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Biology
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New Sight in Cancer Genetics
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New Sight in Cancer Genetics

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Cancer Biology".

Deadline for manuscript submissions: 31 January 2025 | Viewed by 11573

Special Issue Editors

Prof. Dr. Ilda Patrícia Ribeiro

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Guest Editor
1. Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
2. Institute for Clinical and Biomedical Research (iCBR), Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine (FMUC), University of Coimbra, 3004-531 Coimbra, Portugal
Interests: genomic; omics in cancer; head and neck cancer; methylation and genetic mechanisms; oncobiology; copy number alterations; prognosis biomarkers
Prof. Dr. Isabel Marques Carreira

E-Mail Website
Guest Editor
1. Cytogenetics and Genomics Laboratory, Institute of Cellular and Molecular Biology, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
2. Institute for Clinical and Biomedical Research (iCBR), Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine (FMUC), University of Coimbra, 3004-531 Coimbra, Portugal
Interests: cytogenetics; human genetics, cancer genetics, oncobiology
Prof. Dr. Alberto Orfao

E-Mail Website1 Website2
Guest Editor
Department of Medicine, Cancer Research Center (IBMCC-CSIC/USAL), CIBERONC and Institute for Biomedical Research of Salamanca (IBSAL), University of Salamanca (USAL), Salamanca, Spain
Interests: leukemia; lymphoma; early cancer diagnosis; immunophenotyping; genetics; diagnosis; prognosis; minimal residual disease; immune monitoring; CART; EuroFlow
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In general, it has remained challenging to treat cancer despite the innovative and revolutionary research taking place worldwide. The remarkable advances over the last decade in multi-omics technologies, especially next-generation sequencing (NGS) and genome analysis, have led to significant improvements in our knowledge of the molecular mechanisms of cancer. Together with bioinformatic tools and Artificial Intelligence, it is possible to use computer programming to improve cancer diagnosis, drug development, and precision medicine.

This Special Issue aims to present robust molecular signatures and biomarkers of unmet clinical problems in cancer field, mostly focusing on predicting treatment response, making early diagnosis and assessing disease prognosis through the use of different omics approaches, such as genomic, epigenomic, transcriptomis, proteomic, metabolomic methods. We welcome original research articles and reviews to this Special Issue. Research areas may include (but are not limited to) the following topics: new developments in cancer research in order to identify biomarkers and molecular signatures with high possibility of clinical application and therapeutic development.

We look forward to receiving your contributions.

Prof. Dr. Ilda Patrícia Ribeiro
Prof. Dr. Isabel Marques Carreira
Prof. Dr. Alberto Orfao
Guest Editors

Manuscript Submission Information

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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. Biology is an international peer-reviewed open access monthly journal published by MDPI.

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Keywords

  • genomic and epigenetic characterization
  • diagnosis and prognosis biomarkers
  • omics profiles
  • genetic and genomic signature
  • molecular heterogeneity
  • molecular targeted therapy
  • oncogenic signaling pathways
  • copy number alterations and mutational landscape
  • chromosome abnormalities

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Published Papers (6 papers)

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Research

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15 pages, 1265 KiB  
Article
Polygenic Risk Score Improves Melanoma Risk Assessment in a Patient Cohort from the Veneto Region of Italy
by Stefania Pellegrini, Thomas P. Potjer, Paola Del Bianco, Antonella Vecchiato, Alessio Fabozzi, Luisa Piccin, Debora Tonello, Nienke van der Stoep, Emily Tinsley, Maria Teresa Landi, Mark M. Iles and Chiara Menin
Biology 2024, 13(11), 954; https://doi.org/10.3390/biology13110954 - 20 Nov 2024
Viewed by 264
Abstract
Recent genome-wide association studies (GWASs) have identified many single nucleotide polymorphisms (SNPs) that alone weakly affect melanoma risk, but their combined effect on a polygenic risk score (PRS) can have a far bigger impact on estimating risk. However, the PRS is not yet [...] Read more.
Recent genome-wide association studies (GWASs) have identified many single nucleotide polymorphisms (SNPs) that alone weakly affect melanoma risk, but their combined effect on a polygenic risk score (PRS) can have a far bigger impact on estimating risk. However, the PRS is not yet at the stage of being utilized in clinical practice, and further evidence is needed. In this study, 270 melanoma patients fulfilling the criteria for a suspected genetic predisposition but with a negative genetic test for high/medium-penetrance genes were genotyped for 57 SNPs selected in previous GWASs to construct a PRS model. We found a significantly higher mean PRS57 in all melanoma cases than in controls (0.58 vs. 0.00, p < 0.001), and the mean PRS57 in multiple primary melanoma cases was twice that in single melanoma cases (0.689 vs. 0.362, p = 0.025). Interestingly, our results confirm the association of the PRS57 not only with other melanoma risk factors but also with a younger age at diagnosis. This evidence supports the potentially powerful discriminative role of PRS in the selection of high-risk patients who should undergo stricter surveillance protocols. Full article
(This article belongs to the Special Issue New Sight in Cancer Genetics)
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18 pages, 3069 KiB  
Article
Paired Primary and Recurrent Rhabdoid Meningiomas: Cytogenetic Alterations, BAP1 Gene Expression Profile and Patient Outcome
by Patricia Alejandra Garrido Ruiz, Álvaro Otero Rodriguez, Luis Antonio Corchete, Victoria Zelaya Huerta, Alejandro Pasco Peña, Cristina Caballero Martínez, Joaquín González-Carreró Fojón, Inmaculada Catalina Fernández, Juan Carlos López Duque, Laura Zaldumbide Dueñas, Lorena Mosteiro González, María Aurora Astudillo, Aurelio Hernández-Laín, Emma Natalia Camacho Urkaray, María Amparo Viguri Diaz, Alberto Orfao and María Dolores Tabernero
Biology 2024, 13(5), 350; https://doi.org/10.3390/biology13050350 - 16 May 2024
Viewed by 1073
Abstract
Rhabdoid meningiomas (RM) are a rare meningioma subtype with a heterogeneous clinical course which is more frequently associated with recurrence, even among tumors undergoing-complete surgical removal. Here, we retrospectively analyzed the clinical-histopathological and cytogenetic features of 29 tumors, from patients with recurrent (seven [...] Read more.
Rhabdoid meningiomas (RM) are a rare meningioma subtype with a heterogeneous clinical course which is more frequently associated with recurrence, even among tumors undergoing-complete surgical removal. Here, we retrospectively analyzed the clinical-histopathological and cytogenetic features of 29 tumors, from patients with recurrent (seven primary and 14 recurrent tumors) vs. non-recurrent RM (n = 8). Recurrent RM showed one (29%), two (29%) or three (42%) recurrences. BAP1 loss of expression was found in one third of all RM at diagnosis and increased to 100% in subsequent tumor recurrences. Despite both recurrent and non-recurrent RM shared chromosome 22 losses, non-recurrent tumors more frequently displayed extensive losses of chromosome 19p (62%) and/or 19q (50%), together with gains of chromosomes 20 and 21 (38%, respectively), whereas recurrent RM (at diagnosis) displayed more complex genotypic profiles with extensive losses of chromosomes 1p, 14q, 18p, 18q (67% each) and 21p (50%), together with focal gains at chromosome 17q22 (67%). Compared to paired primary tumors, recurrent RM samples revealed additional losses at chromosomes 16q and 19p (50% each), together with gains at chromosomes 1q and 17q in most recurrent tumors (67%, each). All deceased recurrent RM patients corresponded to women with chromosome 17q gains, although no statistical significant differences were found vs. the other RM patients. Full article
(This article belongs to the Special Issue New Sight in Cancer Genetics)
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23 pages, 7697 KiB  
Article
An Exploration of Small Molecules That Bind Human Single-Stranded DNA Binding Protein 1
by Zachariah P. Schuurs, Alexander P. Martyn, Carl P. Soltau, Sam Beard, Esha T. Shah, Mark N. Adams, Laura V. Croft, Kenneth J. O’Byrne, Derek J. Richard and Neha S. Gandhi
Biology 2023, 12(11), 1405; https://doi.org/10.3390/biology12111405 - 6 Nov 2023
Cited by 3 | Viewed by 2324
Abstract
Human single-stranded DNA binding protein 1 (hSSB1) is critical to preserving genome stability, interacting with single-stranded DNA (ssDNA) through an oligonucleotide/oligosaccharide binding-fold. The depletion of hSSB1 in cell-line models leads to aberrant DNA repair and increased sensitivity to irradiation. hSSB1 is over-expressed in [...] Read more.
Human single-stranded DNA binding protein 1 (hSSB1) is critical to preserving genome stability, interacting with single-stranded DNA (ssDNA) through an oligonucleotide/oligosaccharide binding-fold. The depletion of hSSB1 in cell-line models leads to aberrant DNA repair and increased sensitivity to irradiation. hSSB1 is over-expressed in several types of cancers, suggesting that hSSB1 could be a novel therapeutic target in malignant disease. hSSB1 binding studies have focused on DNA; however, despite the availability of 3D structures, small molecules targeting hSSB1 have not been explored. Quinoline derivatives targeting hSSB1 were designed through a virtual fragment-based screening process, synthesizing them using AlphaLISA and EMSA to determine their affinity for hSSB1. In parallel, we further screened a structurally diverse compound library against hSSB1 using the same biochemical assays. Three compounds with nanomolar affinity for hSSB1 were identified, exhibiting cytotoxicity in an osteosarcoma cell line. To our knowledge, this is the first study to identify small molecules that modulate hSSB1 activity. Molecular dynamics simulations indicated that three of the compounds that were tested bound to the ssDNA-binding site of hSSB1, providing a framework for the further elucidation of inhibition mechanisms. These data suggest that small molecules can disrupt the interaction between hSSB1 and ssDNA, and may also affect the ability of cells to repair DNA damage. This test study of small molecules holds the potential to provide insights into fundamental biochemical questions regarding the OB-fold. Full article
(This article belongs to the Special Issue New Sight in Cancer Genetics)
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13 pages, 1753 KiB  
Article
3D Chromatin Architecture Re-Wiring at the CDH3/CDH1 Loci Contributes to E-Cadherin to P-Cadherin Expression Switch in Gastric Cancer
by Celina São José, Carla Pereira, Marta Ferreira, Ana André, Hugo Osório, Irene Gullo, Fátima Carneiro and Carla Oliveira
Biology 2023, 12(6), 803; https://doi.org/10.3390/biology12060803 - 31 May 2023
Cited by 1 | Viewed by 1917
Abstract
Cadherins are cell–cell adhesion molecules, fundamental for cell architecture and polarity. E-cadherin to P-cadherin switch can rescue adherens junctions in epithelial tumours. Herein, we disclose a mechanism for E-cadherin to P-cadherin switch in gastric cancers. CDH1 and CDH3 mRNA expression was obtained from [...] Read more.
Cadherins are cell–cell adhesion molecules, fundamental for cell architecture and polarity. E-cadherin to P-cadherin switch can rescue adherens junctions in epithelial tumours. Herein, we disclose a mechanism for E-cadherin to P-cadherin switch in gastric cancers. CDH1 and CDH3 mRNA expression was obtained from 42 gastric tumours’ RNA-seq data. CRISPR-Cas9 was used to knock out CDH1 and a putative regulatory element. CDH1-depleted and parental cells were submitted to proteomics and enrichment GO terms analysis; ATAC-seq/4C-seq with a CDH1 promoter viewpoint to assess chromatin accessibility and conformation; and RT-PCR/flow cytometry to assess CDH1/E-cadherin and CDH3/P-cadherin expression. In 42% of gastric tumours analysed, CDH1 to CDH3 switch was observed. CDH1 knockout triggered CDH1/E-cadherin complete loss and CDH3/P-cadherin expression increase at plasma membrane. This switch, likely rescuing adherens junctions, increased cell migration/proliferation, commonly observed in aggressive tumours. E- to P-cadherin switch accompanied increased CDH1 promoter interactions with CDH3–eQTL, absent in normal stomach and parental cells. CDH3–eQTL deletion promotes CDH3/CDH1 reduced expression. These data provide evidence that loss of CDH1/E-cadherin expression alters the CDH3 locus chromatin conformation, allowing a CDH1 promoter interaction with a CDH3-eQTL, and promoting CDH3/P-cadherin expression. These data highlight a novel mechanism triggering E- to P-cadherin switch in gastric cancer. Full article
(This article belongs to the Special Issue New Sight in Cancer Genetics)
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Review

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33 pages, 1407 KiB  
Review
Proteomic Profile of Endometrial Cancer: A Scoping Review
by Beatriz Serambeque, Catarina Mestre, Kristina Hundarova, Carlos Miguel Marto, Bárbara Oliveiros, Ana Rita Gomes, Ricardo Teixo, Ana Sofia Carvalho, Maria Filomena Botelho, Rune Matthiesen, Maria João Carvalho and Mafalda Laranjo
Biology 2024, 13(8), 584; https://doi.org/10.3390/biology13080584 - 1 Aug 2024
Viewed by 1660
Abstract
Proteomics can be a robust tool in protein identification and regulation, allowing the discovery of potential biomarkers. In clinical practice, the management of endometrial cancer can be challenging. Thus, identifying promising markers could be beneficial, helping both in diagnosis and prognostic stratification, even [...] Read more.
Proteomics can be a robust tool in protein identification and regulation, allowing the discovery of potential biomarkers. In clinical practice, the management of endometrial cancer can be challenging. Thus, identifying promising markers could be beneficial, helping both in diagnosis and prognostic stratification, even predicting the response to therapy. Therefore, this manuscript systematically reviews the existing evidence of the proteomic profile of human endometrial cancer. The literature search was conducted via Medline (through PubMed) and the Web of Science. The inclusion criteria were clinical, in vitro, and in vivo original studies reporting proteomic analysis using all types of samples to map the human endometrial cancer proteome. A total of 55 publications were included in this review. Most of the articles carried out a proteomic analysis on endometrial tissue, serum and plasma samples, which enabled the identification of several potential diagnostic and prognostic biomarkers. In addition, eight articles were analyzed regarding the identified proteins, where three studies showed a strong correlation, sharing forty-five proteins. This analysis also allowed the identification of the 10 most frequently reported proteins in these studies: EGFR, PGRMC1, CSE1L, MYDGF, STMN1, CASP3 ANXA2, YBX1, ANXA1, and MYH11. Proteomics-based approaches pointed out potential diagnostic and prognostic candidates for endometrial cancer. However, there is a lack of studies exploring novel therapeutic targets. Full article
(This article belongs to the Special Issue New Sight in Cancer Genetics)
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15 pages, 816 KiB  
Review
Current Applications and Challenges of Next-Generation Sequencing in Plasma Circulating Tumour DNA of Ovarian Cancer
by Ricardo Roque, Ilda Patrícia Ribeiro, Margarida Figueiredo-Dias, Charlie Gourley and Isabel Marques Carreira
Biology 2024, 13(2), 88; https://doi.org/10.3390/biology13020088 - 31 Jan 2024
Viewed by 3295
Abstract
Circulating tumour DNA (ctDNA) facilitates longitudinal study of the tumour genome, which, unlike tumour tissue biopsies, globally reflects intratumor and intermetastatis heterogeneity. Despite its costs, next-generation sequencing (NGS) has revolutionised the study of ctDNA, ensuring a more comprehensive and multimodal approach, increasing data [...] Read more.
Circulating tumour DNA (ctDNA) facilitates longitudinal study of the tumour genome, which, unlike tumour tissue biopsies, globally reflects intratumor and intermetastatis heterogeneity. Despite its costs, next-generation sequencing (NGS) has revolutionised the study of ctDNA, ensuring a more comprehensive and multimodal approach, increasing data collection, and introducing new variables that can be correlated with clinical outcomes. Current NGS strategies can comprise a tumour-informed set of genes or the entire genome and detect a tumour fraction as low as 10−5. Despite some conflicting studies, there is evidence that ctDNA levels can predict the worse outcomes of ovarian cancer (OC) in both early and advanced disease. Changes in those levels can also be informative regarding treatment efficacy and tumour recurrence, capable of outperforming CA-125, currently the only universally utilised plasma biomarker in high-grade serous OC (HGSOC). Qualitative evaluation of sequencing shows that increasing copy number alterations and gene variants during treatment may correlate with a worse prognosis in HGSOC. However, following tumour clonality and emerging variants during treatment poses a more unique opportunity to define treatment response, select patients based on their emerging resistance mechanisms, like BRCA secondary mutations, and discover potential targetable variants. Sequencing of tumour biopsies and ctDNA is not always concordant, likely as a result of clonal heterogeneity, which is better captured in the plasma samples than it is in a large number of biopsies. These incoherences may reflect tumour clonality and reveal the acquired alterations that cause treatment resistance. Cell-free DNA methylation profiles can be used to distinguish OC from healthy individuals, and NGS methylation panels have been shown to have excellent diagnostic capabilities. Also, methylation signatures showed promise in explaining treatment responses, including BRCA dysfunction. ctDNA is evolving as a promising new biomarker to track tumour evolution and clonality through the treatment of early and advanced ovarian cancer, with potential applicability in prognostic prediction and treatment selection. While its role in HGSOC paves the way to clinical applicability, its potential interest in other histological subtypes of OC remains unknown. Full article
(This article belongs to the Special Issue New Sight in Cancer Genetics)
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