The Evolution, Functions and Applications of the Breast Cancer Genes BRCA1 and BRCA2

Novel Pathogenic Mutation of P209L in TRPC6 Gene Causes Adult Focal Segmental Glomerulosclerosis

Focal segmental glomerulosclerosis (FSGS) is a leading kidney disease, clinically associated with proteinuria and progressive renal failure. The occurrence of this disease is partly related to gene mutations. We describe a single affected family member who presented with FSGS. We used high-throughput sequencing, sanger sequencing to identify the pathogenic mutations, and a systems genetics analysis in the BXD mice was conducted to explore the genetic regulatory mechanisms of pathogenic genes in the development of FSGS. We identified high urinary protein (++++) and creatinine levels (149 μmol/L) in a 29-year-old male diagnosed with a 5-year history of grade 2 hypertension. Histopathology of the kidney biopsy showed stromal hyperplasia at the glomerular segmental sclerosis and endothelial cell vacuolation degeneration. Whole-exome sequencing followed by Sanger sequencing revealed a heterozygous missense mutation (c.643C > T) in exon 2 of TRPC6, leading to the substitution of arginine with tryptophan at position 215 (p.Arg215Trp). Systems genetics analysis of the 53 BXD mice kidney transcriptomes identified Pygm as the upstream regulator of Trpc6. Those two genes are jointly involved in the regulation of FSGS mainly via Wnt and Hippo signaling pathways. We present a novel variant in the TRPC6 gene that causes FSGS. Moreover, our data suggested TRPC6 works with PYGM, as well as Wnt and Hippo signaling pathways to regulate renal function, which could guide future clinical prevention and targeted treatment for FSGS outcomes.

Essential role of the BRCA2B gene in somatic homologous recombination in Arabidopsis thaliana

Constant exposure to various environmental and endogenous stresses can cause structural DNA damage, resulting in genome instability. Higher eukaryotic cells deploy conserved DNA repair systems, which include various DNA repair pathways, to maintain genome stability. Homologous recombination (HR), one of these repair pathways, involves multiple proteins. BRCA2, one of the proteins in the HR pathway, is of substantial research interest in humans because it is an oncogene. However, the study of this gene is limited due to the lack of availability of homozygous BRCA2-knockout mutants in mammals, which results in embryonic lethality. Arabidopsis thaliana has two copies of the BRCA2 homologs: BRCA2A and BRCA2B . Therefore, the single mutants remain nonlethal and fertile in Arabidopsis. The BRCA2A homolog, which plays a significant role in the HR pathway of germline cells and during the defense response, is well-studied in Arabidopsis. Our study focuses on the functional characterization of the BRCA2B homolog in the somatic cells of Arabidopsis, using the homozygous ΔBRCA2B mutant line. The phenotypic differences of ΔBRCA2B mutants were characterized and compared with wild Arabidopsis plants. The role of BRCA2B in spontaneous somatic HR (SHR) was studied using the ΔBRCA2B-gus detector line. ΔBRCA2B plants have a 6.3-fold lower SHR frequency than the control detector plants. Expression of four other HR pathway genes, including BRE, BRCC36A, RAD50, and RAD54, was significantly reduced in ΔBRCA2B mutants. Thus, our findings convey that the BRCA2B homolog plays an important role in maintaining spontaneous SHR rates and has a direct or indirect regulatory effect on the expression of other HR-related genes.

Human BRCA pathogenic variants were originated during recent human history

BRCA1 and BRCA2 (BRCA) play essential roles in maintaining genome stability. BRCA germline pathogenic variants increase cancer risk. However, the evolutionary origin of human BRCA pathogenic variants remains largely elusive. We tested the 2,972 human BRCA1 and 3,652 human BRCA2 pathogenic variants from ClinVar database in 100 vertebrates across eight clades, but failed to find evidence to show cross-species evolution conservation as the origin; we searched the variants in 2,792 ancient human genome data, and identified 28 BRCA1 and 22 BRCA2 pathogenic variants in 44 cases dated from 45,000 to 300 yr ago; we analyzed the haplotype-dated human BRCA pathogenic founder variants, and observed that they were mostly arisen within the past 3,000 yr; we traced ethnic distribution of human BRCA pathogenic variants, and found that the majority were present in single or a few ethnic populations. Based on the data, we propose that human BRCA pathogenic variants were highly likely arisen in recent human history after the latest out-of-Africa migration, and the expansion of modern human population could largely increase the variation spectrum.

Homologous Recombination Deficiencies and Hereditary Tumors

Homologous recombination (HR) is a vital process for repairing DNA double-strand breaks. Germline variants in the HR pathway, comprising at least 10 genes, such as BRCA1, BRCA2, ATM, BARD1, BRIP1, CHEK2, NBS1(NBN), PALB2, RAD51C, and RAD51D, lead to inherited susceptibility to specific types of cancers, including those of the breast, ovaries, prostate, and pancreas. The penetrance of germline pathogenic variants of each gene varies, whereas all their associated protein products are indispensable for maintaining a high-fidelity DNA repair system by HR. The present review summarizes the basic molecular mechanisms and components that collectively play a role in maintaining genomic integrity against DNA double-strand damage and their clinical implications on each type of hereditary tumor.

Heterogeneity in conservation of multifunctional partner enzymes with meiotic importance, CDK2 kinase and BRCA1 ubiquitin ligase

The evolution of proteins can be accompanied by changes not only to their amino acid sequences, but also their structural and spatial molecular organization. Comparison of the protein conservation within different taxonomic groups (multifunctional, or highly specific) allows to clarify their specificity and the direction of evolution. Two multifunctional enzymes, cyclin-dependent kinase 2 (CDK2) and BRCA1 ubiquitin ligase, that are partners in some mitotic and meiotic processes were investigated in the present work. Two research methods, bioinformatics and immunocytochemical, were combined to examine the conservation levels of the two enzymes. It has been established that CDK2 is a highly conserved protein in different taxonomic lineages of the eukaryotic tree. Immunocytochemically, a conserved CDK2 pattern was revealed in the meiotic autosomes of five rodent species and partially in domestic turkey and clawed frog. Nevertheless, variable CDK2 distribution was detected at the unsynapsed segments of the rodent X chromosomes. BRCA1 was shown to be highly conserved only within certain mammalian taxa. It was also noted that in those rodent nuclei, where BRCA1 specifically binds to antigens, asynaptic regions of sex chromosomes were positive. BRCA1 staining was not always accompanied by specific binding, and a high nonspecificity in the nucleoplasm was observed. Thus, the studies revealed different conservation of the two enzymes at the level of protein structure as well as at the level of chromosome behavior. This suggests variable rates of evolution due to both size and configuration of the protein molecules and their multifunctionality.

Single-Strand Annealing in Cancer

DNA double-strand breaks (DSBs) are among the most serious forms of DNA damage. In humans, DSBs are repaired mainly by non-homologous end joining (NHEJ) and homologous recombination repair (HRR). Single-strand annealing (SSA), another DSB repair system, uses homologous repeats flanking a DSB to join DNA ends and is error-prone, as it removes DNA fragments between repeats along with one repeat. Many DNA deletions observed in cancer cells display homology at breakpoint junctions, suggesting the involvement of SSA. When multiple DSBs occur in different chromosomes, SSA may result in chromosomal translocations, essential in the pathogenesis of many cancers. Inhibition of RAD52 (RAD52 Homolog, DNA Repair Protein), the master regulator of SSA, results in decreased proliferation of BRCA1/2 (BRCA1/2 DNA Repair Associated)-deficient cells, occurring in many hereditary breast and ovarian cancer cases. Therefore, RAD52 may be targeted in synthetic lethality in cancer. SSA may modulate the response to platinum-based anticancer drugs and radiation. SSA may increase the efficacy of the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 (CRISPR associated 9) genome editing and reduce its off-target effect. Several basic problems associated with SSA, including its evolutionary role, interplay with HRR and NHEJ and should be addressed to better understand its role in cancer pathogenesis and therapy.

A Phylogenetic Approach to Analyze the Conservativeness of BRCA1 and BRCA2 Mutations

Identifying pathogenic mutations in BRCA1 and BRCA2 is a critical step for breast cancer prediction. Genome-wide association studies (GWAS) are the most commonly used method for inferring pathogenic mutations. However, identifying pathogenic mutations using GWAS can be difficult. The hypothesis of this study is that the pathogenic mutations in human BRCA1/BRCA2, which are present in many species, are more likely to be located in the evolutionarily conserved sites. This study defines the evolutionary conservativeness based on the previously developed Characteristic Attribute Organization System (CAOS) software. ClinVar is used to identify human pathogenic mutations in BRCA1 and BRCA2. Statistical tests suggest that compared to the non-pathogenic mutations, human pathogenic mutations were more likely to locate at the evolutionary conserved positions. The approach presented in this study shows promise in identifying pathogenic mutations in humans, suggesting that the methodology may be applied to other disease-related genes to identify putative pathogenic mutations.

Rice OsBRCA2 Is Required for DNA Double-Strand Break Repair in Meiotic Cells

The mammalian BREAST CANCER 2 (BRCA2) gene is a tumor suppressor that plays a crucial role in DNA repair and homologous recombination (HR). Here, we report the identification and characterization of OsBRCA2, the rice orthologue of human BRCA2. Osbrca2 mutant plants exhibit normal vegetative growth but experience complete male and female sterility as a consequence of severe meiotic defects. Pairing, synapsis and recombination are impaired in osbrca2 male meiocytes, leading to chromosome entanglements and fragmentation. In the absence of OsBRCA2, localization to the meiotic chromosome axes of the strand-invasion proteins OsRAD51 and OsDMC1 is severely reduced and in vitro OsBRCA2 directly interacts with OsRAD51 and OsDMC1. These results indicate that OsBRCA2 is essential for facilitating the loading of OsRAD51 and OsDMC1 onto resected ends of programmed double-strand breaks (DSB) during meiosis to promote single-end invasions of homologous chromosomes and accurate recombination. In addition, treatment of osbrca2-1 seedlings with mitomycin C (MMC) led to hypersensitivity. As MMC is a genotoxic agent that creates DNA lesions in the somatic cells that can only be repaired by HR, these results suggest that OsBRCA2 has a conserved role in DSB repair and HR in rice.

A novel signature of two long non-coding RNAs in BRCA mutant ovarian cancer to predict prognosis and efficiency of chemotherapy

BACKGROUND

In this study we aimed to identify a prognostic signature in BRCA1/2 mutations to predict disease progression and the efficiency of chemotherapy ovarian cancer (OV), the second most common cause of death from gynecologic cancer in women worldwide.

METHODS

Univariate Cox proportional-hazards and multivariate Cox regression analyses were used to identifying prognostic factors from data obtained from The Cancer Genome Atlas (TCGA) database. The area under the curve of the receiver operating characteristic curve was assessed, and the sensitivity and specificity of the prediction model were determined.

RESULTS

A signature consisting of two long noncoding RNAs(lncRNAs), Z98885.2 and AC011601.1, was selected as the basis for classifying patients into high and low-risk groups (median survival: 7.2 years vs. 2.3 years). The three-year overall survival (OS) rates for the high- and low-risk group were approximately 38 and 100%, respectively. Chemotherapy treatment survival rates indicated that the high-risk group had significantly lower OS rates with adjuvant chemotherapy than the low-risk group. The one-, three-, and five-year OS were 100, 40, and 15% respectively in the high-risk group. The survival rate of the high-risk group declined rapidly after 2 years of OV chemotherapy treatment. Multivariate Cox regression associated with other traditional clinical factors showed that the 2-lncRNA model could be used as an independent OV prognostic factor. Analyses of data from the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) indicated that these signatures are pivotal to cancer development.

CONCLUSION

In conclusion, Z98885.2 and AC011601.1 comprise a novel prognostic signature for OV patients with BRCA1/2 mutations, and can be used to predict prognosis and the efficiency of chemotherapy.

Revealing the selective mechanisms of inhibitors to PARP-1 and PARP-2 via multiple computational methods

Background

Research has shown that Poly-ADP-ribose polymerases 1 (PARP-1) is a potential therapeutic target in the clinical treatment of breast cancer. An increasing number of studies have focused on the development of highly selective inhibitors that target PARP-1 over PARP-2, its closest isoform, to mitigate potential side effects. However, due to the highly conserved and similar binding sites of PARP-1 and PARP-2, there is a huge challenge for the discovery and design of PARP-1 inhibitors. Recently, it was reported that a potent PARP-1 inhibitor named NMS-P118 exhibited greater selectivity to PARP-1 over PARP-2 compared with a previously reported drug (Niraparib). However, the mechanisms underlying the effect of this inhibitor remains unclear.

Methods

In the present study, classical molecular dynamics (MD) simulations and accelerated molecular dynamics (aMD) simulations combined with structural and energetic analysis were used to investigate the structural dynamics and selective mechanisms of PARP-1 and PARP-2 that are bound to NMS-P118 and Niraparib with distinct selectivity.

Results

The results from classical MD simulations indicated that the selectivity of inhibitors may be controlled by electrostatic interactions, which were mainly due to the residues of Gln-322, Ser-328, Glu-335, and Tyr-455 in helix αF. The energetic differences were corroborated by the results from aMD simulations.

Conclusion

This study provides new insights about how inhibitors specifically bind to PARP-1 over PARP-2, which may help facilitate the design of highly selective PARP-1 inhibitors in the future.

The Role of Circulating Adiponectin and SNP276G>T at ADIPOQ Gene in BRCA-mutant Women

BACKGROUND

Environmental factors may influence the lifetime risk of cancer (penetrance) in women with a BRCA mutation.

MATERIALS AND METHODS

In 89 BRCA-mutant women, affected or unaffected by breast/ovarian cancer, we explored serum levels of adipokines and their relation with the polymorphism SNP276G>T as modulators of BRCA penetrance.

RESULTS

Affected women had significantly lower adiponectin than healthy women. Affected women with rs1501299 TT had significantly lower adiponectin and higher leptin than GT and GG genotypes. GT genotype was significantly associated with the disease status [odds ratio (OR)=3.24, 95% confidence interval (95% CI)=1.03-10.17]. Women in the lower tertile of serum adiponectin had a RR of BRCA-associated cancer of 2.80, 95% CI=1.1-7.1 (p for trend=0.03) compared with women in the higher tertile.

CONCLUSION

In the SNP rs1501299 the T allele was significantly associated with lower serum levels of adiponectin in affected women, suggesting that the T allele might be related to cancer.

Fanconi Anemia Pathway: Mechanisms of Breast Cancer Predisposition Development and Potential Therapeutic Targets

The maintenance of genomic stability is crucial for species survival, and its failure is closely associated with tumorigenesis. The Fanconi anemia (FA) pathway, involving 22 identified genes, plays a central role in repairing DNA interstrand cross-links. Importantly, a germline defect in any of these genes can cause Fanconi's anemia, a heterogeneous genetic disorder, characterized by congenital growth abnormalities, bone marrow failure, and predisposition to cancer. On the other hand, the breast cancer susceptibility genes, BRCA1 and BRCA2, also known as FANCS and FANCD1, respectively, are involved in the FA pathway; hence, researchers have studied the association between the FA pathway and cancer predisposition. Here, we mainly focused on and systematically reviewed the clinical and mechanistic implications of the predisposition of individuals with abnormalities in the FA pathway to cancer, especially breast cancer.

The BRCA1 c.4096+3A>G Variant Displays Classical Characteristics of Pathogenic BRCA1 Mutations in Hereditary Breast and Ovarian Cancers, But Still Allows Homozygous Viability

Mutations in BRCA1 result in predisposal to breast and ovarian cancers, but many variants exist with unknown clinical significance (VUS). One is BRCA1 c.4096+3A>G, which affects production of the full-length BRCA1 transcript, while augmenting transcripts lacking most or all of exon 11. Nonetheless, homozygosity of this variant has been reported in a healthy woman. We saw this variant cosegregate with breast and ovarian cancer in several family branches of four Icelandic pedigrees, with instances of phenocopies and a homozygous woman with lung cancer. We found eight heterozygous carriers (0.44%) in 1820 unselected breast cancer cases, and three (0.15%) in 1968 controls (p = 0.13). Seeking conclusive evidence, we studied tumors from carriers in the pedigrees for wild-type-loss of heterozygosity (wtLOH) and BRCA1-characteristic prevalence of estrogen receptor (ER) negativity. Of 15 breast and six ovarian tumors, wtLOH occurred in nine breast and all six ovarian tumours, and six of the nine breast tumors with wtLOH were ER-negative. These data accord with a pathogenic BRCA1-mutation. Our findings add to the current knowledge of BRCA1, and the role of its exon 11 in cancer pathogenicity, and will be of use in clinical genetic counselling.

DNA Damage Response Pathways in Dinoflagellates

Dinoflagellates are a general group of phytoplankton, ubiquitous in aquatic environments. Most dinoflagellates are non-obligate autotrophs, subjected to potential physical and chemical DNA-damaging agents, including UV irradiation, in the euphotic zone. Delay of cell cycles by irradiation, as part of DNA damage responses (DDRs), could potentially lead to growth inhibition, contributing to major errors in the estimation of primary productivity and interpretations of photo-inhibition. Their liquid crystalline chromosomes (LCCs) have large amount of abnormal bases, restricted placement of coding sequences at the chromosomes periphery, and tandem repeat-encoded genes. These chromosome characteristics, their large genome sizes, as well as the lack of architectural nucleosomes, likely contribute to possible differential responses to DNA damage agents. In this study, we sought potential dinoflagellate orthologues of eukaryotic DNA damage repair pathways, and the linking pathway with cell-cycle control in three dinoflagellate species. It appeared that major orthologues in photoreactivation, base excision repair, nucleotide excision repair, mismatch repair, double-strand break repair and homologous recombination repair are well represented in dinoflagellate genomes. Future studies should address possible differential DNA damage responses of dinoflagellates over other planktonic groups, especially in relation to possible shift of life-cycle transitions in responses to UV irradiation. This may have a potential role in the persistence of dinoflagellate red tides with the advent of climatic change.

Identifying a BRCA2 c.5722_5723del mutation in a Han-Chinese family with breast cancer

Breast cancer (BC) is the most common female cancer found worldwide. It is responsible for 25% of all cancer patients in females. Hereditary BC accounts for about 5–10% of all BC cases. The breast cancer 1 gene (BRCA1) and the breast cancer 2 gene (BRCA2) are the two most-studied BC susceptibility genes. Genetic testing for disease-causing mutations in BRCA1, BRCA2, and other BC susceptibility genes is strongly recommended for members of families having a BC family history. The present study found a heterozygous c.5722_5723del mutation in the BRCA2 exon 11 of a large Han-Chinese BC family using whole exome sequencing and Sanger sequencing. It may cause DNA double-strand breaks repair dysfunction by disturbing homologous recombination, further resulting in BC. The study findings may help supplement and further improve genetic testing strategies and BC risk estimation methodologies in China.