Untangling the clinicopathological significance of MRE11-RAD50-NBS1 complex in sporadic breast cancers

Role of MRE11 in DNA damage repair pathway dynamics and its diagnostic and prognostic significance in hereditary breast and ovarian cancer

BACKGROUND

DNA damage repair pathway genes are key components for maintaining genomic stability and are mainly associated with hereditary breast and ovarian cancer.

METHODS

The present study aimed to investigate the gene expression profile of DNA damage repair pathway genes, including BRCA1, BRCA2, ATM, TP53, CHEK2, MRE11, RAD50, BARD1, PALB2, and NBN, in hereditary breast and ovarian cancer patients using quantitative real-time PCR.

RESULTS

The study showed significant upregulation of most DNA damage repair genes in HBOC patients compared to controls, except MRE11, which was downregulated. Receiver operating characteristic (ROC) curve analysis revealed that MRE11 (p < 0.001), BRCA1 (p < 0.001), BRCA2 (p < 0.001), and PALB2 (p < 0.001) can be used as potential diagnostic biomarkers for hereditary breast and ovarian cancer. Spearman correlation analysis showed that RAD50 was significantly associated with the BRCA1/2 mutation status (p = 0.05). Furthermore, bivariate analysis revealed a strong positive correlation between BARD1 gene expression and the expression of BRCA1, PALB2, and NBN genes. Kaplan-Meier survival analysis showed that reduces expression of the MRE11 gene was associated with better overall survival.

CONCLUSIONS

The study findings may lead to a better understanding of the molecular mechanisms underlying hereditary breast and ovarian cancer, suggesting its role as a potential diagnostic and prognostic marker.

Targeting protein arginine methyltransferases in breast cancer: Promising strategies

Protein arginine methyltransferases (PRMTs) catalyze arginine methylation, an essential protein posttranslational modification involved in a variety of biological processes, such as transcription, RNA splicing and the DNA damage response (DDR), protein stability, and signal transduction. Due to their significant roles in these processes, PRMTs have emerged as promising therapeutic targets in cancer. Among all cancer types, breast cancer has been the most extensively studied in relation to PRMTs dysregulation. Previous studies have reported that several PRMTs are overexpressed in breast cancer and play critical roles in tumor growth, metastasis, and the maintenance of breast cancer stem cells. Moreover, an increasing number of PRMT inhibitors are undergoing clinical trials for breast cancer treatment, demonstrating significant progress. This review aims to provide a comprehensive overview of the biological functions of PRMTs in breast cancer and to summarize the latest clinical developments of PRMT inhibitors for cancer therapy.

Comprehensive structural and functional analyses of RAD50 nsSNPs: from prediction to impact assessment

Background

The RAD50 gene on chromosome 5q3.11 plays an important role in the MRN (Mre11-Rad50-Nbs1) complex. This complex orchestrates cellular responses to the DNA double-strand breaks (DSBs) through several pathways for genome stability. This study aims to investigate the functional impact of non-synonymous single-nucleotide polymorphisms (nsSNPs) in RAD50 (a breast cancer-associated gene) and focuses on their consequences on protein structure and interaction within the MRN complex.

Methods

A total of 1,806 nsSNPs were retrieved and subjected to variant analysis using a set of computational tools and ConSurf. Pathogenicity and protein stability criteria were established based on specific tools. Highly conserved damaging nsSNPs were prioritized for the structural analysis. GOR-IV was used for secondary structure prediction, whereas AlphaFold, RoseTTAFold, and I-TASSER were used for protein structure prediction. The docking of RAD50-Mre11A complexes was performed using HADDOCK to assess the impact of nsSNPs on protein-protein interactions. Molecular dynamic simulation was performed to verify the role of mutants in molecular docking analysis.

Results

A subset of pathogenic and disease-associated nsSNPs in the RAD50 gene altered the protein stability and interactions with the Mre11A protein. Substantial alterations in the interacting profiles of mutants (A73P, V117F, L518P, L1092R, N1144S, and A1209T) suggest potential implications for DNA repair mechanisms and genome stability.

Conclusion

The study discloses the normative impact of RAD50 mutations on the pathophysiology of breast cancer. It can provide the basis to treat RAD50 mutation-deficient cells.

NERINE reveals rare variant associations in gene networks across multiple phenotypes and implicates an SNCA-PRL-LRRK2 subnetwork in Parkinson's disease

Gene networks encapsulate biological knowledge, often linked to polygenic diseases. While model system experiments generate many plausible gene networks, validating their role in human phenotypes requires evidence from human genetics. Rare variants provide the most straightforward path for such validation. While single-gene analyses often lack power due to rare variant sparsity, expanding the unit of association to networks offers a powerful alternative, provided it integrates network connections. Here, we introduce NERINE, a hierarchical model-based association test that integrates gene interactions that integrates gene interactions while remaining robust to network inaccuracies. Applied to biobanks, NERINE uncovers compelling network associations for breast cancer, cardiovascular diseases, and type II diabetes, undetected by single-gene tests. For Parkinson's disease (PD), NERINE newly substantiates several GWAS candidate loci with rare variant signal and synergizes human genetics with experimental screens targeting cardinal PD pathologies: dopaminergic neuron survival and alpha-synuclein pathobiology. CRISPRi-screening in human neurons and NERINE converge on PRL, revealing an intraneuronal α-synuclein/prolactin stress response that may impact resilience to PD pathologies.

A systematic review of candidate genes and their relevant pathways for metastasis among adults diagnosed with breast cancer

BACKGROUND

Presently incurable, metastatic breast cancer is estimated to occur in as many as 30% of those diagnosed with early-stage breast cancer. Timely and accurate identification of those at risk for developing metastasis using validated biomarkers has the potential to have profound impact on overall survival rates. Our primary goal was to conduct a systematic review and synthesize the existing body of scientific knowledge on the candidate genes and their respective single nucleotide polymorphisms associated with metastasis-related outcomes among patients diagnosed with breast cancer. This knowledge is critical to inform future hypothesis-driven and validation research aimed at enhancing clinical decision-making for breast cancer patients.

METHODS

Using PRISMA guidelines, literature searches were conducted on September 13th, 2023, using PubMed and Embase databases. The systematic review protocol was registered with INPLASY (DOI: https://doi.org/10.37766/inplasy2024.8.0014 ). Covidence software was used to facilitate the screening and article extraction processes. Peer-reviewed articles were selected if authors reported on single nucleotide polymorphisms directly associated with metastasis among adults diagnosed with breast cancer.

FINDINGS

We identified 451 articles after 44 duplicates were removed resulting in 407 articles to be screened for study inclusion. Three reviewers completed the article screening process which resulted in 86 articles meeting the study inclusion criteria. Sampling varied across studies with the majority utilizing a case-control design (n = 75, 87.2%), with sample sizes ranging from 23 to 1,017 participants having mean age 50.65 ± 4.50 (min-max: 20-75). The synthesis of this internationally generated evidence revealed that the scientific area on the underlying biological contributions to breast cancer metastasis remains predominantly exploratory in nature (n = 74, 86%). Of the 12 studies with reported power analyses, only 9 explicitly stated the power values which ranged from 47.88 to 99%.

DISCUSSION

Understanding the underlying biological mechanisms contributing to metastasis is a critical component for precision oncological therapeutics and treatment approaches. Current evidence investigating the contribution of SNPs to the development of metastasis is characterized by underpowered candidate gene studies. To inform individualized precision health practices and improve breast cancer survival outcomes, future hypothesis-driven research is needed to replicate these associations in larger, more diverse datasets.

Differential methylation of circulating free DNA assessed through cfMeDiP as a new tool for breast cancer diagnosis and detection of BRCA1/2 mutation

BACKGROUND

Recent studies have highlighted the importance of the cell-free DNA (cfDNA) methylation profile in detecting breast cancer (BC) and its different subtypes. We investigated whether plasma cfDNA methylation, using cell-free Methylated DNA Immunoprecipitation and High-Throughput Sequencing (cfMeDIP-seq), may be informative in characterizing breast cancer in patients with BRCA1/2 germline mutations for early cancer detection and response to therapy.

METHODS

We enrolled 23 BC patients with germline mutation of BRCA1 and BRCA2 genes, 19 healthy controls without BRCA1/2 mutation, and two healthy individuals who carried BRCA1/2 mutations. Blood samples were collected for all study subjects at the diagnosis, and plasma was isolated by centrifugation. Cell-free DNA was extracted from 1 mL of plasma, and cfMeDIP-seq was performed for each sample. Shallow whole genome sequencing was performed on the immuno-precipitated samples. Then, the differentially methylated 300-bp regions (DMRs) between 25 BRCA germline mutation carriers and 19 non-carriers were identified. DMRs were compared with tumor-specific regions from public datasets to perform an unbiased analysis. Finally, two statistical classifiers were trained based on the GLMnet and random forest model to evaluate if the identified DMRs could discriminate BRCA-positive from healthy samples.

RESULTS

We identified 7,095 hypermethylated and 212 hypomethylated regions in 25 BRCA germline mutation carriers compared to 19 controls. These regions discriminate tumors from healthy samples with high accuracy and sensitivity. We show that the circulating tumor DNA of BRCA1/2 mutant breast cancers is characterized by the hypomethylation of genes involved in DNA repair and cell cycle. We uncovered the TFs associated with these DRMs and identified that proteins of the Erythroblast Transformation Specific (ETS) family are particularly active in the hypermethylated regions. Finally, we assessed that these regions could discriminate between BRCA positives from healthy samples with an AUC of 0.95, a sensitivity of 88%, and a specificity of 94.74%.

CONCLUSIONS

Our study emphasizes the importance of tumor cell-derived DNA methylation in BC, reporting a different methylation profile between patients carrying mutations in BRCA1, BRCA2, and wild-type controls. Our minimally invasive approach could allow early cancer diagnosis, assessment of minimal residual disease, and monitoring of response to therapy.

Mutual regulation of TGFβ-induced oncogenic EMT, cell cycle progression and the DDR

TGFβ signaling and the DNA damage response (DDR) are two cellular toolboxes with a strong impact on cancer biology. While TGFβ as a pleiotropic cytokine affects essentially all hallmarks of cancer, the multifunctional DDR mostly orchestrates cell cycle progression, DNA repair, chromatin remodeling and cell death. One oncogenic effect of TGFβ is the partial activation of epithelial-to-mesenchymal transition (EMT), conferring invasiveness, cellular plasticity and resistance to various noxae. Several reports show that both individual networks as well as their interface affect chemo-/radiotherapies. However, the underlying mechanisms remain poorly resolved. EMT often correlates with TGFβ-induced slowing of proliferation, yet numerous studies demonstrate that particularly the co-activated EMT transcription factors counteract anti-proliferative signaling in a partially non-redundant manner. Collectively, evidence piled up over decades underscore a multifaceted, reciprocal inter-connection of TGFβ signaling / EMT with the DDR / cell cycle progression, which we will discuss here. Altogether, we conclude that full cell cycle arrest is barely compatible with the propagation of oncogenic EMT traits and further propose that 'EMT-linked DDR plasticity' is a crucial, yet intricate facet of malignancy, decisively affecting metastasis formation and therapy resistance.

The Multiple Faces of the MRN Complex: Roles in Medulloblastoma and Beyond

Hypomorphic mutations in MRN complex genes are frequently found in cancer, supporting their role as oncosuppressors. However, unlike canonical oncosuppressors, MRN proteins are often overexpressed in tumor tissues, where they actively work to counteract DSBs induced by both oncogene-dependent RS and radio-chemotherapy. Moreover, at the same time, MRN genes are also essential genes, since the constitutive KO of each component leads to embryonic lethality. Therefore, even though it is paradoxical, MRN genes may work as oncosuppressive, oncopromoting, and essential genes. In this review, we discussed how alterations in the MRN complex impact the physiopathology of cancer, in light of our recent discoveries on the gene-dosage-dependent effect of NBS1 in Medulloblastoma. These updates aim to understand whether MRN complex can be realistically used as a prognostic/predictive marker and/or as a therapeutic target for the treatment of cancer patients in the future.

In Silico-Based Structural Evaluation to Categorize the Pathogenicity of Mutations Identified in the RAD Class of Proteins

RAD genes, known as double-strand break repair proteins, play a major role in maintaining the genomic integrity of a cell by carrying out essential DNA repair functions via double-strand break repair pathways. Mutations in the RAD class of proteins show high susceptibility to breast and ovarian cancers; however, adequate research on the mutations identified in these genes has not been extensively reported for their deleterious effects. Changes in the folding pattern of RAD proteins play an important role in protein-protein interactions and also functions. Missense mutations identified from four cancer databases, cBioPortal, COSMIC, ClinVar, and gnomAD, cause aberrant conformations, which may lead to faulty DNA repair mechanisms. It is therefore necessary to evaluate the effects of pathogenic mutations of RAD proteins and their subsequent role in breast and ovarian cancers. In this study, we have used eight computational prediction servers to analyze pathogenic mutations and understand their effects on the protein structure and function. A total of 5122 missense mutations were identified from four different cancer databases, of which 1165 were predicted to be pathogenic using at least five pathogenicity prediction servers. These mutations were characterized as high-risk mutations based on their location in the conserved domains and subsequently subjected to structural stability characterization. The mutations included in the present study were selected from clinically relevant mutants in breast cancer pedigrees. Comparative folding patterns and intra-atomic interaction results showed alterations in the structural behavior of RAD proteins, specifically RAD51C triggered by mutations G125V and L138F and RAD51D triggered by mutations S207L and E233G.

DNA Repair Mechanisms, Protein Interactions and Therapeutic Targeting of the MRN Complex

Repair of a DNA double-strand break relies upon a pathway of proteins to identify damage, regulate cell cycle checkpoints, and repair the damage. This process is initiated by a sensor protein complex, the MRN complex, comprised of three proteins-MRE11, RAD50, and NBS1. After a double-stranded break, the MRN complex recruits and activates ATM, in-turn activating other proteins such as BRCA1/2, ATR, CHEK1/2, PALB2 and RAD51. These proteins have been the focus of many studies for their individual roles in hereditary cancer syndromes and are included on several genetic testing panels. These panels have enabled us to acquire large amounts of genetic data, much of which remains a challenge to interpret due to the presence of variants of uncertain significance (VUS). While the primary aim of clinical testing is to accurately and confidently classify variants in order to inform medical management, the presence of VUSs has led to ambiguity in genetic counseling. Pathogenic variants within MRN complex genes have been implicated in breast, ovarian, prostate, colon cancers and gliomas; however, the hundreds of VUSs within MRE11, RAD50, and NBS1 precludes the application of these data in genetic guidance of carriers. In this review, we discuss the MRN complex's role in DNA double-strand break repair, its interactions with other cancer predisposing genes, the variants that can be found within the three MRN complex genes, and the MRN complex's potential as an anti-cancer therapeutic target.

Identification of miRNA biomarkers for breast cancer by combining ensemble regularized multinomial logistic regression and Cox regression

BACKGROUND

Breast cancer is one of the most common cancers in women. It is necessary to classify breast cancer subtypes because different subtypes need specific treatment. Identifying biomarkers and classifying breast cancer subtypes is essential for developing appropriate treatment methods for patients. MiRNAs can be easily detected in tumor biopsy and play an inhibitory or promoting role in breast cancer, which are considered promising biomarkers for distinguishing subtypes.

RESULTS

A new method combing ensemble regularized multinomial logistic regression and Cox regression was proposed for identifying miRNA biomarkers in breast cancer. After adopting stratified sampling and bootstrap sampling, the most suitable sample subset for miRNA feature screening was determined via ensemble 100 regularized multinomial logistic regression models. 124 miRNAs that participated in the classification of at least 3 subtypes and appeared at least 50 times in 100 integrations were screened as features. 22 miRNAs from the proposed feature set were further identified as the biomarkers for breast cancer by using Cox regression based on survival analysis. The accuracy of 5 methods on the proposed feature set was significantly higher than on the other two feature sets. The results of 7 biological analyses illustrated the rationality of the identified biomarkers.

CONCLUSIONS

The screened features can better distinguish breast cancer subtypes. Notably, the genes and proteins related to the proposed 22 miRNAs were considered oncogenes or inhibitors of breast cancer. 9 of the 22 miRNAs have been proved to be markers of breast cancer. Therefore, our results can be considered in future related research.

Identification of new RAD51D-regulating microRNAs that also emerge as potent inhibitors of the Fanconi anemia/homologous recombination pathways

The Fanconi anemia (FA) and homologous recombination (HR) pathways, which partially overlap and include RAD51 and its paralogs, are key for the repair of different types of DNA damage, such as DNA interstrand crosslinks. First, to broadly assess the impact of microRNA-mediated regulation, we examined microRNA expression profiles in five isogenic fibroblast cell pairs, either deficient in DNA repair due to germline mutations in FANCA, FANCB, FANCC, FANCI or BRIP1/FANCJ or proficient due to correction with retroviral vectors. In each pair, we observed lower abundance of specific microRNAs in the FA-deficient cells. From the list of microRNAs, we experimentally confirmed the effects of miR-141-3p and miR-369-3p targeting RAD51B and miR-15a-5p, miR-494-3p as well as miR-544a targeting RAD51D. However, by western blotting, only RAD51D protein was reduced by a mixture of its regulating microRNAs. Gene ontology analyses and identification of additional FA/HR factors as targets of miR-15a-5p, miR-494-3p and miR-544a strongly suggested the widespread influence of these microRNAs on HR. Interestingly, only miR-494-3p directly reduced RAD51 foci formation, while a mixture of miR-15a-5p, miR-494-3p and miR-544a strongly reduced HR activity in green fluorescent protein (GFP) repair assays. In summary, by successfully employing this novel loss- and gain-of-function strategy, we have identified new microRNAs strongly inhibiting HR in mammalian cells. Understanding and modulating such miRNA regulation of DNA repair genes/pathways might help to overcome the reduced repair capacity of FA patients with biallelic hypomorphic mutations or help to engineer synthetic lethality strategies for patients with mutations in cancer-associated FA/HR genes.