ENIGMA CHEK2gether Project: A Comprehensive Study Identifies Functionally Impaired CHEK2 Germline Missense Variants Associated with Increased Breast Cancer Risk

PURPOSE

Germline pathogenic variants in CHEK2 confer moderately elevated breast cancer risk (odds ratio, OR ∼ 2.5), qualifying carriers for enhanced breast cancer screening. Besides pathogenic variants, dozens of missense CHEK2 variants of uncertain significance (VUS) have been identified, hampering the clinical utility of germline genetic testing (GGT).

EXPERIMENTAL DESIGN

We collected 460 CHEK2 missense VUS identified by the ENIGMA consortium in 15 countries. Their functional characterization was performed using CHEK2-complementation assays quantifying KAP1 phosphorylation and CHK2 autophosphorylation in human RPE1-CHEK2-knockout cells. Concordant results in both functional assays were used to categorize CHEK2 VUS from 12 ENIGMA case-control datasets, including 73,048 female patients with breast cancer and 88,658 ethnicity-matched controls.

RESULTS

A total of 430/460 VUS were successfully analyzed, of which 340 (79.1%) were concordant in both functional assays and categorized as functionally impaired (N = 102), functionally intermediate (N = 12), or functionally wild-type (WT)-like (N = 226). We then examined their association with breast cancer risk in the case-control analysis. The OR and 95% CI (confidence intervals) for carriers of functionally impaired, intermediate, and WT-like variants were 2.83 (95% CI, 2.35-3.41), 1.57 (95% CI, 1.41-1.75), and 1.19 (95% CI, 1.08-1.31), respectively. The meta-analysis of population-specific datasets showed similar results.

CONCLUSIONS

We determined the functional consequences for the majority of CHEK2 missense VUS found in patients with breast cancer (3,660/4,436; 82.5%). Carriers of functionally impaired missense variants accounted for 0.5% of patients with breast cancer and were associated with a moderate risk similar to that of truncating CHEK2 variants. In contrast, 2.2% of all patients with breast cancer carried functionally wild-type/intermediate missense variants with no clinically relevant breast cancer risk in heterozygous carriers.

Classification of BRCA2 Variants of Uncertain Significance (VUS) Using an ACMG/AMP Model Incorporating a Homology-Directed Repair (HDR) Functional Assay

PURPOSE

The identification of variants of uncertain significance (VUS) in the BRCA1 and BRCA2 genes by hereditary cancer testing poses great challenges for the clinical management of variant carriers. The ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology) variant classification framework, which incorporates multiple sources of evidence, has the potential to establish the clinical relevance of many VUS. We sought to classify the clinical relevance of 133 single-nucleotide substitution variants encoding missense variants in the DNA-binding domain (DBD) of BRCA2 by incorporating results from a validated functional assay into an ACMG/AMP-variant classification model from a hereditary cancer-testing laboratory.

EXPERIMENTAL DESIGN

The 133 selected VUS were evaluated using a validated homology-directed double-strand DNA break repair (HDR) functional assay. Results were combined with clinical and genetic data from variant carriers in a rules-based variant classification model for BRCA2.

RESULTS

Of 133 missense variants, 44 were designated as non-functional and 89 were designated as functional in the HDR assay. When combined with genetic and clinical information from a single diagnostic laboratory in an ACMG/AMP-variant classification framework, 66 variants previously classified by the diagnostic laboratory were correctly classified, and 62 of 67 VUS (92.5%) were reclassified as likely pathogenic (n = 22) or likely benign (n = 40). In total, 44 variants were classified as pathogenic/likely pathogenic, 84 as benign/likely benign, and 5 remained as VUS.

CONCLUSIONS

Incorporation of HDR functional analysis into an ACMG/AMP framework model substantially improves BRCA2 VUS re-classification and provides an important tool for determining the clinical relevance of individual BRCA2 VUS.

Strong functional data for pathogenicity or neutrality classify BRCA2 DNA-binding-domain variants of uncertain significance

Determination of the clinical relevance of rare germline variants of uncertain significance (VUSs) in the BRCA2 cancer predisposition gene remains a challenge as a result of limited availability of data for use in classification models. However, laboratory-based functional data derived from validated functional assays of known sensitivity and specificity may influence the interpretation of VUSs. We evaluated 252 missense VUSs from the BRCA2 DNA-binding domain by using a homology-directed DNA repair (HDR) assay and identified 90 as non-functional and 162 as functional. The functional assay results were integrated with other available data sources into an ACMG/AMP rules-based classification framework used by a hereditary cancer testing laboratory. Of the 186 missense variants observed by the testing laboratory, 154 were classified as VUSs without functional data. However, after applying protein functional data, 86% (132/154) of the VUSs were reclassified as either likely pathogenic/pathogenic (39/132) or likely benign/benign (93/132), which impacted testing results for 1,900 individuals. These results indicate that validated functional assay data can have a substantial impact on VUS classification and associated clinical management for many individuals with inherited alterations in BRCA2.

Norepinephrine-Induced DNA Damage in Ovarian Cancer Cells

Multiple studies have shown that psychological distress in epithelial ovarian cancer (EOC) patients is associated with worse quality of life and poor treatment adherence. This may influence chemotherapy response and prognosis. Moreover, although stress hormones can reduce cisplatin efficacy in EOC treatment, their effect on the integrity of DNA remains poorly understood. In this study, we investigated whether norepinephrine and epinephrine can induce DNA damage and modulate cisplatin-induced DNA damage in three EOC cell lines. Our data show that norepinephrine and epinephrine exposure led to increased nuclear γ-H2AX foci formation in EOC cells, a marker of double-strand DNA breaks. We further characterized norepinephrine-induced DNA damage by subjecting EOC cells to alkaline and neutral comet assays. Norepinephrine exposure caused DNA double-strand breaks, but not single-strand breaks. Interestingly, pre-treatment with propranolol abrogated norepinephrine-induced DNA damage indicating that its effects may be mediated by β-adrenergic receptors. Lastly, we determined the effects of norepinephrine on cisplatin-induced DNA damage. Our data suggest that norepinephrine reduced cisplatin-induced DNA damage in EOC cells and that this effect may be mediated independently of β-adrenergic receptors. Taken together, these results suggest that stress hormones can affect DNA integrity and modulate cisplatin resistance in EOC cells.

Dual Targeting of WEE1 and PLK1 by AZD1775 Elicits Single Agent Cellular Anticancer Activity

Inhibition of the WEE1 tyrosine kinase enhances anticancer chemotherapy efficacy. Accordingly, the WEE1 inhibitor AZD1775 (previously MK-1775) is currently under evaluation in clinical trials for cancer in combination with chemotherapy. AZD1775 has been reported to display high selectivity and is therefore used in many studies as a probe to interrogate WEE1 biology. However, AZD1775 also exhibits anticancer activity as a single agent although the underlying mechanism is not fully understood. Using a chemical proteomics approach, we here describe a proteome-wide survey of AZD1775 targets in lung cancer cells and identify several previously unknown targets in addition to WEE1. In particular, we observed polo-like kinase 1 (PLK1) as a new target of AZD1775. Importantly, in vitro kinase assays showed PLK1 and WEE1 to be inhibited by AZD1775 with similar potency. Subsequent loss-of-function experiments using RNAi for WEE1 and PLK1 suggested that targeting PLK1 enhances the pro-apoptotic and antiproliferative effects observed with WEE1 knockdown. Combination of RNAi with AZD1775 treatment suggested WEE1 and PLK1 to be the most relevant targets for mediating AZD1775's anticancer effects. Furthermore, disruption of WEE1 by CRISPR-Cas9 sensitized H322 lung cancer cells to AZD1775 to a similar extent as the potent PLK1 inhibitor BI-2536 suggesting a complex crosstalk between PLK1 and WEE1. In summary, we show that AZD1775 is a potent dual WEE1 and PLK1 inhibitor, which limits its use as a specific molecular probe for WEE1. However, PLK1 inhibition makes important contributions to the single agent mechanism of action of AZD1775 and enhances its anticancer effects.

Integration of Population-Level Genotype Data with Functional Annotation Reveals Over-Representation of Long Noncoding RNAs at Ovarian Cancer Susceptibility Loci

BACKGROUND

Genome-wide association studies (GWAS) have identified multiple loci associated with epithelial ovarian cancer (EOC) susceptibility, but further progress requires integration of epidemiology and biology to illuminate true risk loci below genome-wide significance levels (P < 5 × 10-8). Most risk SNPs lie within non-protein-encoding regions, and we hypothesize that long noncoding RNA (lncRNA) genes are enriched at EOC risk regions and represent biologically relevant functional targets.

METHODS

Using imputed GWAS data from about 18,000 invasive EOC cases and 34,000 controls of European ancestry, the GENCODE (v19) lncRNA database was used to annotate SNPs from 13,442 lncRNAs for permutation-based enrichment analysis. Tumor expression quantitative trait locus (eQTL) analysis was performed for sub-genome-wide regions (1 × 10-5 > P > 5 × 10-8) overlapping lncRNAs.

RESULTS

Of 5,294 EOC-associated SNPs (P < 1.0 × 10-5), 1,464 (28%) mapped within 53 unique lncRNAs and an additional 3,484 (66%) SNPs were correlated (r2 > 0.2) with SNPs within 115 lncRNAs. EOC-associated SNPs comprised 130 independent regions, of which 72 (55%) overlapped with lncRNAs, representing a significant enrichment (P = 5.0 × 10-4) that was more pronounced among a subset of 5,401 lncRNAs with active epigenetic regulation in normal ovarian tissue. EOC-associated lncRNAs and their putative promoters and transcription factors were enriched for biologically relevant pathways and eQTL analysis identified five novel putative risk regions with allele-specific effects on lncRNA gene expression.

CONCLUSIONS

lncRNAs are significantly enriched at EOC risk regions, suggesting a mechanistic role for lncRNAs in driving predisposition to EOC.

IMPACT

lncRNAs represent key candidates for integrative epidemiologic and functional studies. Further research on their biologic role in ovarian cancer is indicated. Cancer Epidemiol Biomarkers Prev; 26(1); 116-25. ©2016 AACR.

Inherited variants affecting RNA editing may contribute to ovarian cancer susceptibility: results from a large-scale collaboration

RNA editing in mammals is a form of post-transcriptional modification in which adenosine is converted to inosine by the adenosine deaminases acting on RNA (ADAR) family of enzymes. Based on evidence of altered ADAR expression in epithelial ovarian cancers (EOC), we hypothesized that single nucleotide polymorphisms (SNPs) in ADAR genes modify EOC susceptibility, potentially by altering ovarian tissue gene expression. Using directly genotyped and imputed data from 10,891 invasive EOC cases and 21,693 controls, we evaluated the associations of 5,303 SNPs in ADAD1, ADAR, ADAR2, ADAR3, and SND1. Unconditional logistic regression was used to estimate odds ratios (OR) and 95% confidence intervals (CI), with adjustment for European ancestry. We conducted gene-level analyses using the Admixture Maximum Likelihood (AML) test and the Sequence-Kernel Association test for common and rare variants (SKAT-CR). Association analysis revealed top risk-associated SNP rs77027562 (OR (95% CI)= 1.39 (1.17-1.64), P=1.0x10-4) in ADAR3 and rs185455523 in SND1 (OR (95% CI)= 0.68 (0.56-0.83), P=2.0x10-4). When restricting to serous histology (n=6,500), the magnitude of association strengthened for rs185455523 (OR=0.60, P=1.0x10-4). Gene-level analyses revealed that variation in ADAR was associated (P<0.05) with EOC susceptibility, with PAML=0.022 and PSKAT-CR=0.020. Expression quantitative trait locus analysis in EOC tissue revealed significant associations (P<0.05) with ADAR expression for several SNPs in ADAR, including rs1127313 (G/A), a SNP in the 3' untranslated region. In summary, germline variation involving RNA editing genes may influence EOC susceptibility, warranting further investigation of inherited and acquired alterations affecting RNA editing.

A high frequency of BRCA mutations in young black women with breast cancer residing in Florida

BACKGROUND

Black women are disproportionately affected with triple-negative breast cancer and have relatively poor survival. To the authors' knowledge, it is not known to what extent differences in the clinical presentation of breast cancer between non-Hispanic white women and black women can be accounted for by the presence of mutations in the BRCA1 and BRCA2 genes. The authors sought to evaluate the frequency of BRCA pathogenic variants in a population-based sample of young black women with breast cancer.

METHODS

Black women diagnosed with invasive breast cancer at age ≤50 years from 2009 to 2012 were recruited to the study through the Florida Cancer Registry. Participants underwent genetic counseling, completed a study questionnaire, and consented to release of their medical records. Saliva specimens were collected for BRCA sequencing and large rearrangement testing through multiplex ligation-dependent probe amplification.

RESULTS

A DNA sample was evaluated for 396 women, 49 of whom (12.4%) had a mutation in BRCA1 or BRCA2. Eight recurrent mutations accounted for 49% of all pathogenic variants.

CONCLUSIONS

To the authors' knowledge, the prevalence of BRCA mutations among the Florida-based sample of young black women with breast cancer in the current study exceeds that previously reported for non-Hispanic white women. It is appropriate to recommend BRCA testing in all young black women with invasive breast cancer.

Epithelial-Mesenchymal Transition (EMT) Gene Variants and Epithelial Ovarian Cancer (EOC) Risk

Epithelial-mesenchymal transition (EMT) is a process whereby epithelial cells assume mesenchymal characteristics to facilitate cancer metastasis. However, EMT also contributes to the initiation and development of primary tumors. Prior studies that explored the hypothesis that EMT gene variants contribute to epithelial ovarian carcinoma (EOC) risk have been based on small sample sizes and none have sought replication in an independent population. We screened 15,816 single-nucleotide polymorphisms (SNPs) in 296 genes in a discovery phase using data from a genome-wide association study of EOC among women of European ancestry (1,947 cases and 2,009 controls) and identified 793 variants in 278 EMT-related genes that were nominally (P < 0.05) associated with invasive EOC. These SNPs were then genotyped in a larger study of 14,525 invasive-cancer patients and 23,447 controls. A P-value <0.05 and a false discovery rate (FDR) <0.2 were considered statistically significant. In the larger dataset, GPC6/GPC5 rs17702471 was associated with the endometrioid subtype among Caucasians (odds ratio (OR) = 1.16, 95% CI = 1.07-1.25, P = 0.0003, FDR = 0.19), whereas F8 rs7053448 (OR = 1.69, 95% CI = 1.27-2.24, P = 0.0003, FDR = 0.12), F8 rs7058826 (OR = 1.69, 95% CI = 1.27-2.24, P = 0.0003, FDR = 0.12), and CAPN13 rs1983383 (OR = 0.79, 95% CI = 0.69-0.90, P = 0.0005, FDR = 0.12) were associated with combined invasive EOC among Asians. In silico functional analyses revealed that GPC6/GPC5 rs17702471 coincided with DNA regulatory elements. These results suggest that EMT gene variants do not appear to play a significant role in the susceptibility to EOC.

Abstract 3779: Mutational analysis of MCPH1 C-terminal tandem BRCT domain reveals residues essential for cell cycle arrest

In this study, the C-terminal tandem BRCT domain of human microcephalin 1 protein (MCPH1) was mutagenized in Saccharomyces cerevisiae yeast to identify residues critical for the cell cycle arrest. Deleterious variants in MCPH1 causing the loss of the protein function are associated with primary microcephaly, characterized by decreased cerebral cortex size and mild mental retardation. The tandem BRCT domain of MCPH1 (amino acids 640-833) recognizes phospho-serine/threonine motifs, including □-H2AX, necessary for DNA damage response and cell cycle regulation. Expression of this region of human MCPH1 tethered to DNA in yeast through the Gal4 DNA binding domain (and not through the interaction with the Gal4 activation domain), results in growth inhibition and a small colony phenotype. To detect the essential residues of the MCPH1 tandem BRCT, mutations were randomly introduced into this region using error-prone polymerase chain reaction. The mutants were then transformed into yeast and transformants showing abrogation of the small colony phenotype were isolated and the specific mutations were assessed by sequencing. Screening revealed 34 missense, 4 nonsense, and 8 frameshift variants, and one large deletion of 72 base pairs. The 34 missense variants were further analyzed in silico by alignment with the BRCA1 tandem BRCT. Out of 34 missense variants, four (T694A, L755P, F756V, and S819P) were identified in two or more colonies. One of the mutated residues (T653) is involved in direct hydrogen bonding with □-H2AX, which is likely disrupted by the amino acid change induced during mutagenesis (T653I). Interestingly, when aligned with BRCA1, 16 (47%) of MCPH1 missense variants matched to a corresponding site in BRCA1 previously reported as a missense variant with a functional impact. MCPH1 residues 653, 756, and 819 all corresponded to amino acids in BRCA1 known for their likely pathogenicity. Thus, this study identifies functional determinants in MCPH1 C-terminal domain potentially involved in cell cycle regulation. Taken together, our results suggest that variants in BRCT domain containing proteins, can be clinically annotated by making comparative alignments with the conserved residues of BRCA1 BRCT. Structural inference using BRCT paralogs might aid in the clinical annotation for variants lacking genetic data.

Citation Format: Volha A. Golubeva, Nicholas T. Woods, Alvaro N.A. Monteiro. Mutational analysis of MCPH1 C-terminal tandem BRCT domain reveals residues essential for cell cycle arrest. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3779. doi:10.1158/1538-7445.AM2015-3779

Abstract 5483: Implications of the type of BRCA1 germline mutation in the treatment of patients with hereditary breast cancer

Carrying an inherited mutation in BRCA1 or BRCA2 genes significantly increases individual´s lifetime risk to develop breast or ovarian cancer. However, there are considerable differences in disease manifestation among mutation carriers, suggesting the existence of other factors which could modify the risk of cancer development.

Since BRCA1 is an important component of DNA repair, BRCA1-deficient cells have to rely on other members of the DNA repair machinery. This makes them sensitive to drugs which target specific repair pathways, such as inhibitors of poly (ADP-ribose) polymerase (PARP). Several PARP inhibitors are currently being tested in preclinical or clinical trials, either as a monotherapy or in combination with chemo- or radiotherapy. Taking into account the promising results in patients with germline mutation in BRCA1 or BRCA2 genes, we aimed to investigate which BRCA1 mutation carriers, depending on the mutation type, might benefit from treatment with PARP inhibitors the most. In addition, we were also interested in identifying markers of sensitivity/resistance to PARP inhibitors.

We have used lymphoblastoid cell lines (LCLs) derived from lymphocytes of healthy women heterozygous for different BRCA1 mutations and healthy women from the same families with no mutation. In total, 23 LCLs were characterized according to their DNA repair capacity, growth rate, gene/miRNA expression and sensitivity to PARP inhibitors. Our preliminary results have shown significantly higher sensitivity to PARP inhibitor olaparib in cells harbouring missense mutation in comparison to cells with truncating or no mutation. The ongoing functional studies on these BRCA1 missense variants indicate that these mutations could act in a dominant negative manner. Importantly, the observed differences in sensitivity to olaparib among mutation carriers could be also relevant for recently proposed use of PARP inhibitors as prophylactic agent for mutation carriers.

Our ongoing work may help us to better understand the mechanisms of action of PARP inhibitors and lead to improvement of therapeutic strategies for BRCA1-associated cancers with extension to other tumors.

Citation Format: Tereza Vaclova, Nicholas T. Woods, Fernando Setién, José María García Bueno, José Antonio Macías, Alicia Barroso, Miguel Urioste, Manel Esteller, Alvaro N.A. Monteiro, Javier Benítez, Ana Osorio. Implications of the type of BRCA1 germline mutation in the treatment of patients with hereditary breast cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5483. doi:10.1158/1538-7445.AM2014-5483

Abstract 3285: Functional analysis of the 9p22 locus implicates the transcriptional regulation of BNC2 as a mechanism in ovarian cancer predisposition

An ovarian cancer Genome Wide Association Study (GWAS) identified 9p22.2 as a novel susceptibility locus with the most statistically significant single nucleotide polymorphisms (SNPs) located in an intergenic region near the Basonuclin 2 (BNC2) gene, which codes for a putative transcription regulator containing three pairs of zinc finger (ZF) domains. The minor alleles are protective in terms of ovarian cancer susceptibility. However, the molecular mechanisms by which these SNPs modify susceptibility remain largely unknown. The significant SNPs in the 9p22.2 locus lie in non-coding regions and therefore are hypothesized to affect the activity of regulatory elements and modify the expression of a target gene(s). In order to test this hypothesis we conducted fine mapping for the locus which delimited a ∼74kb region containing SNPs with a p-value less than 10-8. FAIRE-Seq and ChIP-Seq experiments for histone markers conducted in immortalized ovarian surface epithelial cells (IOSE) and fallopian tube epithelial cells (IFTE) were used to prioritize functional SNP candidates which overlap with regulatory elements. Luciferase assays tested the ability of these regulatory elements to activate transcription. Chromosome conformation capture (3C) experiments demonstrate a physical interaction between the BNC2 promoter and candidate regulatory elements containing risk-associated SNPs. Methylation Quantification at Trait Loci (mQTL) revealed an association between decreased methylation at the BNC2 promoter and the protective minor alleles. Expression analysis shows decreased expression of BNC2 in cancer versus normal tissue implicating tumor suppressor function of BNC2. Therefore the protective minor allele likely increases expression of BNC2 which in turn contains tumor suppressing properties that decrease ovarian cancer risk. BNC2 protein is in complex with transcriptional regulatory proteins, in particular the NURD complex components. Moreover, BNC2 acts as a transcriptional repressor in in vitro transfection assays indicating that it functions in transcriptional repression. We then used protein binding microarrays and CHIP-Seq experiments to identify its putative DNA binding motifs and its downstream target genes. Analysis of this data suggests that BNC2 functions in a regulatory transcription network that impacts on genes implicated in ovarian cancer with enrichment for genes in the TGF-beta response pathway.

Citation Format: Melissa A. Buckley, Howard C. Shen, Gustavo A. Mendoza-Fandino, Nicholas T. Woods, Anxhela Gjyshi, Juliet French, Kate Lawrenson, Honglin Song, Jonathan Tyrer, Renato S. Carvalho, Alexandra Valle, Ann Chen, Sean Yoder, Gregory Bloom, Ya-Yu Tsai, Ally Yang, Timothy R. Hughes, Xiaotao Qu, Mine Cicek, Melissa Larson, Ellen Goode, Brooke Fridley, Susan Ramus, Georgia Chenevix-Trench, Paul Pharoah, Thomas A. Sellers, Simon Gayther, Alvaro N.A. Monteiro, Ovarian Cancer Association Consortium. Functional analysis of the 9p22 locus implicates the transcriptional regulation of BNC2 as a mechanism in ovarian cancer predisposition. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3285. doi:10.1158/1538-7445.AM2014-3285

Abstract 946: Exome genotyping array identifies rare and low-frequency variants that may be associated with ovarian cancer risk

Background: Common genetic variants identified by genome-wide association studies and follow-up genotyping initiatives only explain a small proportion of the heritability of epithelial ovarian cancer (EOC). We hypothesized that some of the missing heritability may be explained by rare (minor allele frequency (MAF) &lt;0.5%) and low-frequency (MAF 0.5-5%) protein-coding variants that are not well captured by genotyping arrays that focus on common variants. Methods: To examine the association between uncommon variants and EOC susceptibility, we genotyped 7,060 EOC cases and 6,712 controls from the Ovarian Cancer Association Consortium using the Affymetrix Axiom Exome Genotyping Array. This platform contains 300,785 putative functional coding variants selected from exome sequences of 12,000+ individuals representing multiple ethnicities and complex traits. After performing quality control (QC), we used unconditional logistic regression treating the number of minor alleles carried as an ordinal variable (log-additive model) to evaluate SNP-EOC risk associations. Genotype cluster plots were visually inspected for top-ranking variants to determine assay success, and allele frequencies of samples from the 1000 Genomes Project and other cohorts were evaluated for QC purposes. Results: A total of 13,318 samples (97%) passed QC, and 12,779 eligible samples (6,293 invasive serous and endometrioid cases and 6,486 controls) were included in the analyses. 280,737 (93%) of the 300,785 attempted markers were successfully genotyped and had call rates &gt;90%. After removing 31,436 monomorphic markers, the 249,301 remaining markers were included in association analyses. We confirmed variants at previously reported EOC susceptibility loci (9p22, 3q25, 17cen-q21.3, and 8q24), with p-values between 10-5 and 10-11. Several correlated low-frequency non-synonymous variants (MAF=5%) residing in a novel EOC susceptibility gene at 3q25.31 were risk-associated. The most significant variant at 3q25.31 had an OR=1.36 and p = 5.58x10-8. Also noteworthy is a rare variant at 15q15.1-q21.1 (MAF=0.5%) that introduces a stop codon in a gene belonging to the tyrosine kinase family (OR=0.39, CI=0.26-0.58, p = 4.52x10-6). We also identified a more common synonymous coding variant in a phosphatase at 6q21.3 that was associated with increased risk (OR=1.22, CI=1.13-1.33, p = 1.84x10-6, MAF=9.6%). Population stratification and gene-based analyses are underway to further examine the impact of the newly-identified variants on EOC risk. A meta-analysis to include data from an additional 2104 EOC cases and 2516 controls genotyped with Illumina's HumanExome Beadchip rare variant array is also underway. Functional analysis of the most promising variants will follow. Conclusions: Preliminary data from this large-scale study reveals novel rare and low-frequency variants that may influence susceptibility to epithelial ovarian cancer.

Citation Format: Jennifer Permuth-Wey, Y. Ann Chen, Zhihua Chen, Andrew Berchuck, Georgia Chenevix-Trench, Jennifer Doherty, Simon Gayther, Ellen L. Goode, Edwin Iversen, Alvaro N.A. Monteiro, Leigh Pearce, Paul D.P. Pharoah, Catherine M. Phelan, Ailith Pirie, Susan Ramus, Mary Ann Rossing, Joellen M. Schildkraut, Thomas A. Sellers, on behalf of the Ovarian Cancer Association Consortium. Exome genotyping array identifies rare and low-frequency variants that may be associated with ovarian cancer risk. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 946. doi:10.1158/1538-7445.AM2014-946

Identification and molecular characterization of a new ovarian cancer susceptibility locus at 17q21.31

Epithelial ovarian cancer (EOC) has a heritable component that remains to be fully characterized. Most identified common susceptibility variants lie in non-protein-coding sequences. We hypothesized that variants in the 3' untranslated region at putative microRNA (miRNA)-binding sites represent functional targets that influence EOC susceptibility. Here, we evaluate the association between 767 miRNA-related single-nucleotide polymorphisms (miRSNPs) and EOC risk in 18,174 EOC cases and 26,134 controls from 43 studies genotyped through the Collaborative Oncological Gene-environment Study. We identify several miRSNPs associated with invasive serous EOC risk (odds ratio=1.12, P=10(-8)) mapping to an inversion polymorphism at 17q21.31. Additional genotyping of non-miRSNPs at 17q21.31 reveals stronger signals outside the inversion (P=10(-10)). Variation at 17q21.31 is associated with neurological diseases, and our collaboration is the first to report an association with EOC susceptibility. An integrated molecular analysis in this region provides evidence for ARHGAP27 and PLEKHM1 as candidate EOC susceptibility genes.

Epigenetic analysis leads to identification of HNF1B as a subtype-specific susceptibility gene for ovarian cancer

HNF1B is overexpressed in clear cell epithelial ovarian cancer, and we observed epigenetic silencing in serous epithelial ovarian cancer, leading us to hypothesize that variation in this gene differentially associates with epithelial ovarian cancer risk according to histological subtype. Here we comprehensively map variation in HNF1B with respect to epithelial ovarian cancer risk and analyse DNA methylation and expression profiles across histological subtypes. Different single-nucleotide polymorphisms associate with invasive serous (rs7405776 odds ratio (OR)=1.13, P=3.1 × 10(-10)) and clear cell (rs11651755 OR=0.77, P=1.6 × 10(-8)) epithelial ovarian cancer. Risk alleles for the serous subtype associate with higher HNF1B-promoter methylation in these tumours. Unmethylated, expressed HNF1B, primarily present in clear cell tumours, coincides with a CpG island methylator phenotype affecting numerous other promoters throughout the genome. Different variants in HNF1B associate with risk of serous and clear cell epithelial ovarian cancer; DNA methylation and expression patterns are also notably distinct between these subtypes. These findings underscore distinct mechanisms driving different epithelial ovarian cancer histological subtypes.

Abstract IA19: The GAME-ON (Genetic Associations and Mechanisms in Oncology) Consortium: Assessing the functional relevance of genetic variation

Recently, significant advances in genetics, in particular in genome-wide association studies (GWAS), have uncovered a large number of chromosomal loci associated with cancer risk. Despite these advances the determination of the molecular mechanism behind the detected associations has proven to be a significant challenge. The design of most GWAS genotyping chips take advantage of well characterized tagging single nucleotide polymorphisms (SNPs). These “tags” represent specific proxy markers for a series of other SNPs in high linkage disequilibrium with the tagging SNP in a defined chromosomal region. While the use of tagging SNPs result in reproducible and robust signals during genotyping and minimize the number of SNPs to be tested, the expectation is that they may not necessarily constitute the causal SNP, the nucleotide change that result in a relevant biological activity responsible for cancer predisposition.

Identification of predisposition loci in prostate, ovary, and breast have been accelerated by the COGS (Collaborative Oncologic Gene-Environment Study) project which typed 200,000 SNPs and genotyped an unprecedented number of cancer cases and controls (˜200,000). The GAME-ON (Genetic Associations and Mechanisms in Oncology) consortium has poured over GWAS data for prostate, ovary, breast, lung, and colorectal cancers to develop systematic procedures to dissect functional contribution of SNPs and their target genes. Here I describe our experience in conducting functional analyses for these loci, focusing on ovarian cancer susceptibility loci.

The overall approach can be loosely divided in three stages: in the first we use the most significant SNP found in GWAS analyses or meta-analyses as a starting point to interrogate other candidate functional SNPs in the region. The second stage explores potential target genes in the region. Finally, we focus on tying the candidate functional SNP to the candidate target gene. This final stage may also focus on, depending on the availability of in vivo models, attempts to uncover direct evidence for the participation of the SNP/target gene pairs in the mechanism of oncogenesis. Although in some cases the analytic approaches and tools might be specific to the cancer in question, we feel that the main framework can be utilized for different cancers. Most importantly, perhaps, are the lessons learned during this process as well as identifying the limitations and challenges that lay ahead.

Citation Format: Alvaro N.A. Monteiro. The GAME-ON (Genetic Associations and Mechanisms in Oncology) Consortium: Assessing the functional relevance of genetic variation. [abstract]. In: Proceedings of the AACR Special Conference on Post-GWAS Horizons in Molecular Epidemiology: Digging Deeper into the Environment; 2012 Nov 11-14; Hollywood, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2012;21(11 Suppl):Abstract nr IA19.

Abstract 1649: Genome-wide association study of copy number variations in serous epithelial ovarian cancer susceptibility

DNA copy number variations (CNVs) are a significant and ubiquitous source of human genetic variation. However, the influence of CNVs on cancer susceptibility remains poorly understood. Out of 83 genome-wide association studies (GWAS) on cancer to date, only a few studies found significant associations on germline CNVs and cancer. Here we analyzed data from our ongoing two-stage GWAS of four North American case-control studies to test the hypothesis that CNVs in germline DNA from peripheral blood lymphocytes may serve as risk factors for epithelial ovarian cancer (EOC). To reduce disease heterogeneity, we focused on the subset of cases with serous histology. The analysis was therefore based on 942 serous ovarian cancer patients and 1,682 healthy controls who were genotyped using the Illumina 610K quad array. Subjects with extreme noise and genomic waviness in log R ratio (LR) were excluded prior to segmentation; principal component analysis was performed to adjust for batch effects. CNV segmentation was performed on LR data from 22 autosomes using circular binary segmentation embedded in the Copy Number Analysis Module from Golden Helix SNP Variation Suite version 7. Copy number segment covariates were discretized based on the thresholds that signify a transition between copy number states (deletion/no deletion; duplication/no duplication) after the segmentation. Unconditional logistic regression on a log-additive model was used to evaluate the association between copy number states and serous EOC risk after adjusting for study sites. By comparing single marker copy number states at 388,958 SNPs on 22 autosomes, we observed a total of 134 SNPs significantly associated with risk of serous EOC with a p value below 10−6. Associations with deletion polymorphisms were observed on chromosomes 7, 8, 14, and 18 when controlling for false discovery rate at 1%; no duplication polymorphisms were significant. We observed a large deletion at chromosome 14 that occurred in 8.9% of cases but in only 3.9% of controls, with a p value of 5.59×10−8 (Odds Ratio (OR): 2.56, 95% confidence interval (CI): 1.82-3.60). Another common deletion on chromosome 7 occurred in 8.8% of cases and only 4.3% of controls (p=3.83×10−6; OR: 2.23, 95% CI: 1.60-3.10). Two additional regions on chromosomes 8 and 18 with deletion events less than 5% were also identified. Women who harbored the deletion on chromosome 8 were at lower risk of developing serous ovarian cancer (p=4.83×10−8; OR: 0.04, 95% CI: 0.01-0.30). Women who carried the deletion on chromosome 18 had an increased risk for serous EOC (p=9.04×10−7; OR: 7.26, 95% CI: 2.94-17.97). Further validation of these four regions using independent data sets is currently underway. In summary, this is the largest reported genome-wide study of CNVs and serous EOC risk. These preliminary results suggested that germline CNVs may play an important role in ovarian cancer susceptibility.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1649. doi:1538-7445.AM2012-1649

LIN28B polymorphisms influence susceptibility to epithelial ovarian cancer

Defective microRNA (miRNA) biogenesis contributes to the development and progression of epithelial ovarian cancer (EOC). In this study, we examined the hypothesis that single nucleotide polymorphisms (SNP) in miRNA biogenesis genes may influence EOC risk. In an initial investigation, 318 SNPs in 18 genes were evaluated among 1,815 EOC cases and 1,900 controls, followed up by a replicative joint meta-analysis of data from an additional 2,172 cases and 3,052 controls. Of 23 SNPs from 9 genes associated with risk (empirical P < 0.05) in the initial investigation, the meta-analysis replicated 6 SNPs from the DROSHA, FMR1, LIN28, and LIN28B genes, including rs12194974 (G>A), an SNP in a putative transcription factor binding site in the LIN28B promoter region (summary OR = 0.90, 95% CI: 0.82-0.98; P = 0.015) which has been recently implicated in age of menarche and other phenotypes. Consistent with reports that LIN28B overexpression in EOC contributes to tumorigenesis by repressing tumor suppressor let-7 expression, we provide data from luciferase reporter assays and quantitative RT-PCR to suggest that the inverse association among rs12194974 A allele carriers may be because of reduced LIN28B expression. Our findings suggest that variants in LIN28B and possibly other miRNA biogenesis genes may influence EOC susceptibility.

Identification of Filamin A as a BRCA1-interacting protein required for efficient DNA repair

The product of the breast and ovarian cancer susceptibility gene BRCA1 has been implicated in several aspects of the DNA damage response but its biochemical function in these processes has remained elusive. In order to probe BRCA1 function we conducted a yeast two-hybrid screening to identify interacting partners to a conserved motif (Motif 6) in the central region of BRCA1. Here we report the identification of the actin-binding protein Filamin A (FLNA) as BRCA1 partner and demonstrate that FLNA is required for efficient regulation of early stages of DNA repair processes. Cells lacking FLNA display a diminished BRCA1 IR-induced focus formation and a delayed kinetics of Rad51 focus formation. In addition, our data also demonstrate that FLNA is required to stabilize the interaction between components of the DNA-PK holoenzyme, DNA-PKcs and Ku86 in a BRCA1-independent fashion. Our data is consistent with a model in which absence of FLNA compromises homologous recombination and non-homologous end joining. Our findings have implications for the response to irradiation induced DNA damage.

In situ protein expression of RRM1, ERCC1, and BRCA1 in metastatic breast cancer patients treated with gemcitabine-based chemotherapy

Ribonucleotide reductase 1 (RRM1) is a determinant of gemcitabine efficacy in non-small-cell lung cancer and pancreatic cancer. We investigated the protein levels of RRM1 and two other DNA repair enzymes, ERCC1 and BRCA1, in 55 metastatic breast cancer (MBC) patients undergoing gemcitabine-based chemotherapy. With automated in situ protein quantification (AQUA v1.6), the average scores for RRM1, ERCC1, and BRCA1 ranged from 245.6-2774.1, 74.0-410.3, and 54.4-1833.1, respectively. They were significantly associated with each other (Spearman's rho > or = .36; p < or = .007). Given their pattern of distribution, RRM1 and BRCA1 are potentially suitable markers for clinical decision making in MBC.

Three-color intranuclear staining for measuring mitosis and apoptosis in cells transfected with a GFP-tagged histone

Green fluorescent protein (GFP) has become a powerful tool for monitoring the expression of transfected genes by flow cytometry including GFP-tagged histones for tracking chromatin and elucidating histone function. We describe here a method for simultaneous detection of three nucleus-localized signals: a GFP-tagged histone, DNA content and detection of phosphorylated histone H3, which labels mitotic cells. We also demonstrate another application of this method for simultaneous detection of a GFP-tagged histone, DNA content, and cleaved caspase-3.

Somatic alterations in brain tumors

Mutations in TP53 and RB1 have been shown to participate in the development of malignant brain tumors. Emerging evidence shows that mutations are involved in LGI1 in brain tumor progression. Herein we present data from the sequencing of a series of high- and low-grade gliomas with matched normal DNA. We report on 35 unique missense mutations in TP53, RB1 and LGI1 genes and use available information for each mutation in order to classify them as likely to be 'driver' or 'passenger' mutations. The identification of putatively deleterious mutations in LGI1 supports the notion that this locus may play a role in brain cancer development.

Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis

Germ line inactivating mutations in BRCA1 confer susceptibility for breast and ovarian cancer. However, the relevance of the many missense changes in the gene for which the effect on protein function is unknown remains unclear. Determination of which variants are causally associated with cancer is important for assessment of individual risk. We used a functional assay that measures the transactivation activity of BRCA1 in combination with analysis of protein modeling based on the structure of BRCA1 BRCT domains. In addition, the information generated was interpreted in light of genetic data. We determined the predicted cancer association of 22 BRCA1 variants and verified that the common polymorphism S1613G has no effect on BRCA1 function, even when combined with other rare variants. We estimated the specificity and sensitivity of the assay, and by meta-analysis of 47 variants, we show that variants with <45% of wild-type activity can be classified as deleterious whereas variants with >50% can be classified as neutral. In conclusion, we did functional and structure-based analyses on a large series of BRCA1 missense variants and defined a tentative threshold activity for the classification missense variants. By interpreting the validated functional data in light of additional clinical and structural evidence, we conclude that it is possible to classify all missense variants in the BRCA1 COOH-terminal region. These results bring functional assays for BRCA1 closer to clinical applicability.

Cancer risks in first degree relatives of BRCA1 mutation carriers: effects of mutation and proband disease status

BACKGROUND

Mutations in the BRCA1 (MIM 113705) gene are found in many families with multiple cases of breast and ovarian cancer, and women with a BRCA1 mutation are at significantly higher risk of developing breast and ovarian cancer than are the general public.

METHODS

We obtained blood samples and pedigree information from 3568 unselected cases of early-onset breast cancer and 609 unselected patients with ovarian cancer from hospitals throughout Poland. Genetic testing was performed for three founder BRCA1 mutations. We also calculated the risk of breast and ovarian cancer to age 75 in the first degree relatives of carriers using Kaplan-Meier methods.

RESULTS

The three founder BRCA1 mutations were identified in 273 samples (187 with 5382insC, 22 with 4153delA, and 64 with C61G). A mutation was present in 4.3% of patients with breast cancer and 12.3% of patients with ovarian cancer. The overall risk of breast cancer to age 75 in relatives was 33% and the risk of ovarian cancer was 15%. The risk for breast cancer was 42% higher among first degree relatives of carriers of the C61G missense mutation compared to other mutations (HR = 1.42; p = 0.10) and the risk for ovarian cancer was lower than average (OR = 0.26; p = 0.03). Relatives of women diagnosed with breast cancer had a higher risk of breast cancer than relatives of women diagnosed with ovarian cancer (OR = 1.7; p = 0.03).

CONCLUSIONS

The risk of breast cancer in female relatives of women with a BRCA1 mutation depends on whether the proband was diagnosed with breast or ovarian cancer.

Yeast-based assays for detection and characterization of mutations in BRCA1

Germ-line mutations in BRCA1 account for the majority of families with breast and ovarian cancer predisposition. BRCA1 encodes a 1,863 amino acid protein with no ascribed function. Due to its size and the fact that mutations are evenly scattered along the sequence, screening for mutations is particularly challenging. Here we review recently published yeast-based assays that may form the basis of an alternative diagnostic test for BRCA1. Although individually limited, these assays may, when combined, become a useful method to screen for cancer predisposing mutations. In any event, the yeast-based assays could complement results from direct sequencing providing functional information about unique mutations.

Functional analysis of BRCA1 C-terminal missense mutations identified in breast and ovarian cancer families

Germline mutations in the breast and ovarian cancer susceptibility gene BRCA1 are responsible for the majority of cases involving hereditary breast and ovarian cancer. Whereas all truncating mutations are considered as functionally deleterious, most of the missense variants identified to date cannot be readily distinguished as either disease-associated mutations or benign polymorphisms. The C-terminal domain of BRCA1 displays an intrinsic transactivation activity, and mutations linked to disease predisposition have been shown to confer loss of such activity in yeast and mammalian cells. In an attempt to clarify the functional importance of the BRCA1 C-terminus as a transcription activator in cancer predisposition, we have characterized the effect of C-terminal germline variants identified in Scandinavian breast and ovarian cancer families. Missense variants A1669S, C1697R, R1699W, R1699Q, A1708E, S1715R and G1738E and a truncating mutation, W1837X, were characterized using yeast- and mammalian-based transcription assays. In addition, four additional missense variants (V1665M, D1692N, S1715N and D1733G) and one in-frame deletion (V1688del) were included in the study. Our findings demonstrate that transactivation activity may reflect a tumor-suppressing function of BRCA1 and further support the role of BRCA1 missense mutations in disease predisposition. We also report a discrepancy between results from yeast- and mammalian-based assays, indicating that it may not be possible to unambiguously characterize variants with the yeast assay alone. We show that transcription-based assays can aid in the characterization of deleterious mutations in the C-terminal part of BRCA1 and may form the basis of a functional assay.

BRCA1: exploring the links to transcription

Progress on determining the function of the breast and ovarian cancer susceptibility gene BRCA1 suggests it might be involved in two fundamental cellular processes: DNA repair and transcriptional regulation. Recent developments indicate that BRCA1 is a multifunctional protein, and disruption of its transcriptional activity could be crucial for tumor development.

BRCA1 can stimulate gene transcription by a unique mechanism

Most familial breast and ovarian cancers have been linked to mutations in the BRCA1 gene. BRCA1 has been shown to affect gene transcription but how it does so remains elusive. Here we show that BRCA1 can stimulate transcription without the requirement for a DNA-tethering function in mammalian and yeast cells. Furthermore, the BRCA1 C-terminal region can stimulate transcription of the p53-responsive promoter, MDM2. Unlike many enhancer-specific activators, non-tethered BRCA1 does not require a functional TATA element to stimulate transcription. Our results suggest that BRCA1 can enhance transcription by a function additional to recruiting the transcriptional machinery to a targeted gene.

Functional assay for BRCA1: mutagenesis of the COOH-terminal region reveals critical residues for transcription activation

The breast and ovarian cancer susceptibility gene product BRCA1 is a tumor suppressor, but its precise biochemical function remains unknown. The BRCA1 COOH terminus acts as a transcription activation domain, and germ-line cancer- predisposing mutations in this region abolish transcription activation, whereas benign polymorphisms do not. These results raise the possibility that loss of transcription activation by BRCA1 is crucial for oncogenesis. Therefore, identification of residues involved in transcription activation by BRCA1 will help understand why particular germ-line missense mutations are deleterious and may provide more reliable presymptomatic risk assessment. The BRCA1 COOH terminus (amino acids 1560-1863) consists of two BRCTs preceded by a region likely to be nonglobular. We combined site-directed and random mutagenesis, followed by a functional transcription assay in yeast: (a) error-prone PCR-induced random mutagenesis generated eight unique missense mutations causing loss of function, six of which targeted hydrophobic residues conserved in canine, mouse, rat, and human BRCA1; (b) random insertion of a variable pentapeptide cassette generated 21 insertion mutants. All pentapeptide insertions NH2-terminal to the BRCTs retained wild-type activity, whereas insertions in the BRCTs were, with few exceptions, deleterious; and (c) site-directed mutagenesis was used to characterize five known germ-line mutations and to perform deletion analysis of the COOH terminus. Deletion analysis revealed that the integrity of the most COOH-terminal hydrophobic cluster (I1855, L1854, and Y1853) is necessary for activity. We conclude that the integrity of the BRCT domains is crucial for transcription activation and that hydrophobic residues may be important for BRCT function. Therefore, the yeast-based assay for transcription activation can be used successfully to provide tools for structure-function analysis of BRCA1 and may form the basis of a BRCA1 functional assay.

A nuclear function for the tumor suppressor BRCA1

The breast and ovarian cancer susceptibility gene BRCA1 has been recently cloned and revealed an open reading frame of 1863 amino acids, but a lack of significant homology to any known protein in the database has led to few clues about its functions. One of the first steps to investigate the function of BRCA1 was to define its subcellular localization. Several reports have led to contradictory findings that include: nuclear localization in normal cells and cytoplasmic in breast and ovarian cancer cells; nuclear in both normal and cancer cells; cytoplasmic and secreted to the extracellular space; present in tube-like invaginations of the nucleus; and colocalizing with the centrosome. As is apparent, the subcellular localization has been the most controversial aspect of BRCA1 biology and is a key point to uncover its functions. In this paper we review the published data on subcellular localization of BRCA1 with special emphasis on the antibodies and techniques used. We conclude that there is now overwhelming evidence to support a nuclear localization for BRCA1, both in normal and cancer cells. In addition, several BRCA1-interacting proteins have been isolated and they are preferentially located in the nucleus. Evidence supporting a physiological function for BRCA1 during DNA repair and transcriptional activation is also discussed.

BRCA1 regulates p53-dependent gene expression

Mutations in BRCA1 are present in 45% of families that segregate with susceptibility for breast cancer and in 80-90% of families with both breast and ovarian cancer. Here we report that BRCA1 stimulates artificial and genomic promoter constructs containing p53-responsive elements. This activity of BRCA1 depends on the presence of wild-type p53, which was shown by using mouse fibroblasts expressing temperature-sensitive forms of p53, or p53(+/+) and p53(-/-) fibroblasts obtained from p53 knockout mice. Furthermore, mutant forms of BRCA1 lacking the C-terminal second BRCA1 C-terminal (BRCT) domain showed reduced p53-mediated transcriptional activation. Finally, we found that BRCA1 coimmunoprecipitates with p53, in vitro and in vivo. These findings suggest a function of BRCA1 as a p53 coactivator.

Evidence for a transcriptional activation function of BRCA1 C-terminal region

Mutations in BRCA1 account for 45% of families with high incidence of breast cancer and for 80-90% of families with both breast and ovarian cancer. BRCA1 protein includes an amino-terminal zinc finger motif as well as an excess of negatively charged amino acids near the C terminus. In addition, BRCA1 contains two nuclear localization signals and localizes to the nucleus of normal cells. While these features suggest a role in transcriptional regulation, no function has been assigned to BRCA1. Here, we show that the C-terminal region, comprising exons 16-24 (aa 1560-1863) of BRCA1 fused to GAL4 DNA binding domain can activate transcription both in yeast and mammalian cells. Furthermore, we define the region comprising exons 21-24 (aa 1760-1863) as the minimal transactivation domain. Any one of four germ-line mutations in the C-terminal region found in patients with breast or ovarian cancer (Ala-1708-->Glu, Gln-1756 C+, Met-1775-->Arg, Tyr-1853 ->Stop), had markedly impaired transcription activity. Together these data underscore the notion that one of the functions of BRCA1 may be the regulation of transcription.

Clonal heterogeneity in murine liver myofibroblasts

GR primary cells cultures were isolated from hepatic granulomas induced in C3H mice livers by Schistosoma mansoni infection; the GRX continuous cell line was derived from GR cells after long-term culture and a progressive drift towards a rapidly proliferating cell population. These cells were analyzed and compared in terms of their clonal heterogeneity. Clones were classified on the basis of cell substrate, cell-cell adhesion (growth morphology of the clone) and fat droplet accumulation. GR cells were composed of two slow-growing clone types, while GRX cells gave rise to clones with several phenotypes, including the two found in the GR cells. The overall proportion of different clones in the GRX cell population was stable in long-term cultures, as well as after recloning of the highly proliferating, but not the slowly proliferating, clones. We propose that the slow-growing clones are maintained in the overall population by continuous contribution of new slow-growing cells from the rapidly growing ones. The slow-growing clones may represent the basal population of liver connective tissue cells that can be mobilized into injured tissues and that are involved in tissue repair. The highly proliferating clones with a broad capacity of phenotype expression that arise after long-term growth stimulation of the local cell population may represent the hypertrophic connective tissue cells, such as those observed in progressive fibrotic reactions associated with chronic liver tissue inflammation.

Complement-dependent induction of DNA synthesis and cell proliferation in human liver connective tissue cells in vitro

Liver connective tissue cells (LCTC) isolated from patients with fibrotic livers have morphological and biochemical characteristics of myofibroblasts. We have examined the proliferation of LCTC derived from normal livers and from livers with fibrosis of different etiologies, as well as proliferation of skin fibroblasts. We have compared proliferation rates in the presence of fresh human serum and heat-inactivated serum. While skin fibroblast and LCTC from normal liver showed no difference, proliferation of LCTC from fibrotic livers was markedly decreased in the presence of heat-inactivated serum. We demonstrate that the native complement component C1 is a factor involved in the induction of DNA synthesis and proliferation of LCTC isolated from fibrotic livers. We propose that native C1, acting probably in cooperation with other growth factors, is involved in the expansion of connective tissue cells during the development of liver fibrosis.

In vitro collagen synthesis by liver connective tissue cells isolated from schistosomal granulomas

Hepatic injury elicits an excessive deposition of extracellular matrix probably due to a loss of control mechanisms in mesenchymal cells in fibrotic lesions, or a local activity of growth factors. To study collagen synthesis in an in vitro model of fibrotic lesions, we isolated liver connective tissue cells (LCTC) from murine schistosomal granulomas in C3H/HeN mice. Collagen was quantified in culture supernatants using a sirius red dye assay. LCTC and skin fibroblasts (SF) secreted similar amounts of collagen per cell and secretion was inversely proportional to the cell density. Cells cultured at low density (10,000 cells/cm2) secreted two- to three-times more collagen per cell when compared to cells grown in high-density cultures (60,000 cells/cm2). Collagen secretion was stimulated by transforming growth factor-beta (TGF-beta) in both cell lines, but the response of LCTC was detected from 1 ng/ml on, while SF responded only to higher concentrations (2.5 and 5 ng/ml). These data do not support the hypothesis that cells from fibrotic livers have lost the normal control mechanisms and suggest that their control is disturbed locally by the presence of peptide growth factors during the development of fibrosis.

Effect of various factors and substrates on the growth of a human hepatoblastoma cell line, HuH-6 in a serum-free medium

The effect of various factors and substrates on the growth of a human hepatoblastoma cell line, HuH-6, which was inoculated at low density in a serum-free medium was examined. Several supplements were required to enhance cell growth of HuH-6. These included cholera toxin (CT), glucagon (Glu) and selenium (Se). Type IV collagen (C-IV) provided the most conductive environment tested for cell growth. These results suggest that CT, Glu, Se, and C-IV are important stimulators for the continuous growth of HuH-6 in a serum-free medium at low density.

Interaction of human liver connective tissue cells, skin fibroblasts and smooth muscle cells with collagen gels

Interactions of liver connective tissue cells, skin fibroblasts and smooth muscle cells with collagen gels in vitro were studied and compared. Liver connective tissue cells showed the lowest rate of migration into the gel and the highest speed of gel contraction, reflecting their high adhesiveness to the substrate as compared to the other cell lines studied. The analysis of their ultrastructural morphology showed that liver connective tissue cells and smooth muscle cells developed cytoskeletal and cytoplasmic organelle polarities, in response to the contact with gel surface. This polarity was lost when cells were embedded in the gel. Skin fibroblasts did not show this characteristic, neither on top nor in the gel. Although liver connective tissue cells have been recognized as analogous to smooth muscle cells, they represent a defined cell population, present in fibrotic livers, with specific behavior and with particular relationship to the extracellular matrix.

In vitro formation of fibrous septa by liver connective tissue cells

Active fibrous septa are a common feature in liver fibrosis and cirrhosis. Their etiology and formation were studied using cultures of tissue fragments or cells included in collagen gels. Liver fragments obtained from patients with cirrhosis or severe schistosomal fibrosis were able to reorganize the gel and to form discrete, interconnecting fibrous septa composed of parallel arrays of collagen, subsequently colonized by migrating connective tissue cells. The same was obtained in cultures of fibrogranulomatous lesions isolated from schistosome-infected mice livers. However, fragments of normal human and murine liver tissue did not show the capacity to form fibrous septa. Septa formation was also obtained in cultures of cell spheroids formed by liver connective tissue cells isolated from human fibrotic or cirrhotic liver tissues, but not with spheroids of normal skin fibroblasts or smooth muscle cells. This experimental model may represent the fibrous septa formation in vivo, depending on the activity of liver connective tissue cells. The ability of tissue fragments or cell spheroids to form septa in collagen gels might reflect the degree of fibrosis present in the liver tissue in vivo.

Liver connective tissue cells isolated from human schistosomal fibrosis or alcoholic cirrhosis represent a modified phenotype of smooth muscle cells

Hepatic connective tissue cells associated with schistosomal fibrosis and alcoholic cirrhosis were studied in vitro. Primary cell lines were isolated from all biopsies: they were identified as specific homogeneous cell populations, named liver connective tissue cells (LCTC). They were recognized as analogous to smooth muscle cells, different from true fibroblasts by morphological and physiological criteria. The proliferative capacity of LCTC is directly proportional to the degree of fibrosis in hepatic tissues. LCTC are able to secrete type I, III and IV collagen, fibronectin, laminin and amyloid P component. Their relationship with specific pathology of intrahepatic vascular tree in schistosomiasis is hypothesized.