Sequence Variants in Breast/Ovarian Cancer Susceptibility Genes: From Risk Assessment to Clinical Management in Carrier Individuals and Their Blood Relatives

A special issue of Cancers (ISSN 2072-6694). This special issue belongs to the section "Cancer Epidemiology and Prevention".

Deadline for manuscript submissions: 31 December 2024 | Viewed by 1209

Special Issue Editors


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Guest Editor
Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
Interests: hereditary breast/ovarian cancer; BRCA1 and BRCA2 genes; variant classification and reporting; variants of uncertain significance; molecular mechanisms of carcinogenesis; sporadic breast cancer

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Guest Editor
Molecular Oncology Laboratory, IdISSC (San Carlos Biomedical Research Institute), Madrid, Spain
Interests: hereditary breast/ovarian cancer; ATM; BARD1; BRCA1; BRCA2; BRIP1; CHEK2; PALB2; RAD51C; RAD51D; alternative splicing in control populations and variant carriers; ACMG/AMP classification of genetic variants
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Special Issue Information

Dear Colleagues,

Genetic testing for breast/ovarian cancer susceptibility plays a crucial role in personalized medicine. The BRCA1 and BRCA2 genes stand as a model for variant-associated cancer risk assessment and management. The implementation of massively parallel sequencing in cancer genetics has increased the amount of information that needs to be deciphered prior to potential clinical use. The elucidation of the biological and clinical significance of sequence variants—a prerequisite for effective cancer prevention and treatment—can be challenging for certain genes and variant types, thus limiting the clinical value of test results. Transnational collaborative efforts, the collection of multi-layered evidence, and ad hoc in depth analyses are often required to achieve variant classification, which, in turn, informs clinical decision-making.

This Special Issue aims to advance our knowledge of both basic and clinically relevant aspects pertaining to the assessment and management of the cancer risk associated with sequence variants in breast/ovarian cancer susceptibility genes. We welcome original articles and reviews covering a broad spectrum of research topics, including the following:

  • High- and moderate-risk gene variants and the clinical management of carrier individuals and their non-carrier blood relatives;
  • Other cancer phenotypes associated with (likely) pathogenic variants in breast/ovarian cancer susceptibility genes;
  • Uses of PRS for risk refinement (real-world studies on models integrating multiple risk factors are encouraged);
  • Evidence supporting variant classification, e.g., segregation analyses, functional studies, or the characterization of splice-site variants (multifactorial analyses are especially welcome);
  • Molecular mechanisms of response/resistance to platinum and PARP inhibitors;
  • Preventive and therapeutic (surgical and medical) options for carrier individuals.

Dr. Arcangela De Nicolo
Dr. Miguel De la Hoya
Guest Editors

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Keywords

  • breast/ovarian cancer susceptibility genes
  • risk assessment and clinical management of carrier individuals and their blood relatives
  • risk models
  • variant classification
  • multifactorial approaches

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Published Papers (1 paper)

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Research

14 pages, 3221 KiB  
Article
Splicing Dysregulation of Non-Canonical GC-5′ Splice Sites of Breast Cancer Susceptibility Genes ATM and PALB2
by Inés Llinares-Burguet, Lara Sanoguera-Miralles, Alberto Valenzuela-Palomo, Alicia García-Álvarez, Elena Bueno-Martínez and Eladio A. Velasco-Sampedro
Cancers 2024, 16(21), 3562; https://doi.org/10.3390/cancers16213562 - 22 Oct 2024
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Abstract
Background/Objectives: The non-canonical GC-5′ splice sites (5′ss) are the most common exception (~1%) to the classical GT/AG splicing rule. They constitute weak 5′ss and can be regulated by splicing factors, so they are especially sensitive to genetic variations inducing the misrecognition of [...] Read more.
Background/Objectives: The non-canonical GC-5′ splice sites (5′ss) are the most common exception (~1%) to the classical GT/AG splicing rule. They constitute weak 5′ss and can be regulated by splicing factors, so they are especially sensitive to genetic variations inducing the misrecognition of their respective exons. We aimed to investigate the GC-5′ss of the breast/ovarian cancer susceptibility genes, ATM (exon 50), BRIP1 (exon 1), and PALB2 (exon 12), and their dysregulation induced by DNA variants. Methods: Splicing assays of the minigenes, mgATM_49-52, mgBRIP1_1-2, and mgPALB2_5-12, were conducted to study the regulation of the indicated GC-5′ss. Results: A functional map of the splicing regulatory elements (SRE) formed by overlapping exonic microdeletions revealed three essential intervals, ATM c.7335_7344del, PALB2 c.3229_3258del, and c.3293_3322del, which are likely targets for spliceogenic SRE-variants. We then selected 14 ATM and 9 PALB2 variants (Hexplorer score < −40) located at these intervals that were assayed in MCF-7 cells. Nine ATM and three PALB2 variants affected splicing, impairing the recognition of exons 50 and 12, respectively. Therefore, these variants likely disrupt the active SREs involved in the inclusion of both exons in the mature mRNA. DeepCLIP predictions suggested the participation of several splicing factors in exon recognition, including SRSF1, SRSF2, and SRSF7, involved in the recognition of other GC sites. The ATM spliceogenic variants c.7336G>T (p.(Glu2446Ter)) and c.7340T>A (p.(Leu2447Ter)) produced significant amounts of full-length transcripts (55–59%), which include premature termination stop codons, so they would inactivate ATM through both splicing disruption and protein truncation mechanisms. Conclusions: ATM exon 50 and PALB2 exon 12 require specific sequences for efficient recognition by the splicing machinery. The mapping of SRE-rich intervals in minigenes is a valuable approach for the identification of spliceogenic variants that outperforms any prediction software. Indeed, 12 spliceogenic SRE-variants were identified in the critical intervals. Full article
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