abstract
Breast cancer is one of the leading causes of death in women around the world. Over time, many genes and mutations that are associated with the development of this disease have been identified. However, the specific role of many genes has not yet [...] Read more.
Breast cancer is one of the leading causes of death in women around the world. Over time, many genes and mutations that are associated with the development of this disease have been identified. However, the specific role of many genes has not yet been fully elucidated. Higher ARID4B expression has been identified as a risk factor for diverse cancer types. Silencing experiments also showed that ARID4B is associated with developing cancer-associated characteristics. However, no transcriptomic studies have shown the overall cellular effect of loss of function in breast cancer in humans. This study addresses the impact of loss-of-function mutations in breast cancer MCF-7 cells. Using the CRISPR/Cas9 system, we generated mutations that caused heterozygous truncated proteins, isolating three monoclonal lines carrying insertions and deletions in ARID4B. We observed reduced proliferation and migration in in vitro experiments. In addition, from RNA-seq assays, a differential expression analysis shows known and novel deregulated cancer-associate pathways in mutated cells supporting the impact of ARID4B. For example, we found the AKT-PI3K pathway to be altered at the transcript level but through different genes than those reported for ARID4B. Our transcriptomic results also suggest new insights into the role of ARID4B in aggressiveness by the epithelial-to-mesenchymal transition and TGF-β pathways and in metabolism through cholesterol and mevalonate pathways. We also performed exome sequencing to show that no off-target effects were apparent. In conclusion, the ARID4B gene is associated with some aggressive phenotypes in breast cancer cells. Full article
(This article belongs to the Special Issue Cancer Risk and Gene Variations)
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