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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 (15 January 2022) | Viewed by 53121

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Prof. Dr. Paola Ghiorzo

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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

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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 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
Prof. Dr. William Bruno
Guest Editors

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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.

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Published Papers (12 papers)

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Editorial

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3 pages, 171 KiB

Open AccessEditorial

A Glance at Molecular Advances in Cancer Genetics: A Baffling Puzzle Still to Be Solved

by Paola Ghiorzo and William Bruno

Int. J. Mol. Sci. 2023, 24(2), 1394; https://doi.org/10.3390/ijms24021394 - 11 Jan 2023

Viewed by 1612

Abstract

The purpose of this first Special Issue is to provide a glance at the molecular advances in cancer genetics to untangle the complexity of tumorigenesis [...] Full article

(This article belongs to the Special Issue Molecular Advances in Cancer Genetics)

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Research

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13 pages, 1069 KiB

Open AccessArticle

Determination of BRCAness Phenotype in Breast Tumors for the Appointment of Neoadjuvant Chemotherapy Based on Platinum and Taxanes

by Matvey Mihajlovich Tsyganov, Marina K. Ibragimova, Evgeniy Y. Garbukov, Olga D. Bragina, Ariana A. Karchevskaya, Evgeny A. Usynin and Nikolai V. Litvyakov

Int. J. Mol. Sci. 2023, 24(1), 207; https://doi.org/10.3390/ijms24010207 - 22 Dec 2022

Cited by 3 | Viewed by 2115

Abstract

The concept of BRCAness was developed because of similarities between sporadic and hereditary breast cancer. BRCAness defines the pathogenesis and treatment sensitivity of many types of cancer, as well as the presence of a defect in the homologous recombination repair of tumor cells simulating the loss of BRCA1 or BRCA2, as in the presence of germline mutations. The question of treatment effectiveness for BRCA-like tumors is controversial and open. Thus, the aim of this work was to study the effectiveness of neoadjuvant chemotherapy (NAC) in BRCA-deficient breast cancer patients without germline mutations. The study involved 130 patients with breast cancer in stages IIA–IIIB. The treatment regimen included neoadjuvant chemotherapy, surgery, and adjuvant chemotherapy. The materials used were tumor samples from before and after chemotherapy. DNA and RNA were isolated from the tumor material. RNA was used to assess the expression level of BRCA1, while DNA was used for methyl-sensitive PCR. A microarray analysis was performed on high-density DNA chips from an Affymetrix CytoScan^TM HD Array to assess DNA copy number aberration (CNA status) and loss of heterozygosity. A statistical analysis was performed using the Statistica 8.0 application package. It was noted that the existence of copy number aberrations in genes was statistically significantly associated with tumor treatment response and disease prognosis. Patients with partial regression had a statistically significantly higher amount of deletion than patients without an objective response (5/25 patients; 16%), as shown in the general sample of patients (52.9% versus 27.1%, respectively) at p = 0.0001 and in patients treated with anthracycline-containing regimen (p = 0.0001). In addition, it was shown that patients with BRCA1 deletion had higher rates of metastatic-free survival (log rank test, p = 0.009). BRCAness patients had a higher rate of 5-year metastatic survival, but not of treatment efficacy. The prospective study showed the positive effect of assessing the BRCAness phenotype of a tumor before treatment and of prescribing personalized NAC regimens. The objective response rate was statistically significantly more often observed in the group of patients with personalized chemotherapy (85.0% (34/40 patients) versus 62.3% (56/90 patients); p = 0.007). Despite the controversial effectiveness of BRCA-like tumor treatment, our data showed high predictive and prognostic significance of the BRCAness phenotype for the personalization of platinum and taxane regimens. Full article

(This article belongs to the Special Issue Molecular Advances in Cancer Genetics)

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13 pages, 746 KiB

Open AccessArticle

The Absence of Retroelement Activity Is Characteristic for Childhood Acute Leukemias and Adult Acute Lymphoblastic Leukemia

by Shamil Urazbakhtin, Anastasia Smirnova, Anastasiya Volakhava, Elena Zerkalenkova, Maria Salyutina, Michael Doubek, Hana Jelinkova, Nelly Khudainazarova, Egor Volchkov, Laima Belyaeva, Ekaterina Komech, Sarka Pavlova, Yuri Lebedev, Karla Plevova, Yulia Olshanskaya, Alexander Komkov and Ilgar Mamedov

Int. J. Mol. Sci. 2022, 23(3), 1756; https://doi.org/10.3390/ijms23031756 - 3 Feb 2022

Cited by 1 | Viewed by 3030

Abstract

Retroelements (RE) have been proposed as important players in cancerogenesis. Different cancer types are characterized by a different level of tumor-specific RE insertions. In previous studies, small cohorts of hematological malignancies, such as acute myeloid leukemia, multiple myeloma, and chronic lymphocytic leukemia have been characterized by a low level of RE insertional activity. Acute lymphoblastic leukemia (ALL) in adults and childhood acute leukemias have not been studied in this context. We performed a search for new RE insertions (Alu and L1) in 44 childhood ALL, 14 childhood acute myeloid leukemia, and 14 adult ALL samples using a highly sensitive NGS-based approach. First, we evaluated the method sensitivity revealing the 1% detection threshold for the proportion of cells with specific RE insertion. Following this result, we did not identify new tumor-specific RE insertions in the tested cohort of acute leukemia samples at the established level of sensitivity. Additionally, we analyzed the transcription levels of active L1 copies and found them increased. Thus, the increased transcription of active L1 copies is not sufficient for overt elevation of L1 retrotranspositional activity in leukemia. Full article

(This article belongs to the Special Issue Molecular Advances in Cancer Genetics)

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17 pages, 1223 KiB

Open AccessArticle

Comprehensive Genomic and Transcriptomic Analysis of Three Synchronous Primary Tumours and a Recurrence from a Head and Neck Cancer Patient

by Luisa Bresadola, David Weber, Christoph Ritzel, Martin Löwer, Valesca Bukur, Özlem Akilli-Öztürk, Julia Becker, Hisham Mehanna, Barbara Schrörs, Fulvia Vascotto, Ugur Sahin and Anthony Kong

Int. J. Mol. Sci. 2021, 22(14), 7583; https://doi.org/10.3390/ijms22147583 - 15 Jul 2021

Cited by 3 | Viewed by 3002

Abstract

Synchronous primary malignancies occur in a small proportion of head and neck squamous cell carcinoma (HNSCC) patients. Here, we analysed three synchronous primaries and a recurrence from one patient by comparing the genomic and transcriptomic profiles among the tumour samples and determining the recurrence origin. We found remarkable levels of heterogeneity among the primary tumours, and through the patterns of shared mutations, we traced the origin of the recurrence. Interestingly, the patient carried germline variants that might have predisposed him to carcinogenesis, together with a history of alcohol and tobacco consumption. The mutational signature analysis confirmed the impact of alcohol exposure, with Signature 16 present in all tumour samples. Characterisation of immune cell infiltration highlighted an immunosuppressive environment in all samples, which exceeded the potential activity of T cells. Studies such as the one described here have important clinical value and contribute to personalised treatment decisions for patients with synchronous primaries and matched recurrences. Full article

(This article belongs to the Special Issue Molecular Advances in Cancer Genetics)

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15 pages, 1862 KiB

Open AccessArticle

Detecting Variants in the NBN Gene While Testing for Hereditary Breast Cancer: What to Do Next?

by Roberta Zuntini, Elena Bonora, Laura Maria Pradella, Laura Benedetta Amato, Michele Vidone, Sara De Fanti, Irene Catucci, Laura Cortesi, Veronica Medici, Simona Ferrari, Giuseppe Gasparre, Paolo Peterlongo, Marco Sazzini and Daniela Turchetti

Int. J. Mol. Sci. 2021, 22(11), 5832; https://doi.org/10.3390/ijms22115832 - 29 May 2021

Cited by 10 | Viewed by 4270

Abstract

The NBN gene has been included in breast cancer (BC) multigene panels based on early studies suggesting an increased BC risk for carriers, though not confirmed by recent research. To evaluate the impact of NBN analysis, we assessed the results of NBN sequencing in 116 BRCA-negative BC patients and reviewed the literature. Three patients (2.6%) carried potentially relevant variants: two, apparently unrelated, carried the frameshift variant c.156_157delTT and another one the c.628G>T variant. The latter was subsequently found in 4/1390 (0.3%) BC cases and 8/1580 (0.5%) controls in an independent sample, which, together with in silico predictions, provided evidence against its pathogenicity. Conversely, the rare c.156_157delTT variant was absent in the case-control set; moreover, a 50% reduction of NBN expression was demonstrated in one carrier. However, in one family it failed to co-segregate with BC, while the other carrier was found to harbor also a probably pathogenic TP53 variant that may explain her phenotype. Therefore, the c.156_157delTT, although functionally deleterious, was not supported as a cancer-predisposing defect. Pathogenic/likely pathogenic NBN variants were detected by multigene panels in 31/12314 (0.25%) patients included in 15 studies. The risk of misinterpretation of such findings is substantial and supports the exclusion of NBN from multigene panels. Full article

(This article belongs to the Special Issue Molecular Advances in Cancer Genetics)

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14 pages, 2343 KiB

Open AccessArticle

The GNAQ T96S Mutation Affects Cell Signaling and Enhances the Oncogenic Properties of Hepatocellular Carcinoma

by Eugene Choi, Sung Jean Park, Gunhee Lee, Seung Kew Yoon, Minho Lee and Suk Kyeong Lee

Int. J. Mol. Sci. 2021, 22(6), 3284; https://doi.org/10.3390/ijms22063284 - 23 Mar 2021

Cited by 6 | Viewed by 3484

Abstract

Hepatocellular carcinoma (HCC), the most common malignant tumor in the liver, grows and metastasizes rapidly. Despite advances in treatment modalities, the five-year survival rate of HCC remains less than 30%. We sought genetic mutations that may affect the oncogenic properties of HCC, using The Cancer Genome Atlas (TCGA) data analysis. We found that the GNAQ T96S mutation (threonine 96 to serine alteration of the Gαq protein) was present in 12 out of 373 HCC patients (3.2%). To examine the effect of the GNAQ T96S mutation on HCC, we transfected the SK-Hep-1 cell line with the wild-type or the mutant GNAQ T96S expression vector. Transfection with the wild-type GNAQ expression vector enhanced anchorage-independent growth, migration, and the MAPK pathways in the SK-Hep-1 cells compared to control vector transfection. Moreover, cell proliferation, anchorage-independent growth, migration, and the MAPK pathways were further enhanced in the SK-Hep-1 cells transfected with the GNAQ T96S expression vector compared to the wild-type GNAQ-transfected cells. In silico structural analysis shows that the substitution of the GNAQ amino acid threonine 96 with a serine may destabilize the interaction between the regulator of G protein signaling (RGS) protein and GNAQ. This may reduce the inhibitory effect of RGS on GNAQ signaling, enhancing the GNAQ signaling pathway. Single nucleotide polymorphism (SNP) genotyping analysis for Korean HCC patients shows that the GNAQ T96S mutation was found in only one of the 456 patients (0.22%). Our data suggest that the GNAQ T96S hotspot mutation may play an oncogenic role in HCC by potentiating the GNAQ signal transduction pathway. Full article

(This article belongs to the Special Issue Molecular Advances in Cancer Genetics)

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9 pages, 1090 KiB

Open AccessArticle

BRCA Methylation Testing Identifies a Subset of Ovarian Carcinomas without Germline Variants That Can Benefit from PARP Inhibitor

by Nora Sahnane, Ileana Carnevali, Giorgio Formenti, Jvan Casarin, Sofia Facchi, Raffaella Bombelli, Eleonora Di Lauro, Domenico Memoli, Annamaria Salvati, Francesca Rizzo, Fausto Sessa and Maria Grazia Tibiletti

Int. J. Mol. Sci. 2020, 21(24), 9708; https://doi.org/10.3390/ijms21249708 - 19 Dec 2020

Cited by 21 | Viewed by 3408

Abstract

Homologous Recombination Deficiency (HRD) is a frequent feature of high-grade epithelial ovarian carcinoma (EOC), associated with sensitivity to PARP-inhibitors (PARPi). The best characterized causes of HRD in EOCs are germline or somatic mutations in BRCA1 and BRCA2 genes. Although promoter methylation is a well-known mechanism of gene transcriptional repression, few data have been published about BRCA gene methylation in EOCs. In this retrospective study, we quantitatively analyzed by pyrosequencing a selected series of 90 formalin-fixed (FFPE) primary EOCs without BRCA germline mutations. We identified 20/88 (22.7%) EOCs showing BRCA promoter methylation, including 17/88 (19.3%) in BRCA1 and 4/86 (4.6%) in BRCA2 promoters, one of which showing concomitant BRCA1 methylation. Mean methylation levels were 49.6% and 45.8% for BRCA1 and BRCA2, respectively, with methylation levels ≥50% in 10/20 methylated EOCs. Constitutive BRCA methylation was excluded by testing blood-derived DNA. In conclusion, pyrosequencing methylation analysis of BRCA genes is a robust, quantitative and sensitive assay applicable to FFPE samples. Remarkably, a considerable subset of germline BRCA-negative EOCs showed somatic methylation and, likely, HRD. A subpopulation of women with BRCA methylation, even without BRCA mutations, could potentially benefit from PARP-inhibitors; further clinical studies are needed to clarify the predictive role of somatic BRCA methylation of PARP-therapy response. Full article

(This article belongs to the Special Issue Molecular Advances in Cancer Genetics)

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11 pages, 1787 KiB

Open AccessArticle

Genomic Analysis of Hematopoietic Stem Cell at the Single-Cell Level: Optimization of Cell Fixation and Whole Genome Amplification (WGA) Protocol

by Chiara Carretta, Selene Mallia, Elena Genovese, Sandra Parenti, Sebastiano Rontauroli, Elisa Bianchi, Sebastian Fantini, Stefano Sartini, Lara Tavernari, Enrico Tagliafico and Rossella Manfredini

Int. J. Mol. Sci. 2020, 21(19), 7366; https://doi.org/10.3390/ijms21197366 - 6 Oct 2020

Cited by 6 | Viewed by 3435

Abstract

Single-cell genomics has become the method of choice for the study of heterogeneous cell populations and represents an elective application in defining the architecture and clonal evolution in hematological neoplasms. Reconstructing the clonal evolution of a neoplastic population therefore represents the main way to understand more deeply the pathogenesis of the neoplasm, but it is also a potential tool to understand the evolution of the tumor population with respect to its response to therapy. Pre-analytical phase for single-cell genomics analysis is crucial to obtain a cell population suitable for single-cell sorting, and whole genome amplification is required to obtain the necessary amount of DNA from a single cell in order to proceed with sequencing. Here, we evaluated the impact of different methods of cellular immunostaining, fixation and whole genome amplification on the efficiency and yield of single-cell sequencing. Full article

(This article belongs to the Special Issue Molecular Advances in Cancer Genetics)

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Review

Jump to: Editorial, Research

19 pages, 2446 KiB

Open AccessReview

Novel Molecular Insights into Leukemic Evolution of Myeloproliferative Neoplasms: A Single Cell Perspective

by Sebastiano Rontauroli, Chiara Carretta, Sandra Parenti, Matteo Bertesi and Rossella Manfredini

Int. J. Mol. Sci. 2022, 23(23), 15256; https://doi.org/10.3390/ijms232315256 - 3 Dec 2022

Cited by 6 | Viewed by 2982

Abstract

Myeloproliferative neoplasms (MPNs) are clonal disorders originated by the serial acquisition of somatic mutations in hematopoietic stem/progenitor cells. The major clinical entities are represented by polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF), that are caused by driver mutations affecting JAK2, MPL or CALR. Disease progression is related to molecular and clonal evolution. PV and ET can progress to secondary myelofibrosis (sMF) but can also evolve to secondary acute myeloid leukemia (sAML). PMF is associated with the highest frequency of leukemic transformation, which represents the main cause of death. sAML is associated with a dismal prognosis and clinical features that differ from those of de novo AML. The molecular landscape distinguishes sAML from de novo AML, since the most frequent hits involve TP53, epigenetic regulators, spliceosome modulators or signal transduction genes. Single cell genomic studies provide novel and accurate information about clonal architecture and mutation acquisition order, allowing the reconstruction of clonal dynamics and molecular events that accompany leukemic transformation. In this review, we examine our current understanding of the genomic heterogeneity in MPNs and how it affects disease progression and leukemic transformation. We focus on molecular events elicited by somatic mutations acquisition and discuss the emerging findings coming from single cell studies. Full article

(This article belongs to the Special Issue Molecular Advances in Cancer Genetics)

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14 pages, 496 KiB

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Insights into Mechanisms of Tumorigenesis in Neuroendocrine Neoplasms

by Lorenza Pastorino, Federica Grillo, Manuela Albertelli, Paola Ghiorzo and William Bruno

Int. J. Mol. Sci. 2021, 22(19), 10328; https://doi.org/10.3390/ijms221910328 - 25 Sep 2021

Cited by 5 | Viewed by 2694

Abstract

Genomic studies have identified some of the most relevant genetic players in Neuroendocrine Neoplasm (NEN) tumorigenesis. However, we are still far from being able to draw a model that encompasses their heterogeneity, elucidates the different biological effects consequent to the identified molecular events, or incorporates extensive knowledge of molecular biomarkers and therapeutic targets. Here, we reviewed recent insights in NEN tumorigenesis from selected basic research studies on animal models, highlighting novel players in the intergenic cooperation and peculiar mechanisms including splicing dysregulation, chromatin stability, or cell dedifferentiation. Furthermore, models of tumorigenesis based on composite interactions other than a linear progression of events are proposed, exemplified by the involvement in NEN tumorigenesis of genes regulating complex functions, such as MEN1 or DAXX. Although limited by interspecies differences, animal models have proved helpful for the more in-depth study of every facet of tumorigenesis, showing that the identification of driver mutations is only one of the many necessary steps and that other mechanisms are worth investigating. Full article

(This article belongs to the Special Issue Molecular Advances in Cancer Genetics)

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24 pages, 399 KiB

Open AccessReview

Multi-Gene Testing Overview with a Clinical Perspective in Metastatic Triple-Negative Breast Cancer

by Martina Dameri, Lorenzo Ferrando, Gabriella Cirmena, Claudio Vernieri, Giancarlo Pruneri, Alberto Ballestrero and Gabriele Zoppoli

Int. J. Mol. Sci. 2021, 22(13), 7154; https://doi.org/10.3390/ijms22137154 - 1 Jul 2021

Cited by 7 | Viewed by 5351

Abstract

Next-generation sequencing (NGS) is the technology of choice for the routine screening of tumor samples in clinical practice. In this setting, the targeted sequencing of a restricted number of clinically relevant genes represents the most practical option when looking for genetic variants associated with cancer, as well as for the choice of targeted treatments. In this review, we analyze available NGS platforms and clinical applications of multi-gene testing in breast cancer, with a focus on metastatic triple-negative breast cancer (mTNBC). We make an overview of the clinical utility of multi-gene testing in mTNBC, and then, as immunotherapy is emerging as a possible targeted therapy for mTNBC, we also briefly report on the results of the latest clinical trials involving immune checkpoint inhibitors (ICIs) and TNBC, where NGS could play a role for the potential predictive utility of homologous recombination repair deficiency (HRD) and tumor mutational burden (TMB). Full article

(This article belongs to the Special Issue Molecular Advances in Cancer Genetics)

24 pages, 626 KiB

Open AccessReview

Genetic Markers in Lung Cancer Diagnosis: A Review

by Katarzyna Wadowska, Iwona Bil-Lula, Łukasz Trembecki and Mariola Śliwińska-Mossoń

Int. J. Mol. Sci. 2020, 21(13), 4569; https://doi.org/10.3390/ijms21134569 - 27 Jun 2020

Cited by 131 | Viewed by 15476

Abstract

Lung cancer is the most often diagnosed cancer in the world and the most frequent cause of cancer death. The prognosis for lung cancer is relatively poor and 75% of patients are diagnosed at its advanced stage. The currently used diagnostic tools are not sensitive enough and do not enable diagnosis at the early stage of the disease. Therefore, searching for new methods of early and accurate diagnosis of lung cancer is crucial for its effective treatment. Lung cancer is the result of multistage carcinogenesis with gradually increasing genetic and epigenetic changes. Screening for the characteristic genetic markers could enable the diagnosis of lung cancer at its early stage. The aim of this review was the summarization of both the preclinical and clinical approaches in the genetic diagnostics of lung cancer. The advancement of molecular strategies and analytic platforms makes it possible to analyze the genome changes leading to cancer development—i.e., the potential biomarkers of lung cancer. In the reviewed studies, the diagnostic values of microsatellite changes, DNA hypermethylation, and p53 and KRAS gene mutations, as well as microRNAs expression, have been analyzed as potential genetic markers. It seems that microRNAs and their expression profiles have the greatest diagnostic potential value in lung cancer diagnosis, but their quantification requires standardization. Full article

(This article belongs to the Special Issue Molecular Advances in Cancer Genetics)

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