Human Breast Cancer Susceptibility Research Articles

Whole genome sequencing for the investigation of canine mammary tumor inheritance - an initial assessment of high-risk breast cancer genes reveal BRCA2 and STK11 variants potentially associated with risk in purebred dogs

BackgroundAlthough, in general, cancer is considered a multifactorial disease, clustering of particular cancers in pedigrees suggests a genetic predisposition and could explain why some dog breeds appear to have an increased risk of certain cancers. To our knowledge, there have been no published reports of whole genome sequencing to investigate inherited canine mammary tumor (CMT) risk, and with little known about CMT genetic susceptibility, we carried out whole genome sequencing on 14 purebred dogs diagnosed with mammary tumors from four breed-specific pedigrees. Following sequencing, each dog’s data was processed through a bioinformatics pipeline. This initial report highlights variants in orthologs of human breast cancer susceptibility genes.ResultsThe overall whole genome and exome coverage averages were 26.0X and 25.6X, respectively, with 96.1% of the genome and 96.7% of the exome covered at least 10X. Of the average 7.9 million variants per dog, initial analyses involved surveying variants in orthologs of human breast cancer susceptibility genes, BRCA1, BRCA2, CDH1, PTEN, STK11, and TP53, and identified 19 unique coding variants that were validated through PCR and Sanger sequencing. Statistical analyses identified variants in BRCA2 and STK11 that appear to be associated with CMT, and breed-specific analyses revealed the breeds at the highest risk. Several additional BRCA2 variants showed trends toward significance, but have conflicting interpretations of pathogenicity, and correspond to variants of unknown significance in humans, which require further investigation. Variants in other genes were noted but did not appear to be associated with disease.ConclusionsWhole genome sequencing proves to be an effective method to elucidate risk of CMT. Risk variants in orthologs of human breast cancer susceptibility genes have been identified. Ultimately, these whole genome sequencing efforts have provided a plethora of data that can also be assessed for novel discovery and have the potential to lead to breakthroughs in canine and human research through comparative analyses.

Estrogen receptors genotypes and canine mammary neoplasia

BackgroundEstrogens are essential for the development and proper function of several hormone-dependent organs. There are, however, several lines of evidence associating estrogens with mammary carcinogenesis. A marked individual genetic variability concerning estrogens biosynthesis, metabolism and mechanism of action was recognized and associated with human breast cancer susceptibility, clinical features and progression. Although some genetic variations in canine ESR1 gene were reported, their influence in clinicopathological features and progression of canine mammary tumors has not been fully evaluated. This study aims to assess the influence of SNPs in ESR1 gene (rs397512133, rs397510462, rs851327560, rs397510612, rs852887655, rs852684753 and rs852398698) in canine mammary tumors characteristics and progression. A group of 155 non-neutered bitches with mammary tumors was included in the study. Follow-up information was assessed 24 months after surgery.ResultsGenetic profiles associated with a later onset of mammary tumors and less aggressive clinicopathological features, namely smaller tumor size (≤ 3 cm) with extensive tubular differentiation and low canine-adapted prognostic index (vet-NPI), were identified in this study.ConclusionsOur data suggest that the ESR1 genetic profile may help on the decision regarding the selection of individual tailored preventive measures against canine mammary tumors development, such as early neutering.

Canine mammary tumor risk is associated with polymorphisms in RAD51 and STK11 genes.

Cancer is a complex disease involving genetic and phenotypic changes. Several single nucleotide polymorphisms (SNPs) have been associated with the risk of breast cancer development in women; however, little is known regarding their influence on canine mammary tumor risk. We assessed the influence of SNPs in genes related to human breast cancer susceptibility, with respect to the risk of development of mammary tumors in dogs. Sixty-seven canine SNPs in proto-oncogenes, tumor suppressor genes, genes involved in DNA repair, and in hormonal metabolism were evaluated in 212 bitches with mammary tumors and in 161 bitches free of mammary neoplasia. A significant association with mammary neoplasia risk was identified for 2 SNPs in RAD51 ( rs23623251 and rs23642734) and one SNP in the STK11 gene ( rs22928814). None of the other SNPs were related to the risk of mammary tumor development. The identification of genetic profiles associated with risk of mammary neoplasia is of great importance, supporting the implementation of specific clinical management strategies in high-risk animals.

Abstract 1839: TGFBR1*6A mouse model mimics human breast cancer development and progression

Abstract Transforming Growth Factor-ß (TGF-β) is one of the most commonly altered cellular signaling pathways in human cancer. Our group was the first to discover TGFBR1*6A (*6A), a common hypomorphic variant of the type I TGF-ß receptor (TGFBR1), which has been associated with increased risk for breast cancer in multiple epidemiological studies. Functional analysis also suggests that *6A is associated with decreased tumor suppressive TGF-β signaling in early tumor development and is involved with promoting tumorigenesis in advanced carcinomas. To better understand the functional impact of *6A and constitutively reduced TGF-ß signaling on breast cancer development and progression, we have recently developed a series of transgenic knock-in mouse model variants by replacing exon 1 of the mouse Tgfbr1 sequence with human exon 1 sequences harboring both *6A and wild-type (*9A) TGFBR1 variants and crossed them with MMTVneu mice. We generated a total of 5 FVB double and/or triple transgenic mouse strains: MMTVneu;9A/9A, MMTVneu;6A/6A, MMTVneu;9A/6A, MMTVneu;*9A/-, and MMTVneu;6A/-. Following tumor development, measurements were performed three times per week to determine tumor volume. All mice were allowed to live up to 18 months (548 days) or until they died of natural causes. Specimens were collected for later analysis of blood, tumors, normal mammary tissue, and were evaluated for lung metastases. Statistical comparisons performed using Student’s t-test. Only 34.4% of MMTVneu;9A/9A mice (11/32) developed mammary tumors, while 80% of MMTVneu;6A/6A mice (24/30; p=0.0002) and 62.5% of MMTVneu;6A/- mice (19/32, p=0.046) developed tumors. The percentage of MMTVneu;9A/6A and MMTVneu;*9A/- mice that developed tumors was higher than MMTVneu;9A/9A mice (48.3% and 50%, respectively) but was not statistically significant. Additionally, 66.7% of MMTVneu;6A/6A mice (20/30) developed 2 or more tumors, while only 25% of MMTVneu;9A/9A mice (8/32) developed multiple tumors (p=0.0007). Our data suggests that we have developed transgenic mouse strains that accurately mimic human breast cancer susceptibility associated with *6A and constitutively decreased TGFBR1 expression in humans, as evidenced by other studies. These mouse models may be a tool to provide invaluable insight to better understand the role of TGFBR1 variants in the development and progression of breast cancer. Citation Format: Michael James Pennison, Minghui Wang, Hugo Jimenez, Boris Pasche. TGFBR1*6A mouse model mimics human breast cancer development and progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1839. doi:10.1158/1538-7445.AM2017-1839

A monograph proposing the use of canine mammary tumours as a model for the study of hereditary breast cancer susceptibility genes in humans.

Canines are excellent models for cancer studies due to their similar physiology and genomic sequence to humans, companion status and limited intra‐breed heterogeneity. Due to their affliction to mammary cancers, canines can serve as powerful genetic models of hereditary breast cancers. Variants within known human breast cancer susceptibility genes only explain a fraction of familial cases. Thus, further discovery is necessary but such efforts have been thwarted by genetic heterogeneity. Reducing heterogeneity is key, and studying isolated human populations have helped in the endeavour. An alternative is to study dog pedigrees, since artificial selection has resulted in extreme homogeneity. Identifying the genetic predisposition to canine mammary tumours can translate to human discoveries – a strategy currently underutilized. To explore this potential, we reviewed published canine mammary tumour genetic studies and proposed benefits of next generation sequencing canine cohorts to facilitate moving beyond incremental advances.

Interaction with PALB2 Is Essential for Maintenance of Genomic Integrity by BRCA2.

Human breast cancer susceptibility gene, BRCA2, encodes a 3418-amino acid protein that is essential for maintaining genomic integrity. Among the proteins that physically interact with BRCA2, Partner and Localizer of BRCA2 (PALB2), which binds to the N-terminal region of BRCA2, is vital for its function by facilitating its subnuclear localization. A functional redundancy has been reported between this N-terminal PALB2-binding domain and the C-terminal DNA-binding domain of BRCA2, which undermines the relevance of the interaction between these two proteins. Here, we describe a genetic approach to examine the functional significance of the interaction between BRCA2 and PALB2 by generating a knock-in mouse model of Brca2 carrying a single amino acid change (Gly25Arg, Brca2G25R) that disrupts this interaction. In addition, we have combined Brca2G25R homozygosity as well as hemizygosity with Palb2 and Trp53 heterozygosity to generate an array of genotypically and phenotypically distinct mouse models. Our findings reveal defects in body size, fertility, meiotic progression, and genome stability, as well as increased tumor susceptibility in these mice. The severity of the phenotype increased with a decrease in the interaction between BRCA2 and PALB2, highlighting the significance of this interaction. In addition, our findings also demonstrate that hypomorphic mutations such as Brca2G25R have the potential to be more detrimental than the functionally null alleles by increasing genomic instability to a level that induces tumorigenesis, rather than apoptosis.

Significant overlap between human genome-wide association-study nominated breast cancer risk alleles and rat mammary cancer susceptibility loci

IntroductionHuman population-based genome-wide association (GWA) studies identify low penetrance breast cancer risk alleles; however, GWA studies alone do not definitively determine causative genes or mechanisms. Stringent genome- wide statistical significance level requirements, set to avoid false-positive associations, yield many false-negative associations. Laboratory rats (Rattus norvegicus) are useful to study many aspects of breast cancer, including genetic susceptibility. Several rat mammary cancer associated loci have been identified using genetic linkage and congenic strain based-approaches. Here, we sought to determine the amount of overlap between GWA study nominated human breast and rat mammary cancer susceptibility loci.MethodsWe queried published GWA studies to identify two groups of SNPs, one that reached genome-wide significance and one comprised of SNPs failing a validation step and not reaching genome- wide significance. Human genome locations of these SNPs were compared to known rat mammary carcinoma susceptibility loci to determine if risk alleles existed in both species. Rat genome regions not known to associate with mammary cancer risk were randomly selected as control regions.ResultsSignificantly more human breast cancer risk GWA study nominated SNPs mapped at orthologs of rat mammary cancer loci than to regions not known to contain rat mammary cancer loci. The rat genome was useful to predict associations that had met human genome-wide significance criteria and weaker associations that had not.ConclusionsIntegration of human and rat comparative genomics may be useful to parse out false-negative associations in GWA studies of breast cancer risk.

Human MCS5A1 candidate breast cancer susceptibility gene FBXO10 is induced by cellular stress and correlated with lens epithelium-derived growth factor (LEDGF).

Genetic variation and candidate genes associated with breast cancer susceptibility have been identified. Identifying molecular interactions between associated genetic variation and cellular proteins may help to better understand environmental risk. Human MCS5A1 breast cancer susceptibility associated SNP rs7042509 is located in F-box protein 10 (FBXO10). An orthologous Rattus norvegicus DNA-sequence that contains SNV ss262858675 is located in rat Mcs5a1, which is part of a mammary carcinoma susceptibility locus controlling tumor development in a non-mammary cell-autonomous manner via an immune cell-mediated mechanism. Higher Fbxo10 expression in T cells is associated with Mcs5a increased susceptibility alleles. A common DNA-protein complex bound human and rat sequences containing MCS5A1/Mcs5a1 rs7042509/ss262858675 in electrophoretic mobility shift assays (EMSAs). Lens epithelium-derived growth factor (LEDGF), a stress-response protein, was identified as a candidate to bind both human and rat sequences using DNA-pulldown and mass spectrometry. LEDGF binding was confirmed by LEDGF-antibody EMSA and chromatin immunoprecipitation (ChIP). Ectopic expression of LEDGF/p75 increased luciferase activities of co-transfected reporters containing both human and rat orthologs. Over-expressed LEDGF/p75 increased endogenous FBXO10 mRNA levels in Jurkat cells, a human T-cell line, implying LEDGF may be involved in increasing FBXO10 transcript levels. Oxidative and thermal stress of Jurkat cells increased FBXO10 and LEDGF expression, further supporting a hypothesis that LEDGF binds to a regulatory region of FBXO10 and increases expression during conditions favoring carcinogenesis. We conclude that FBXO10, a candidate breast cancer susceptibility associated gene, is induced by cellular stress and LEDGF may play a role in expression of this gene.

Functional evaluation of BRCA2 variants mapping to the PALB2-binding and C-terminal DNA-binding domains using a mouse ES cell-based assay

Single-nucleotide substitutions and small in-frame insertions or deletions identified in human breast cancer susceptibility genes BRCA1 and BRCA2 are frequently classified as variants of unknown clinical significance (VUS) due to the availability of very limited information about their functional consequences. Such variants can most reliably be classified as pathogenic or non-pathogenic based on the data of their co-segregation with breast cancer in affected families and/or their co-occurrence with a pathogenic mutation. Biological assays that examine the effect of variants on protein function can provide important information that can be used in conjunction with available familial data to determine the pathogenicity of VUS. In this report, we have used a previously described mouse embryonic stem (mES) cell-based functional assay to characterize eight BRCA2 VUS that affect highly conserved amino acid residues and map to the N-terminal PALB2-binding or the C-terminal DNA-binding domains. For several of these variants, very limited co-segregation information is available, making it difficult to determine their pathogenicity. Based on their ability to rescue the lethality of Brca2-deficient mES cells and their effect on sensitivity to DNA-damaging agents, homologous recombination and genomic integrity, we have classified these variants as pathogenic or non-pathogenic. In addition, we have used homology-based modeling as a predictive tool to assess the effect of some of these variants on the structural integrity of the C-terminal DNA-binding domain and also generated a knock-in mouse model to analyze the physiological significance of a residue reported to be essential for the interaction of BRCA2 with meiosis-specific recombinase, DMC1.

CODING FOR LIFE - SHOULD ANY ENTITY HAVE THE EXCLUSIVE RIGHT TO USE AND SELL ISOLATED DNA?

Myriad Genetics, Inc. ("Myriad") obtained patents in the 1990s on two "isolated" human breast and ovarian cancer susceptibility genes ("BRCA"). Myriad did not list all the isolated sequences it claims to have a right to monopolize, but instead claims a patent on the physical phenomena itself -- all DNA segments that code for the BRCA1 polypeptide, even the sequences Myriad has not identified and even those someone else in the future creates or isolates the sequences of through a method or methods not contemplated by Myriad. An impressive array of non-profit medical societies, doctors and patients sued to have the Myriad patents declared invalid. In 2010, the District Court for the Southern District of New York held in Association for Molecular Pathology v. United States Patent and Trademark Office that the claimed product patents for isolated DNA segments constituted unpatentable subject matter under 35 U.S.C. §101. On July 29, 2011, a divided panel of the Federal Circuit reversed the District Court and held that the isolated DNA segments constituted patentable subject matter. Of the three member panel, Judge Lourie concluded that the isolated DNA was markedly different than the native DNA, so constituted patentable subject matter. Although Judge Moore agreed that certain DNA segments constituted patentable subject matter, she believed that the longer isolated DNA segments probably did not constitute patentable subject matter. However, primarily in light of the fact that the US Patent and Trademark Office has been granting patents for isolated DNA for years, Judge Moore concurred in the judgment of Judge Lourie. Judge Bryson concurred on one of the product claims (for synthetic cDNA) but dissented on claims pertaining to the isolated DNA segments on the grounds that isolated DNA did not differ markedly from the native DNA and that the function of the isolated DNA was identical to the function of the native DNA.The Supreme Court stated that "Congress may not authorize the issuance of patents whose effects are to remove existent knowledge from the public domain, or to restrict free access to materials already available." This article argues that the Federal Circuit - not Congress - has done just that and has given Myriad a wall to restrict free access to materials that have literally been in humans for centuries. The isolated DNA segments of claim 1 do exactly the same coding as do the native segments--nothing more; nothing less. The segments of claim 1 do not act as primers or probes, so they do not have markedly different characteristics or utility than native DNA, which the Supreme Court has ruled courts must consider. Moreover, the functioning of the sequence of the nucleotide bases is a physical phenomenon that Myriad has not created but has captured in its claim. Judges Lourie and Moore disregarded Supreme Court precedent and the fundamental principle that physical phenomena are not patentable subject matter.

Coding for Life - Should Any Entity Have the Exclusive Right to Use and Sell Isolated DNA?

Myriad Genetics, Inc. (Myriad) obtained patents in the 1990's on two human breast and ovarian cancer susceptibility genes (BRCA). Myriad did not list all the isolated sequences it claims to have a right to monopolize, but instead claims a patent on the physical phenomena itself -- all DNA segments that code for the BRCA1 polypeptide, even the sequences Myriad has not identified and even someone else in the future creates or isolates the sequences through a method or methods not contemplated by Myriad.An impressive array of non-profit medical societies, doctors and patients sued to have the Myriad patents declared invalid. In 2010, the District Court for the Southern District of New York held in Association for Molecular Pathology v. United States Patent and Trademark Office that the claimed product patents for isolated DNA segments constituted unpatentable subject matter under 35 U.S.C. §101. On July 29, 2011, a divided panel of the Federal Circuit reversed the District Court and held that the isolated DNA segments constituted patentable subject matter. Of the three member panel, Judge Lourie concluded that the isolated DNA was markedly different than the native DNA, so constituted patentable subject matter. Although Judge Moore agreed that certain DNA segments constituted patentable subject matter, he believed that the longer isolated DNA segments probably did not constitute patentable subject matter. However, primarily in light of the fact that the US Patent and Trademark Office has been granting patents for isolated DNA for years, Judge Moore concurred in the judgment of Judge Lourie. Judge Bryson concurred on one of the product claims (for synthetic cDNA) but dissented on claims pertaining to the isolated DNA segments on the grounds that isolated DNA did not differ markedly from the native DNA and that the function of the isolated DNA was identical to the function of the native DNA.The Supreme Court has stated that may not authorize the issuance of patents whose effects are to remove existent knowledge from the public domain, or to restrict free access to materials already available. This article argues that the Federal Circuit - not Congress - has done just that and has given Myriad a wall to restrict free access to materials that have literally been in humans for centuries. The isolated DNA segments of claim 1 do exactly the same coding as the do the native segments -- nothing more; nothing less. The segments of claim 1 do not act as primers or probes, so they do not have markedly different characteristics or utility than native DNA, which the Supreme Court has ruled courts must consider. Moreover, the functioning of the sequence of the nucleotide bases is a physical phenomenon that Myriad has not created but has captured in its claim. Judges Lourie and Moore disregarded Supreme Court precedent and the fundamental principle that physical phenomena are not patentable subject matter.

A comprehensive functional characterization of BRCA2 variants associated with Fanconi anemia using mouse ES cell–based assay

AbstractBiallelic mutations in the human breast cancer susceptibility gene, BRCA2, are associated with Fanconi anemia, implying that some persons who inherit 2 deleterious variants of BRCA2 are able to survive even though it is well established that BRCA2 is indispensable for viability in mice. One such variant, IVS7 + 2T > G, results in premature protein truncation because of skipping of exon 7. Surprisingly, the persons who are either IVS7 + 2T > G homozygous or compound heterozygous are born alive but die of malignancy associated with Fanconi anemia. Using a mouse embryonic stem cell–based functional assay, we found that the IVS7 + 2T > G allele produces an alternatively spliced transcript lacking exons 4-7, encoding an in-frame BRCA2 protein with an internal deletion of 105 amino acids (BRCA2Δ105). We demonstrate that BRCA2Δ105 is proficient in homologous recombination-mediated DNA repair as measured by different functional assays. Evaluation of this transcript in normal and leukemia cells suggests that BRCA2Δ105 may contribute to the viability of persons inheriting this mutation. In this study, we have also characterized 5 other BRCA2 variants and found 3 of these (p.L2510P, p.R2336H, and p.W2626C) to be deleterious and 2 (p.I2490T and p.K2729N) probably neutral. Such studies are important to understand the functional significance of unclassified BRCA2 variants.

A HRM-based screening method detects RAD51C germ-line deleterious mutations in Spanish breast and ovarian cancer families

The RAD51C gene has been recently proposed as a high-penetrance breast and ovarian cancer gene. However, early replication studies have failed to confirm the finding. Thus, further studies in larger cohorts should be conducted in order to clarify the role of RAD51C as a cancer susceptibility gene. Here, we describe a high-resolution melting analysis (HRMA)-based method developed for presequence screening of RAD51C sequence variants. We have screened RAD51C sequence variants by HRMA in 492 breast cancer patients with family history of breast and/or ovarian cancer that were previously tested negative for BRCA1/2. All variants were confirmed by direct sequencing. We have detected 12 different RAD51C germ-line sequence variants, including eight transitions, two transversion, and two indels (insA, and delT). All these variants generated melting profiles which differ from wild type homozygous controls. Interestingly, we have identified one clearly pathogenic mutation (c.774delT) in the subset of 101 breast and ovarian cancer families, supporting that RAD51C is a human breast and ovarian cancer susceptibility gene.

Slip-Sliding Away: Serial Changes and Homoplasy in Repeat Number in the Drosophila yakuba Homolog of Human Cancer Susceptibility Gene BRCA2

Several recent studies have examined the function and evolution of a Drosophila homolog to the human breast cancer susceptibility gene BRCA2, named dmbrca2. We previously identified what appeared to be a recent expansion in the RAD51-binding BRC-repeat array in the ancestor of Drosophila yakuba. In this study, we examine patterns of variation and evolution of the dmbrca2 BRC-repeat array within D. yakuba and its close relatives. We develop a model of how unequal crossing over may have produced the expanded form, but we also observe short repeat forms, typical of other species in the D. melanogaster group, segregating within D. yakuba and D. santomea. These short forms do not appear to be identical-by-descent, suggesting that the history of dmbrca2 in the D. melanogaster subgroup has involved repeat unit contractions resulting in homoplasious forms. We conclude that the evolutionary history of dmbrca2 in D. yakuba and perhaps in other Drosophila species may be more complicated than can be inferred from examination of the published single genome sequences per species.

Schizosaccharomyces pombe Dss1p Is a DNA Damage Checkpoint Protein That Recruits Rad24p, Cdc25p, and Rae1p to DNA Double-strand Breaks

Schizosaccharomyces pombe Dss1p and its homologs function in multiple cellular processes including recombinational repair of DNA and nuclear export of messenger RNA. We found that Tap-tagged Rad24p, a member of the 14-3-3 class of proteins, co-purified Dss1p along with mitotic activator Cdc25p, messenger RNA export/cell cycle factor Rae1p, 19 S proteasomal factors, and recombination protein Rhp51p (a Rad51p homolog). Using chromatin immunoprecipitation, we found that Dss1p recruited Rad24p and Rae1p to the double-strand break (DSB) sites. Furthermore, Cdc25p also recruited to the DSB site, and its recruitment was dependent on Dss1p, Rad24p, and the protein kinase Chk1p. Following DSB, all nuclear Cdc25p was found to be chromatin-associated. We found that Dss1p and Rae1p have a DNA damage checkpoint function, and upon treatment with UV light Deltadss1 cells entered mitosis prematurely with indistinguishable timing from Deltarad24 cells. Taken together, these results suggest that Dss1p plays a critical role in linking repair and checkpoint factors to damaged DNA sites by specifically recruiting Rad24p and Cdc25p to the DSBs. We suggest that the sequestration of Cdc25p to DNA damage sites could provide a mechanism for S. pombe cells to arrest at G(2)/M boundary in response to DNA damage.

Brca1 is required for embryonic development of the mouse cerebral cortex to normal size by preventing apoptosis of early neural progenitors

The extent of apoptosis of neural progenitors is known to influence the size of the cerebral cortex. Mouse embryos lacking Brca1, the ortholog of the human breast cancer susceptibility gene BRCA1, show apoptosis in the neural tube, but the consequences of this for brain development have not been studied. Here we investigated the role of Brca1 during mouse embryonic cortical development by deleting floxed Brca1 using Emx1-Cre, which leads to conditional gene ablation specifically in the dorsal telencephalon after embryonic day (E) 9.5. The postnatal Brca1-ablated cerebral cortex was substantially reduced in size with regard to both cortical thickness and surface area. Remarkably, although the thickness of the cortical layers (except for the upper-most layer) was decreased, cortical layering as such was essentially unperturbed. High levels of apoptosis were found at E11.5 and E13.5, but dropped to near-control levels by E16.5. The apoptosis at the early stage of neurogenesis occurred in both BrdU pulse-labeled neural progenitors and the neurons derived therefrom. No changes were observed in the mitotic index of apical (neuroepithelial, radial glial) progenitors and basal (intermediate) progenitors, indicating that Brca1 ablation did not affect cell cycle progression. Brca1 ablation did, however, result in the nuclear translocation of p53 in neural progenitors, suggesting that their apoptosis involved activation of the p53 pathway. Our results show that Brca1 is required for the cerebral cortex to develop to normal size by preventing the apoptosis of early cortical progenitors and their immediate progeny.

HistoneHits: A database for histone mutations and their phenotypes

Histones are the basic protein components of nucleosomes. They are among the most conserved proteins and are subject to a plethora of post-translational modifications. Specific histone residues are important in establishing chromatin structure, regulating gene expression and silencing, and responding to DNA damage. Here we present HistoneHits, a database of phenotypes for systematic collections of histone mutants. This database combines assay results (phenotypes) with information about sequences, structures, post-translational modifications, and evolutionary conservation. The web interface presents the information through dynamic tables and figures. It calculates the availability of data for specific mutants and for nucleosome surfaces. The database currently includes 42 assays on 677 mutants multiply covering 405 of the 498 residues across yeast histones H3, H4, H2A, and H2B. We also provide an interface with an extensible controlled vocabulary for research groups to submit new data. Preliminary analyses confirm that mutations at highly conserved residues and modifiable residues are more likely to generate phenotypes. Buried residues and residues on the lateral surface tend to generate more phenotypes, while tail residues generate significantly fewer phenotypes than other residues. Yeast mutants are cross referenced with known human histone variants, identifying a position where a yeast mutant causes loss of ribosomal silencing and a human variant increases breast cancer susceptibility. All data sets are freely available for download.

Single Nucleotide Polymorphisms in Human Gene icb-1 and Breast Cancer Susceptibility

In this study, we tested the hypothesis that single nucleotide polymorphisms (SNPs) of differentiation-associated human gene icb-1 (C1orf38) may be associated with breast cancer susceptibility. A total of 646 women—323 breast cancer cases and just as many controls—were included. Breast cancer patients more frequently carried the homozygous genotype AA of SNP rs1467465 than did healthy women. Analysis of allele positivity revealed that AG or GG genotypes were significantly less frequent in breast cancer patients, suggesting that presence of G allele might have protective effects. Our data suggest that SNP rs1467465 of human gene icb-1 might affect breast cancer susceptibility.

Toxicogenomic Analyses of Genetic Susceptibility to Mammary Gland Carcinogenesis in Rodents: Implications for Human Breast Cancer

The Human Genome Project and the multitude of genomic technologies that it generated have dramatically altered the face of biological research. Genomic sequence information allowed for the development of high throughput technologies for DNA sequencing, gene expression profiling, genotyping, and detection of epigenetic changes. These technologies provide an unprecedented opportunity to elucidate how genetic variation and cellular responses to insult from environment toxicants and stressors, drugs, infections, co-morbid disease, and dietary factors among others, contribute to complex human diseases, including cancer. Toxicogenomics, which combines classical toxicology and genetics with the tools of modern genomics, promises to help elucidate and classify compounds based on mechanisms of toxicity, predict toxicity of untested compounds, provide improved screening and exposure monitoring, enhance the ability to predict toxicity and disease outcomes following exposure, and identify genetically susceptible individuals. Toxicogenomic data are therefore expected to do much to inform risk assessment. Rodents are excellent models for the study of the molecular and genetic bases for human disease, and are still used extensively to screen for toxic effects of drugs and environmental toxicants. In the present review, we explore how the combination of toxicogenomic approaches with rodent models can accelerate the discovery of human breast cancer susceptibility genes.

Stabilization of RAD51 nucleoprotein filaments by the C-terminal region of BRCA2

The human breast cancer susceptibility gene BRCA2 is required for the regulation of RAD51-mediated homologous recombinational repair. BRCA2 interacts with RAD51 monomers, as well as nucleoprotein filaments, primarily though the conserved BRC motifs. The unrelated C-terminal region of BRCA2 also interacts with RAD51. Here we show that the BRCA2 C terminus interacts directly with RAD51 filaments, but not monomers, by binding an interface created by two adjacent RAD51 protomers. These interactions stabilize filaments so that they cannot be dissociated by association with BRC repeats. Interaction of the BRCA2 C terminus with the RAD51 filament causes a large movement of the flexible RAD51 N-terminal domain that is important in regulating filament dynamics. We suggest that interactions of the BRCA2 C-terminal region with RAD51 may facilitate efficient nucleation of RAD51 multimers on DNA and thereby stimulate recombination-mediated repair.