The extensive use of next-generation sequencing (NGS) multi-gene panels and advanced analysis algorithms have led to the identification of numerous genetic variants associated with breast, ovarian, and pancreatic cancer. Copynumber variations (CNVs), defined as deletions and duplications of specific DNA regions, account for up to 10% of pathogenic variants and can affect any of the cancer-predisposing genes. Despite this, CNVs’ contribution beyond BRCA1 and BRCA2 remains underexplored. This observational study analyzed data from 2949 patients, primarily affected by breast or ovarian cancer, who underwent NGS testing with a 22-gene hereditary cancer panel between 2018 and 2023, with a focus on CNV results. In line with comparison studies, a total diagnostic yield of 14.8% was observed with pathogenic variants in BRCA1, BRCA2, CHEK2, ATM, and PALB2 accounting for most of positive findings. In contrast, CNVs were found in 1.4% of patients, displaying a peculiar distribution pattern. PALB2 exhibited the highest frequency of pathogenic CNVs (66.7%), representing 62.2% of all PALB2 pathogenic variants. Notably, 24 out of 28 PALB2 CNV carriers shared the deletion of Exon 11. Further investigations revealed identical breakpoints and common geographical origins, and moreover, the same haplotype for some of the families suggests a relatively recent founder effect. Simultaneous sequence and copy number analyses resulted in likely higher positive predictive value of the test and, more interestingly, disclosed an unforeseen single contribution of CNVs in PALB2 gene, confirming geography as a key factor in shaping human genetic variations.

EGFR and AXL protein expression in the brain and immunohistochemical characterization of tumors of Lztr1fl/fl;Cdkn2afl/fl;GFAP-Cre+ mice

Aim: To investigate clinical and molecular features of neurofibromatosis type 1 (NF1)-associated breast cancer (BC) in a large multicenter cohort. Methods: Clinical and histopathological data from 86 NF1 patients with BC (69 with molecular data) were collected, and 111 published cases were reviewed. NF1 variants were assessed in silico, and their distribution across neurofibromin domains was compared with the general NF1 population. Results: NF1 patients developed BC earlier than the general population (mean 49 years), with missense variant heterozygotes showing the earliest onset (43.9 vs. 49.5 years for truncating variants, p = 0.014). Tumors were frequently high-grade (49 %), HER2-enriched (31 %) or luminal B subtypes (31 %), with reduced luminal A (28 %) frequency. NF1+BC patients had more subcutaneous (p = 0.006) and plexiform neurofibromas (p < 0.00001). Compared with the general NF1 population, they lacked large deletions (0 % vs. 3 %, p = 0.0148), showed enrichment for N-HEAT missense variants (70 % vs. 42 %; p = 0.0078), and carried recurrent variants significantly enriched in NF1+BC. Structural modeling predicted deleterious effects for >70 % of variants, with proline/arginine substitutions accounting for 83 % of missense variants (vs. 44 % in the general NF1 population, p = 0.0012). Conclusions: NF1-associated BC is characterized by earlier onset, aggressive tumor features, and distinct mutational patterns.

The Kelch domain of LZTR1 and carboxyl tail of EGFR are required for their interaction

Mechanism of LZTR1-mediated degradation of RIT1 and the effect of LZTR1 mutations

Vulnerability of LZTR1 inactive cells to combination treatment of EGFR and AXL inhibitors

LZTR1 co-localized with EGFR and AXL at the cellular membrane upon ligand stimulation

Phenotype alterations in the liver and brain of Lztr1-deleted mice

Table S1. List of ubiquitylated peptides from DiGly proteomics assay. Table S2. List of proteins differentially abundant in LZTR1-/- compared toLZTR1+/+ cells quantified by TMT.Table S3. List of top scoring LZTR1 interacting proteins from immunoprecipitation/mass spectrometry.

Protein expression of LZTR1 substrates and pathway analysis in human schwannoma A

LZTR1 regulates EGFR and AXL protein stability

The identification of structural variant (SV) breakpoints plays a crucial role in understanding the genetic variants, mutagenic mechanisms, and functional consequences that drive various genetic diseases. While next-generation sequencing (NGS) has become a cornerstone in single nucleotide variant (SNP) discovery and characterization, short-read NGS technology faces significant challenges in resolving large genomic rearrangements such as duplications, deletions, inversions, and translocations. Nanopore sequencing offers a promising alternative by enabling precise mapping of chromosomal rearrangement breakpoints, and characterization of chromosomal alterations, thereby improving the genetic diagnosis of such conditions. Using long-read whole-genome sequencing, we examined the breakpoints of a cytogenetically balanced chromosomal translocation, t(8;22)(q13.3;q11.23), initially detected during prenatal diagnosis and later confirmed as de novo in a patient who developed NF2-associated schwannomatosis in late infancy. Nanopore sequencing revealed that the translocation disrupted the NF2 gene. This case highlights the power of nanopore long-read sequencing in detecting the exact consequences of de novo, apparently balanced translocations and in uncovering the genetic underpinnings of abnormal phenotypes. Given its ability to resolve complex SVs with high precision, nanopore sequencing might be considered a valuable complement to conventional genetic diagnostic methods, enhancing our understanding of genetic diseases and potentially improving diagnostic yield and risk assessment.

Nineteen genomic regions have been associated with high-grade serous ovarian cancer (HGSOC). We meta-analyzed >22 million variants for 398,238 women from the Ovarian Cancer Association Consortium (OCAC), UK Biobank (UKBB) and Consortium of Investigators of Modifiers of BRCA1/BRCA2 (CIMBA) to identify novel HGSOC susceptibility loci. Eight novel variants were associated with HGSOC risk. An interesting discovery biologically was TP53 3’-UTR SNP rs78378222-T’s association with HGSOC (per-T-allele relative risk (RR) = 1.44, 95% CI:1.28–1.62, P = 1.76 × 10−9). Polygenic scores (PGS) were developed using OCAC and CIMBA data and trained on FinnGen data. The optimal PGS included 64,518 variants and was associated with an odds ratio of 1.46 (95% CI:1.37–1.54) per standard deviation when validated in the UKBB. This study represents the largest HGSOC GWAS to date – demonstrating that improvements in imputation reference panels and increased sample sizes help to identify HGSOC associated variants that previously went undetected, ultimately improving PGS which can improve personalized HGSOC risk prediction.

Background/Objective: Large genomic rearrangements of PALB2 gene, particularly deletions and duplications, have been linked to hereditary breast-ovarian cancer. Our research specifically focuses on delineating the intronic breakpoints associated with rearrangements of PALB2 exon 11, which is crucial for understanding the mechanisms underlying these genomic changes in patients with hereditary breast and ovarian syndrome. Methods: By using next-generation sequencing, we identified one duplication and three deletions of PALB2 exon 11, confirmed by Multiplex Ligation-Dependent Probe Amplification analysis. To assess the impact on transcription and potential splicing issues, reverse-transcription PCR was performed on patients' RNA. For the detailed characterization of intronic breakpoints, the primer walking approach and long-range PCR were implemented, followed by Sanger sequencing. Results: Our analysis revealed a tandem duplication of 5134 base pairs (bp) mediated by AluY repeats located in introns 10 and 11, respectively. Moreover, identical deletions were identified in three unrelated patients, encompassing an approximate 8050 bp region mediated by AluSx elements. Both genomic alterations resulted in a truncated PALB2 protein due to the introduction of a premature stop codon. Conclusions: This study underscores the remarkable instability of intronic regions flanking exon 11 of PALB2 and identifies a previously unreported hotspot involving Alu repeats with very high sequence homology in introns 10 and 11 of the gene. Our findings suggest avenues for further research, such as investigating the prevalence of similar genomic rearrangements in larger cohorts and exploring functional studies to understand how these alterations contribute to hereditary breast cancer pathogenesis.

Human SCs play a primary role in SWN, a rare genetic disorder in which patients develop multiple schwannomas. So that, their isolation and immortalization could represent an irreplaceable tool to investigate the disease etiopathology. Although few clones of tumoural SCs have been obtained, unfortunately they present genetic, morphological and biological characteristics that do not fully represent the original cells. Herein we isolated, characterized and immortalized primary SCs from human schwannomas. Our immortalized human SCs present typical NF2 and LTZR1 genetic mutations of SWN and retain original phenotype characteristics, representing a valuable tool for further genetic, functional and biomolecular in vitro studies.

PURPOSE:Pathogenic LZTR1 variants cause schwannomatosis and dominant/recessive Noonan syndrome (NS). We aim to establish an association between heterozygous loss-of-function LZTR1 alleles and isolated multiple café-au-lait macules (CaLMs). METHODS:A total of 849 unrelated participants with multiple CaLMs, lacking pathogenic/likely pathogenic NF1 and SPRED1 variants, underwent RASopathy gene panel sequencing. Data on 125 individuals with heterozygous LZTR1 variants were collected for characterizing their clinical features and the associated molecular spectrum. In vitro functional assessment was performed on a representative panel of missense variants and small in-frame deletions. RESULTS:Analysis revealed heterozygous LZTR1 variants in 6.0% (51/849) of participants, exceeding the general population prevalence. LZTR1-related CaLMs varied in number, displayed sharp or irregular borders, and were generally isolated but occasionally associated with features recurring in RASopathies. In 2 families, CaLMs and schwannomas co-occurred. The molecular spectrum mainly consisted of truncating variants, indicating loss-of-function. These variants substantially overlapped with those occurring in schwannomatosis and recessive NS. Functional characterization showed accelerated protein degradation or mislocalization, and failure to downregulate mitogen-activated protein kinase signaling. CONCLUSION:Our findings expand the phenotypic variability associated with LZTR1 variants, which, in addition to conferring susceptibility to schwannomatosis and causing dominant and recessive NS, occur in individuals with isolated multiple CaLMs.