Regulation of BRCA1

BRCA1 promoter deletions in young women with breast cancer and a strong family history: a population-based study

Women diagnosed with breast cancer before the age of 40 years who have a strong family history of breast and/or ovarian cancer were selected from an Australian population-based case-control-family study for large deletion screening within the BRCA1 promoter. Deletions within the BRCA1 promoter region are usually not detected by the methods applied in routine clinical mutation detection strategies. Fifty-one of the 66 women (77%) who met our inclusion criteria were tested for promoter deletions using linkage disequilibrium analysis of two BRCA1 polymorphic sites (C/G1802 and Pro871Leu) and multiplex ligation-dependent probe amplification. Two cases of BRCA1 promoter deletion involving exons 1A-2 and exons 1A-23 were detected. The morphology of the breast cancers arising in these women with BRCA1 promoter deletions was consistent with the morphology associated with other germline BRCA1 mutations. Large genomic deletions that involve the promoter regions of BRCA1 make up 20% (2/10) of all known BRCA1 mutations in this group of young women with a strong family history of breast and ovarian cancer. Our data support the inclusion of testing for large genomic alterations in the BRCA1 promoter region in routine clinical mutation detection within BRCA1.

Regulation of BRCA1 transcription by specific single-stranded DNA binding factors

Since the majority of high-grade breast cancers express reduced levels of BRCA1 mRNA, we investigated the factors regulating BRCA1 transcription. Factors with specific affinity for the previously identified positive regulatory region (PRR) in the BRCA1 promoter were purified from whole-cell extracts. Identified proteins included replication protein A and a series of related factors with affinity for the sense strand of PRR. A subset of the identified factors activated the BRCA1 promoter. Identification of these families of proteins regulating the BRCA1 promoter represents an important step in the comprehension of the mechanisms responsible for breast cancer development.

Hierarchical mutation screening protocol for the BRCA1 gene

The identification of mutations in the BRCA1 gene poses difficulties in achieving a screening outcome that satisfies the twin needs of speed and accuracy. These needs must also take into account the patient's family history and the statistical evaluation of the probability of detecting a mutation. Given the above, we present here a hierarchical mutation screening strategy that comprises two tiers: first, multiplex heteroduplex and exon 13 duplication analysis; second, exon amplification and direct sequencing using a 96-well tray format. The advantages of this strategy are two-fold: first, the division of analytical tools in order to achieve low and high-resolution mutation screening, respectively; second, a streamlined sequencing approach that leads to a sensitive and rapid assay that reduces labor costs and handling errors. The success of this approach is shown by the identification of a novel deletion mutation in exon 14 of the BRCA1 gene, which was not detected by the more conventional protein truncation assay due to the small size of the predicted truncated protein.

Mouse ret finger protein (rfp) proto-oncogene is expressed at specific stages of mouse spermatogenesis

Many proteins involved in the regulation of cell growth and differentiation possess structural motifs that participate in specific molecular interactions. The human rfp (ret finger protein) has a tripartite motif, consisting of two novel zinc fingers (the RING linger and the B box) and a coiled-coil domain, and belongs to the B box zinc finger protein family. Rfp becomes oncogenic when its tripartite motif is recombined with the tyrosine kinase domain from the c-ret proto-oncogene. To further understand the function of rfp during normal development and cellular differentiation, we cloned the mouse rfp cDNA and analyzed its pattern of expression and subcellular distribution. We found that the mouse rfp cDNA shared a 98.4% homology with the human sequence. The gene mapped to human chromosome 6 and mouse chromosome 13 indicating that it was linked to a several other genes encoding proteins that possess common domains. rfp transcripts and protein were ubiquitous in day 10.5-13.5 mouse embryos, however, they were restricted in adult mice, with the highest level of expression in pachytene spermatocytes and round spermatids of differentiating sperm. The rfp protein was detected within cell nuclei as nuclear bodies similar to the PODs (PML oncogenic domains) observed with another B box family member, PML (promyelocytic leukemia protein). These results suggest that rfp may function in the regulation of cell growth and differentiation during mouse embryogenesis and sperm differentiation.

Transcription of BRCA1 is dependent on the formation of a specific protein-DNA complex on the minimal BRCA1 Bi-directional promoter

BRCA1 is the first tumor suppressor gene linked to hereditary breast and ovarian cancers. Its involvement in sporadic breast cancer, however, remains unclear. Recent studies showed that a loss or lowered expression of BRCA1 is not uncommon in nonfamilial breast cancers. In addition, there have been cases of inherited BRCA1-linked breast cancer with as yet unidentified mutation. Misregulation of BRCA1 at the transcription level is a possible mechanism for loss of BRCA1 expression. To understand transcriptional regulation of the BRCA1 gene, we cloned and examined the BRCA1 promoter, by both functional reporter gene analyses and protein-DNA complex formation electrophorectic mobility shift assays. A bi-directional promoter could be located within a 229-base pair (bp) intergenic region between BRCA1 and its neighboring gene, NBR2. Deletion analyses further delineated a minimal 56-bp EcoRI-HaeIII fragment, which could drive transcription in the NBR2 gene direction 2-4-fold higher than in the BRCA1 direction in all cell lines tested. Furthermore, transcriptional activity in the BRCA1 direction was undetectable in the muscle cell line C2C12, whereas activity in the NBR2 direction was maintained. These results were consistent with the expression pattern of the respective genes. A specific protein-DNA complex was detected when nuclear extracts from HeLa cells and Caco2, a colon cell line, were incubated with the 56-bp minimal promoter. This protein binding activity was further localized to an 18-bp fragment and might involve a tissue-specific factor, because binding was not detected in the C2C12 cell line. The correlation of the detection of this protein-DNA complex only in those cell lines that expressed the chloramphenicol acetyltransferase reporter gene in the BRCA1 direction suggests a significant positive role of this complex in the transcription of the BRCA1 gene.

Positive regulation of the BRCA1 promoter

Inherited mutations in the BRCA1 gene, presumably leading to loss of function, confer susceptibility to breast and ovarian neoplasms and are thought to be responsible for approximately 2.5-5% of all breast cancers. It has been suggested that alternative mechanisms, such as disruption of transcription, may also be involved in the suppression of BRCA1 gene expression/function in breast cancers. Therefore, we initiated studies on the BRCA1 transcriptional promoter. Utilizing systematic promoter deletions and transient transfection assays, a 36-base pair region was determined to be important for the positive regulation of BRCA1 transcription. Deletion of this positive regulatory region resulted in a significant loss of promoter activity. Utilizing DNA binding assays, proteins with specific affinities for the positive regulatory region were detected. Disruption of the DNA-protein complexes could affect normal BRCA1 transcription and may contribute to breast cancer susceptibility.

Expression of BRCA1 and BRCA2 in normal and neoplastic cells

Current evidence strongly supports a role for the breast cancer susceptibility genes, BRCA1 and BRCA2, in both normal development and carcinogenesis. Valuable clues regarding the function of these genes have been garnered through studies of their patterns of expression. A central feature of the in vivo pattern of BRCA1 and BRCA2 expression is that each of these putative tumor suppressor genes is expressed at maximal levels in rapidly proliferating cells. This feature is consistent with in vitro observations that BRCA1 and BRCA2 are expressed in a cell cycle-dependent manner. This feature is also well illustrated during mammary gland development wherein the expression of BRCA1 and BRCA2 is induced in rapidly proliferating cellular compartments undergoing differentiation, such as terminal end buds during puberty and developing alveoli during pregnancy. Strikingly, the spatial and temporal patterns of BRCA1 and BRCA2 expression are virtually indistinguishable during embryonic development and in multiple adult tissues despite the fact that these genes are unrelated. These observations have contributed to the emerging hypothesis that these genes function in similar regulatory pathways.

Preferential allelic expression can lead to reduced expression of BRCA1 in sporadic breast cancers

BRCA1 is considered to be a tumor-suppressor gene, yet mutations in this gene are uncommon in sporadic breast tumors. We investigated whether mechanisms other than DNA mutations that affect the coding region might be involved in breast carcinogenesis. Since loss of expression of the BRCA1 gene would lead to lack of protein, we evaluated the level of BRCA1 mRNA in 21 normal epithelial specimens and in 74 breast carcinomas using quantitative reverse-transcription-polymerase-chain-reaction (RT-PCR). All normal breast epithelial samples expressed BRCA1 mRNA. On the other hand, the tumor specimens exhibited approximately 10-fold range of levels of BRCA1, with some specimens expressing barely detectable amounts of BRCA1 mRNA. The distribution in levels was significantly higher in normal breast epithelial cells than in tumor specimens (p = 0.004). Examination of the BRCA1 locus indicated that deletion of the BRCA1 gene may account for low levels of BRCA1 in a number of specimens. In addition, analysis of samples with relatively reduced levels of BRCA1 expression revealed preferential allele-specific expression in a number of cases, suggesting the presence of regulatory mutations. Our data suggest that the BRCA1 gene may be involved in sporadic breast carcinogenesis through a reduction in gene expression.

Complete genomic sequence and analysis of 117 kb of human DNA containing the gene BRCA1

Over 100 distinct disease-associated mutations have been identified in the breast-ovarian cancer susceptibility gene BRCA1. Loss of the wild-type allele in > 90% of tumors from patients with inherited BRCA1 mutations indicates tumor suppressive function. The low incidence of somatic mutations suggests that BRCA1 inactivation in sporadic tumors occurs by alternative mechanisms, such as interstitial chromosomal deletion or reduced transcription. To identify possible features of the BRCA1 genomic region that may contribute to chromosomal instability as well as potential transcriptional regulatory elements, a 117,143-bp DNA sequence encompassing BRCA1 was obtained by random sequencing of four cosmids identified from a human chromosome 17 specific library. The 24 exons of BRCA1 span an 81-kb region that has an unusually high density of Alu repetitive DNA (41.5%), but relatively low density (4.8%) of other repetitive sequences. BRCA1 intron lengths range in size from 403 bp to 9.2 kb and contain the intragenic microsatellite markers D17S1323, D17S1322, and D17S855, which localize to introns 12, 19, and 20, respectively. In addition to BRCA1, the contig contains two complete genes: Rho7, a member of the rho family of GTP binding proteins, and VAT1, an abundant membrane protein of cholinergic synaptic vesicles. Partial sequences of the 1A1-3B B-box protein pseudogene and IFP 35, an interferon induced leucine zipper protein, reside within the contig. An L21 ribosomal protein pseudogene is embedded in BRCA1 intron 13. The order of genes on the chromosome is: centromere-1FP 35-VAT1-Rho7-BRCA1-1A1-3B-telomere.

In vivo and in vitro characterization of the B1 and B2 zinc-binding domains from the acute promyelocytic leukemia protooncoprotein PML

Acute promyelocytic leukemia (APL) has been ascribed to a chromosomal translocation event which results in a fusion protein comprising the PML protein and retinoic acid receptor alpha. PML is normally a component of a nuclear multiprotein complex which is disrupted in the APL disease state. Here, two newly defined cysteine/histidine-rich protein motifs called the B-box (B1 and B2) from PML have been characterized in terms of their effect on PML nuclear body formation, their dimerization, and their biophysical properties. We have shown that both peptides bind Zn2+, which induces changes in the peptides' structures. We demonstrate that mutants in both B1 and B2 do not form PML nuclear bodies in vivo and have a phenotype that is different from that observed in the APL disease state. Interestingly, these mutations do not affect the ability of wild-type PML to dimerize with mutant proteins in vitro, suggesting that the B1 and B2 domains are involved in an additional interaction central to PML nuclear body formation. This report in conjunction with our previous work demonstrates that the PML RING-Bl/B2 motif plays a fundamental role in formation of a large multiprotein complex, a function that may be common to those unrelated proteins which contain the motif.

Hereditary predisposition to breast cancer

The breast cancer susceptibility gene on chromosome 17q, BRCA1, has now been isolated. Mutations in this gene have been detected in many families with a predisposition to breast cancer. Most of these mutations result in truncation and presumed inactivation of the BRCA1 protein. A large number of distinct mutations have been reported, although some families have identical mutations, probably due to a founder effect. Certain evidence suggests that mutations positioned towards the 5' end of the gene carry a higher risk of ovarian cancer than those at the 3' end. BRCA1 is infrequently somatically mutated in sporadic breast or ovarian cancer. The BRCA2 gene has been localized to chromosome 13q12-q13. BRCA2 carries a risk of breast cancer similar to that of BRCA1, but is associated with a lower risk of ovarian cancer and a higher risk of male breast cancer. Additional breast cancer susceptibility genes probably exist, but may be difficult to locate by conventional methods.

BRCA1 mutations in a population-based sample of young women with breast cancer

BACKGROUND

Inherited mutations in the BRCA1 gene are associated with a high risk of breast and ovarian cancer in some families. However, little is known about the contribution of BRCA1 mutations to breast cancer in the general population. We analyzed DNA samples from women enrolled in a population-based study of early-onset breast cancer to assess the spectrum and frequency of germ-line BRCA1 mutations in young women with breast cancer.

METHODS

We studied 80 women in whom breast cancer was diagnosed before the age of 35, and who were not selected on the basis of family history. Genomic DNA was studied for BRCA1 mutations by analysis involving single-strand conformation polymorphisms and with allele-specific assays. Alterations were defined by DNA sequencing.

RESULTS

Germ-line BRCA1 mutations were identified in 6 of the 80 women. Four additional rare sequence variants of unknown functional importance were also identified. Two of the mutations and three of the rare sequence variants were found among the 39 women who reported no family history of breast or ovarian cancer. None of the mutations and only one of the rare variants was identified in a reference population of 73 unrelated subjects.

CONCLUSIONS

Alterations in BRCA1 were identified in approximately 10 percent of this cohort of young women with breast cancer. The risk of harboring a mutation was not limited to women with family histories of breast or ovarian cancer. These results represent a minimal estimate of the frequency of BRCA1 mutations in this population. Comprehensive methods of identifying BRCA1 mutations and understanding their importance will be needed before testing of women in the general population can be undertaken.

Mutations and polymorphisms in the familial early-onset breast cancer (BRCA1) gene. Breast Cancer Information Core

Mutations in the familial early-onset breast cancer gene (BRCA1) account for approximately 2-5% of all breast cancer cases (Easton et al., 1993). Since the isolation of the BRCA1 gene in 1994, many mutations have been identified. We report here a total of 254 BRCA1 mutations, 132 (52%) of which are unique. These represent mutations entered into a database established by the Breast Cancer Information Core (BIC), which have appeared in the literature or have been submitted by BIC members and other contributors prior to publication. A total of 221 (87%) of all mutations or 107 (81%) of the unique mutations are small deletions, insertions, nonsense point mutations, splice variants, and regulatory mutations that result in truncation or absence of the BRCA1 protein. A total of 11 disease-associated missense mutations (5 unique), and 21 variants (19 unique) as yet unclassified as either missense mutations or polymorphisms have been detected. Thirty-five independent benign polymorphisms are also described. The most common mutations are 185delAG and 5382insC, which account for 30 (11.7%) and 26 (10.1%), respectively, of all mutations shown. The biological and clinical relevance of these BRCA1 mutations is discussed.

Long-range interaction between two promoters: activation of the leu-500 promoter by a distant upstream promoter

The leu-500 mutation can be suppressed in S. typhimurium topA. Previous studies have demonstrated that the plasmid-borne leu-500 minimal promoter cannot be activated in topA mutants unless adjacent (< 250 bp) transcription occurs away from the leu-500 promoter (short-range promoter interaction). To search for a potential upstream promoter responsible for activation of leu-500 in the chromosomal context, we have identified the ilvlH promoter, located 1.9 kb upstream of leu-500 (long-range promoter interaction). Different from short-range promoter interaction, which is abolished by DNA sequence insertions, the long-range promoter interaction is mediated by the intervening DNA sequence. These studies suggest that the long-range interaction between a pair of divergently arrayed promoters is probably mediated by a complex process involving relay of DNA supercoiling by the DNA sequence located between the two promoters.

Physical mapping, cloning, and identification of genes within a 500-kb region containing BRCA1

BRCA1 is a breast/ovarian cancer susceptibility gene on human chromosome 17q21. We describe a complete and detailed physical map of a 500-kb region of genomic DNA containing the BRCA1 gene and the partial cloning in phage P1 artificial chromosomes. Approximately 70 exons were isolated from this region, 11 of which were components of the BRCA1 gene. Analysis of the other exons revealed a rho-related G protein and the interferon-induced leucine-zipper protein IFP-35.