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Molecular Advances in Cancer Genetics 3.0
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Molecular Advances in Cancer Genetics 3.0

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 (30 June 2023) | Viewed by 12682

Special Issue Editors

Prof. Dr. Paola Ghiorzo

E-Mail Website1 Website2
Guest Editor
Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy
Interests: cancer genetics and genomics; molecular genetics; functional analysis; melanoma; pancreatic cancer; cancerogenesis; gene regulation; regulatory variants; hereditary cancers; somatic mutations
Special Issues, Collections and Topics in MDPI journals
Dr. William Bruno

E-Mail Website
Guest Editor
Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genova, Italy
Interests: rare cancers; hereditary cancers; genetic testing; molecular genetics; tumor heterogeneity; gene expression; functional genomics; genomic variations
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Recent advances in methodological approaches to the study of cancer genetics and genomics, which have resulted in increased detection of pathogenic variants and variants of unknown significance (VUS), have led to a paradigm shift in cancer susceptibility testing and revealed a substantial number of germline variants across a range of tumors, with a combination of germline testing and tumor mutation assessment helping to discern the clinical relevance of VUS and guide therapeutic implications. Therefore, hereditary predisposition and translation cancer genomics focused on therapeutic implications, previously considered separate, now meet and provide us with the opportunity to extend our identification of actionable germline and somatic variants in hereditary, rare, and common cancers, but also to improve our understanding of the genetic and molecular bases of cancer.

In this new Special Issue, we welcome reviews, original research articles, and short communications that focus on or are relevant to the evolution of methodological approaches to the study of cancer genetics and genomics, the molecular bases of cancer, hereditary cancer syndromes, tumor mutational assessment and interpretation of genomic variants, or potential therapeutic implications of hereditary predisposition.

Prof. Dr. Paola Ghiorzo
Dr. William Bruno
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

  • cancer genetics
  • molecular mechanisms
  • genetics of hereditary and rare cancers
  • evolution of methodological approaches to the study of cancer genetics and genomics
  • variant interpretation
  • actionability of genomic findings in cancer
  • somatic mutation testing

Published Papers (7 papers)

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Editorial

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2 pages, 172 KiB  
Editorial
Special Issue “Molecular Advances in Cancer Genetics 3.0”
by William Bruno and Paola Ghiorzo
Int. J. Mol. Sci. 2024, 25(5), 2717; https://doi.org/10.3390/ijms25052717 - 27 Feb 2024
Viewed by 407
Abstract
The third volume of this Special Issue focuses on new advances in cancer genetics studies and collates papers reporting on a variety of mechanisms of tumorigenesis, the need to explore them from multiple perspectives, and the difficulties in exploring them, as well as [...] Read more.
The third volume of this Special Issue focuses on new advances in cancer genetics studies and collates papers reporting on a variety of mechanisms of tumorigenesis, the need to explore them from multiple perspectives, and the difficulties in exploring them, as well as the challenge of integrating them into a unifying but still different model for each tumor type [...] Full article
(This article belongs to the Special Issue Molecular Advances in Cancer Genetics 3.0)

Research

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19 pages, 1235 KiB  
Article
Epithelial-to-Mesenchymal Transition Gene Signature in Circulating Melanoma Cells: Biological and Clinical Relevance
by Maria Cristina Rapanotti, Elisa Cugini, Elena Campione, Cosimo Di Raimondo, Gaetana Costanza, Piero Rossi, Amedeo Ferlosio, Sergio Bernardini, Augusto Orlandi, Anastasia De Luca and Luca Bianchi
Int. J. Mol. Sci. 2023, 24(14), 11792; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms241411792 - 22 Jul 2023
Cited by 2 | Viewed by 1300
Abstract
The most promising method for monitoring patients with minimal morbidity is the detection of circulating melanoma cells (CMCs). We have shown that CD45−CD146+ABCB5+ CMCs identify a rare primitive stem/mesenchymal CMCs population associated with disease progression. The epithelial-to-mesenchymal transition [...] Read more.
The most promising method for monitoring patients with minimal morbidity is the detection of circulating melanoma cells (CMCs). We have shown that CD45−CD146+ABCB5+ CMCs identify a rare primitive stem/mesenchymal CMCs population associated with disease progression. The epithelial-to-mesenchymal transition (EMT) confers cancer cells a hybrid epithelial/mesenchymal phenotype promoting metastatization. Thus, we investigated the potential clinical value of the EMT gene signature of these primitive CMCs. A reliable quantitative real-time polymerase chain reaction (qRT-PCR) protocol was settled up using tumor cell lines RNA dilutions. Afterwards, immune-magnetically isolated CMCs from advanced melanoma patients, at onset and at the first checkpoint (following immune or targeted therapy), were tested for the level of EMT hallmarks and EMT transcription factor genes. Despite the small cohort of patients, we obtained promising results. Indeed, we observed a deep gene rewiring of the EMT investigated genes: in particular we found that the EMT gene signature of isolated CMCs correlated with patients’ clinical outcomes. In conclusion, We established a reliable qRT-PCR protocol with high sensitivity and specificity to characterize the gene expression of isolated CMCs. To our knowledge, this is the first evidence demonstrating the impact of immune or targeted therapies on EMT hallmark gene expressions in CMCs from advanced melanoma patients. Full article
(This article belongs to the Special Issue Molecular Advances in Cancer Genetics 3.0)
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11 pages, 5276 KiB  
Article
Evolutionary Origin of Human PALB2 Germline Pathogenic Variants
by Jia Sheng Chian, Jiaheng Li and San Ming Wang
Int. J. Mol. Sci. 2023, 24(14), 11343; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms241411343 - 12 Jul 2023
Cited by 2 | Viewed by 1031
Abstract
PALB2 (Partner and localizer of BRCA2) is crucial for repairing DNA double-stranded breaks (DSBs) through homologous recombination (HR). Germline pathogenic variation in PALB2 disrupts DNA damage repair and increases the risk of Fanconi Anemia, breast cancer, and ovarian cancer. Determination of the evolutionary [...] Read more.
PALB2 (Partner and localizer of BRCA2) is crucial for repairing DNA double-stranded breaks (DSBs) through homologous recombination (HR). Germline pathogenic variation in PALB2 disrupts DNA damage repair and increases the risk of Fanconi Anemia, breast cancer, and ovarian cancer. Determination of the evolutionary origin of human PALB2 variants will promote a deeper understanding of the biological basis of PALB2 germline variation and its roles in human diseases. We tested the evolution origin for 1444 human PALB2 germline variants, including 484 pathogenic and 960 benign variants. We performed a phylogenic analysis by tracing the variants in 100 vertebrates. However, we found no evidence to show that cross-species conservation was the origin of PALB2 germline pathogenic variants, but it is indeed a rich source for PALB2 germline benign variants. We performed a paleoanthropological analysis by tracing the variants in over 5000 ancient humans. We identified 50 pathogenic in 71 ancient humans dated from 32,895 to 689 before the present, of which 90.1% were dated within the recent 10,000 years. PALB2 benign variants were also highly shared with ancient humans. Data from our study reveal that human PALB2 pathogenic variants mostly arose in recent human history. Full article
(This article belongs to the Special Issue Molecular Advances in Cancer Genetics 3.0)
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20 pages, 9549 KiB  
Article
MiR-199a-5p-Regulated SMARCA4 Promotes Oral Squamous Cell Carcinoma Tumorigenesis
by Mingyan Xu, Junling Zhang, Xuemei Lu, Fan Liu, Songlin Shi and Xiaoling Deng
Int. J. Mol. Sci. 2023, 24(5), 4756; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24054756 - 01 Mar 2023
Cited by 6 | Viewed by 1912
Abstract
SWI/SNF related, matrix associated, actin-dependent regulator of chromatin, subfamily a, member 4 (SMARCA4, also known as BRG1), an ATPase subunit of the switch/sucrose non-fermentable (SWI/SNF) chromatin remodeling complex, plays an important regulatory role in many cytogenetic and cytological processes during cancer development. However, [...] Read more.
SWI/SNF related, matrix associated, actin-dependent regulator of chromatin, subfamily a, member 4 (SMARCA4, also known as BRG1), an ATPase subunit of the switch/sucrose non-fermentable (SWI/SNF) chromatin remodeling complex, plays an important regulatory role in many cytogenetic and cytological processes during cancer development. However, the biological function and mechanism of SMARCA4 in oral squamous cell carcinoma (OSCC) remain unclear. The present study aimed to investigate the role of SMARCA4 in OSCC and its potential mechanism. Using a tissue microarray, SMARCA4 expression was found to be highly upregulated in OSCC tissues. In addition, SMARCA4 upregulate expression led to increased migration and invasion of OSCC cells in vitro, as well as tumor growth and invasion in vivo. These events were associated with the promotion of epithelial–mesenchymal transition (EMT). Bioinformatic analysis and luciferase reporter assay confirmed that SMARCA4 is a target gene of microRNA miR-199a-5p. Further mechanistic studies showed that the miR-199a-5p regulated SMARCA4 can promote the invasion and metastasis of tumor cells through EMT. These findings indicate that the miR-199a-5p- SMARCA4 axis plays a role in tumorigenesis by promoting OSCC cell invasion and metastasis through EMT regulation. Our findings provide insights into the role of SMARCA4 in OSCC and the mechanism involved, which may have important implications for therapeutic purposes. Full article
(This article belongs to the Special Issue Molecular Advances in Cancer Genetics 3.0)
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20 pages, 1297 KiB  
Article
Whole-Exome Sequencing and cfDNA Analysis Uncover Genetic Determinants of Melanoma Therapy Response in a Real-World Setting
by Irene Vanni, Lorenza Pastorino, Enrica Teresa Tanda, Virginia Andreotti, Bruna Dalmasso, Nicola Solari, Matteo Mascherini, Francesco Cabiddu, Antonio Guadagno, Simona Coco, Eleonora Allavena, William Bruno, Gabriella Pietra, Michela Croce, Rosaria Gangemi, Michele Piana, Gabriele Zoppoli, Lorenzo Ferrando, Francesco Spagnolo, Paola Queirolo and Paola Ghiorzoadd Show full author list remove Hide full author list
Int. J. Mol. Sci. 2023, 24(5), 4302; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24054302 - 21 Feb 2023
Viewed by 2072
Abstract
Although several studies have explored the molecular landscape of metastatic melanoma, the genetic determinants of therapy resistance are still largely unknown. Here, we aimed to determine the contribution of whole-exome sequencing and circulating free DNA (cfDNA) analysis in predicting response to therapy in [...] Read more.
Although several studies have explored the molecular landscape of metastatic melanoma, the genetic determinants of therapy resistance are still largely unknown. Here, we aimed to determine the contribution of whole-exome sequencing and circulating free DNA (cfDNA) analysis in predicting response to therapy in a consecutive real-world cohort of 36 patients, undergoing fresh tissue biopsy and followed during treatment. Although the underpowered sample size limited statistical analysis, samples from non-responders had higher copy number variations and mutations in melanoma driver genes compared to responders in the BRAF V600+ subset. In the BRAF V600− subset, Tumor Mutational Burden (TMB) was twice that in responders vs. non-responders. Genomic layout revealed commonly known and novel potential intrinsic/acquired resistance driver gene variants. Among these, RAC1, FBXW7, GNAQ mutations, and BRAF/PTEN amplification/deletion were present in 42% and 67% of patients, respectively. Both Loss of Heterozygosity (LOH) load and tumor ploidy were inversely associated with TMB. In immunotherapy-treated patients, samples from responders showed higher TMB and lower LOH and were more frequently diploid compared to non-responders. Secondary germline testing and cfDNA analysis proved their efficacy in finding germline predisposing variants carriers (8.3%) and following dynamic changes during treatment as a surrogate of tissue biopsy, respectively. Full article
(This article belongs to the Special Issue Molecular Advances in Cancer Genetics 3.0)
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18 pages, 2140 KiB  
Article
Expression of Selected miRNAs in Normal and Cancer-Associated Fibroblasts and in BxPc3 and MIA PaCa-2 Cell Lines of Pancreatic Ductal Adenocarcinoma
by Václav Mandys, Alexey Popov, Robert Gürlich, Jan Havránek, Lucie Pfeiferová, Michal Kolář, Jana Vránová, Karel Smetana, Jr., Lukáš Lacina and Pavol Szabo
Int. J. Mol. Sci. 2023, 24(4), 3617; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24043617 - 10 Feb 2023
Cited by 1 | Viewed by 1758
Abstract
Therapy for pancreatic ductal adenocarcinoma remains challenging, and the chances of a complete cure are very limited. As in other types of cancer, the expression and role of miRNAs in controlling the biological properties of this type of tumor have been extensively studied. [...] Read more.
Therapy for pancreatic ductal adenocarcinoma remains challenging, and the chances of a complete cure are very limited. As in other types of cancer, the expression and role of miRNAs in controlling the biological properties of this type of tumor have been extensively studied. A better insight into miRNA biology seems critical to refining diagnostics and improving their therapeutic potential. In this study, we focused on the expression of miR-21, -96, -196a, -210, and -217 in normal fibroblasts, cancer-associated fibroblasts prepared from a ductal adenocarcinoma of the pancreas, and pancreatic carcinoma cell lines. We compared these data with miRNAs in homogenates of paraffin-embedded sections from normal pancreatic tissues. In cancer-associated fibroblasts and cancer cell lines, miRNAs differed significantly from the normal tissue. In detail, miR-21 and -210 were significantly upregulated, while miR-217 was downregulated. Similar transcription profiles were earlier reported in cancer-associated fibroblasts exposed to hypoxia. However, the cells in our study were cultured under normoxic conditions. We also noted a relation to IL-6 production. In conclusion, cultured cancer-associated fibroblasts and carcinoma cells reflect miR-21 and -210 expression similarly to the cancer tissue samples harvested from the patients. Full article
(This article belongs to the Special Issue Molecular Advances in Cancer Genetics 3.0)
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Review

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15 pages, 1066 KiB  
Review
BRG1: Promoter or Suppressor of Cancer? The Outcome of BRG1’s Interaction with Specific Cellular Pathways
by Aaron Shaykevich, Isaac Silverman, Gargi Bandyopadhyaya and Radhashree Maitra
Int. J. Mol. Sci. 2023, 24(3), 2869; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24032869 - 02 Feb 2023
Cited by 6 | Viewed by 3470
Abstract
BRG1 is one of two catalytic subunits of the SWI/SNF ATP-dependent chromatin-remodeling complex. In cancer, it has been hypothesized that BRG1 acts as a tumor suppressor. Further study has shown that, under certain circumstances, BRG1 acts as an oncogene. Targeted knockout of BRG1 [...] Read more.
BRG1 is one of two catalytic subunits of the SWI/SNF ATP-dependent chromatin-remodeling complex. In cancer, it has been hypothesized that BRG1 acts as a tumor suppressor. Further study has shown that, under certain circumstances, BRG1 acts as an oncogene. Targeted knockout of BRG1 has proven successful in most cancers in suppressing tumor growth and proliferation. Furthermore, BRG1 effects cancer proliferation in oncogenic KRAS mutated cancers, with varying directionality. Thus, dissecting BRG1’s interaction with various cellular pathways can highlight possible intermediates that can facilitate the design of different treatment methods, including BRG1 inhibition. Autophagy and apoptosis are two important cellular responses to stress. BRG1 plays a direct role in autophagy and apoptosis and likely promotes autophagy and suppresses apoptosis, supporting unfettered cancer growth. PRMT5 inhibits transcription by interacting with ATP-dependent chromatin remodeling complexes, such as SWI/SNF. When PRMT5 associates with the SWI/SNF complex, including BRG1, it represses tumor suppressor genes. The Ras/Raf/MAPK/ERK1/2 pathway in cancers is a signal transduction pathway involved in the transcription of genes related to cancer survival. BRG1 has been shown to effect KRAS-driven cancer growth. BRG1 associates with several proteins within the signal transduction pathway. In this review, we analyze BRG1 as a promising target for cancer inhibition and possible synergy with other cancer treatments. Full article
(This article belongs to the Special Issue Molecular Advances in Cancer Genetics 3.0)
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