Genome-wide and transcriptome-wide association studies of mammographic density phenotypes reveal novel loci

BACKGROUND

Mammographic density (MD) phenotypes, including percent density (PMD), area of dense tissue (DA), and area of non-dense tissue (NDA), are associated with breast cancer risk. Twin studies suggest that MD phenotypes are highly heritable. However, only a small proportion of their variance is explained by identified genetic variants.

METHODS

We conducted a genome-wide association study, as well as a transcriptome-wide association study (TWAS), of age- and BMI-adjusted DA, NDA, and PMD in up to 27,900 European-ancestry women from the MODE/BCAC consortia.

RESULTS

We identified 28 genome-wide significant loci for MD phenotypes, including nine novel signals (5q11.2, 5q14.1, 5q31.1, 5q33.3, 5q35.1, 7p11.2, 8q24.13, 12p11.2, 16q12.2). Further, 45% of all known breast cancer SNPs were associated with at least one MD phenotype at p < 0.05. TWAS further identified two novel genes (SHOX2 and CRISPLD2) whose genetically predicted expression was significantly associated with MD phenotypes.

CONCLUSIONS

Our findings provided novel insight into the genetic background of MD phenotypes, and further demonstrated their shared genetic basis with breast cancer.

168 Expanding and characterizing tumor infiltrating lymphocytes from myxofibrosarcoma and undifferentiated pleomorphic sarcoma

Background

Sarcoma is a group of rare bone and soft tissue tumors with over 50 distinct subtypes. Survival rate ranges widely due to the lack of efficacious treatments. Immunotherapy, such as adoptive cell therapy (ACT), has drawn significant interest due to its minimal toxicity. In ACT, tumor infiltrating lymphocytes (TILs) are isolated from patients, expanded, and autologously infused back. We recently observed TILs’ presence in Undifferentiated Pleomorphic Sarcoma (UPS) and Myxofibrosarcoma (MFS) tumors and found that tumor’s PD-L1 overexpression is correlated with better clinical outcome in UPS but not MFS.1 The Th1 anti-tumoral inflammatory pathway was highly activated in the former cohort, which may explain the favorable outcome. We hypothesize that there are phenotypic and functional differences between TILs of UPS with differential PD-L1 expression, which may be related to clinical outcomes. However, sarcoma TILs are rare and challenging to culture, which significantly impedes their studies. We first aim to robustly expand sarcoma TILs to sufficient numbers.

Methods

Tumors’ PD-L1 expression was determined by RT-qPCR (table 1). To initiate the tumor-fragment (TF) method of TIL culturing, primary tumors were fragmented and cultured in IMDM, IL-2, and 10% HSA. We further optimized the TF protocol to expand rare sarcoma TILs. Rapid expansion protocol (REP) with anti-CD3/anti-CD28 co-stimulating beads was employed for additional expansion. During REP, TILs were co-treated with gamma-chain cytokines (IL-2, 7, 15, 21).

Results

Of the 15 MFS TIL populations expanded, only 40% achieved sufficient growth (1x106) for analysis (figure 1A). Our optimized TF protocol expanded TILs from 8 UPS cases with a 62.5% success rate (figure 1B). UPS TILs were further stimulated with REP and various gamma-chain cytokine treatments. In ACT, prolonged culturing with IL-2 is known to cause activation-induced cell death, problematic in clinical treatments. We demonstrated that treatments with a Trio-cocktail (IL-7, 15, and 21) or IL-15 alone can achieve TIL proliferation comparable to that of IL-2 (figure 2).

Abstract 168 Figure 1

Initial TIL Culturing with Tumor Fragment Method. Figure A.. The traditional tumor fragment protocol was used to expand TILs of four MFS cases. TILs were cultured and expanded from primary tumor fragments in IL-2 (6000IU/mL) supplemented complete media (CM) over four weeks in duration. Fifteen TIL populations were derived from the four MFS cases. Populations were categorized based on their growth rates and labeled as ‘1’ or ‘2’ representing ‘fast’ or ‘slow’ growing TILs, respectively. Additional populations ‘A’ and ‘B’ represent biological replicates. Population TIL164 ‘2’ had no replicates. At Week 4, populations’ cell counts were determined via hemocytometer. As shown, only 6 out of 15 populations achieved > 1x10^6 cells (40% success rate). Figure B. An optimized tumor fragment protocol was used to expand TILs of eight UPS cases. Optimization includes shortening the culturing duration from four weeks to two weeks, reducing frequency of cell culture disruption, and adjusting cell culture environments. TILs were expanded from primary tumor fragments in CM over two weeks in duration. At Week 2, populations’ cell counts were determined via hemocytometer. As shown, 5 out of 8 cases achieved >1x10^6 cells (62.5% success rate).

Abstract 168 Figure 2

Gamma-chain cytokine treatments of UPS TILs. Gamma-chain cytokine treatments of UPS TILs with CD3/CD28 stimulation. Magnetic Dynabeads coated with CD3 and CD28 monoclonal antibodies were used to stimulate cells at a bead to cell ratio of 1:3. In ACT, IL-2 is a gold-standard cytokine that facilitates potent T-cell growth. However, it is known to cause activation-induced cell death. Resulting TIL population also possesses an exhausted-effector phenotype with low durability. UPS TIL Case 52 and Case 166 were treated with various interleukins during two weeks of REP, including gamma-chain IL-7, 15, 21 and inflammatory IL-12. IL-7, IL-12, and IL-21 individually did not elicit significant T-cell growth. IL-15 alone and in combination with IL-7 and IL-21 yield growth comparable to IL-2. IL-2 was obtained from Novartis (50ng/mL). All other cytokines were obtained from PeproTech (25ng/mL).

Abstract 168 Table 1

Tumor PD-L1 RNA Expression. Four MFS and eight UPS cases were processed. Tumors’ PD-L1 RNA expression was determined via RT-qPCR and evaluated as a ratio with the housekeeping gene STAM2. TIL359’s PD-L1 status has yet to be evaluated.

Conclusions

Sarcoma infiltrates are difficult to culture, and their roles remain largely unstudied. By optimizing the TF protocol in conjunction with anti-CD3/CD28 treatments, we developed a robust in vitro pipeline to expand rare sarcoma TILs, enabling downstream characterization. We also demonstrated the potential for alternate gamma-chain cytokines to favorably replace IL-2 during TIL expansion. Future phenotypic and functional evaluation of UPS TILs would elucidate the impact of tumors’ differential PD-L1 expression on UPS patients‘ prognoses. These findings would inform the implementation of ACT in sarcoma treatments.

References

Wunder J, Lee M, Nam J, Lau B, Dickson B, Pinnaduwage D, Bull S, Ferguson P, Seto A, Gokgoz N, Andrulis I. Osteosarcoma and soft-tissue sarcomas with an immune infiltrate express PD-L1: relation to clinical outcome and Th1 pathway activation. Onco Immunology 2020;9: e1737385-1- e1737385-13.

Ethics Approval

Patients provided signed consent before study entry, as approved by Mount Sinai Hospital’s Ethics Board (REB#01-0138-U).

A competing risks model with binary time varying covariates for estimation of breast cancer risks in BRCA1 families

Mammographic screening and prophylactic surgery such as risk-reducing salpingo oophorectomy can potentially reduce breast cancer risks among mutation carriers of BRCA families. The evaluation of these interventions is usually complicated by the fact that their effects on breast cancer may change over time and by the presence of competing risks. We introduce a correlated competing risks model to model breast and ovarian cancer risks within BRCA1 families that accounts for time-varying covariates. Different parametric forms for the effects of time-varying covariates are proposed for more flexibility and a correlated gamma frailty model is specified to account for the correlated competing events.We also introduce a new ascertainment correction approach that accounts for the selection of families through probands affected with either breast or ovarian cancer, or unaffected. Our simulation studies demonstrate the good performances of our proposed approach in terms of bias and precision of the estimators of model parameters and cause-specific penetrances over different levels of familial correlations. We applied our new approach to 498 BRCA1 mutation carrier families recruited through the Breast Cancer Family Registry. Our results demonstrate the importance of the functional form of the time-varying covariate effect when assessing the role of risk-reducing salpingo oophorectomy on breast cancer. In particular, under the best fitting time-varying covariate model, the overall effect of risk-reducing salpingo oophorectomy on breast cancer risk was statistically significant in women with BRCA1 mutation.

Abstract LB-307: Translational and mechanistic implications of osteosarcoma genomics: A TARGET report

Osteosarcoma (OS) is the most common malignant bone tumor of children and young adults. Although the optimization of combination chemotherapy has led to significantly improved prognosis, survival remains poor for patients with recurrent tumor or metastatic disease at diagnosis. The international TARGET (Therapeutically Applicable Research to Generate Effective Therapy) OS project team collected 285 clinically annotated samples (age &lt;40 years) for integrative genomics analyses. Eighty-nine cases, the discovery set, were characterized with paired tumor and normal DNA sequencing as well as profiling of transcriptomes, DNA methylation, and miRNA. An additional 196 validation cases were used for copy number analysis and targeted DNA sequencing guided by results from the discovery set. The most frequent recurrent somatic mutations cause loss of function in the tumor suppressors TP53, RB1, CDKN2A, PTEN, and NF1 as well as the chromatin remodeler ATRX. Structural rearrangements are an important mechanism of inactivation for all of these genes. In the discovery set, every case carried at least one mutation of a cell cycle regulator, with TP53 somatically altered in 87/89 cases. Analysis of TP53 mutations suggests that these are often truncal. OS genomes are strikingly complex and contain copy number aberrations (CNA) arising from aneuploidy and extensive structural rearrangements. Transcriptome analysis revealed profound remodeling of gene expression with statistically significant correlation of CNA and gene expression of 3340 genes (FDR&lt;0.001). Regions of high copy number amplification include known therapeutically relevant cancer drivers (e.g. PDGFRA, MYC, CDK4, MDM2, IGF1R, and CCNE1). In contrast, activating mutations of signal transduction genes were rare. With few exceptions (e.g. MYC amplification), mutations or CNA of individual genes were not predictive of outcome. The pattern of significant co-occurrence or mutual exclusion of frequent mutations and amplifications allowed partitioning of 240 cases into four distinct genomic groups. One of these, characterized by relatively simple genomes lacking high copy number amplification, had a more favorable outcome. Unsupervised transcriptome analysis by NMF separated the discovery set into two groups with significantly different outcomes. A pathway-based approach identified a high-risk bone differentiation signature comprised of genes highly correlated with the expression of the osteogenic transcription factors. NMF analysis of DNA methylation and miRNA data also partitioned the discovery set into two groups with the methylation groups significantly correlated with clinical outcome. Our results provide a detailed picture of the genomic complexity and heterogeneity of these tumors that suggests a model wherein most OS are initiated by TP53 loss in a proliferative cell of the osteoblast lineage. TP53 deficiency leads directly to impairment of cell cycle control, DNA repair, and terminal differentiation, a state permissive for the development of secondary CNA and epigenetic changes. The TARGET OS data are publicly available (phs000218) and of immediate relevance to future investigations of the molecular mechanisms driving osteosarcoma. Findings suggest a path forward to improved assessment of risk for individual patients and support a precision medicine approach to future clinical trial development.

Citation Format: Paul S. Meltzer, Sean Davis, Jack Zhu, Yonghong Wang, Sven Bilke, Joshua Waterfall, Robert Walker, Marbin Pineda, Yuan Jiang, Sharon Savage, Lisa Mirabello, Tsz-Kwong Man, Aaron Taylor, Monika J. Sun, Jay Wunder, Irene Andrulis, Nalan Gokgoz, Shintaro Iwata, Miki Ohira, Mark Krailo, Don Barkauskas, Lisa Teot, Timothy Triche, Silvia de Toledo, Antonio S. Petrilli, Jaime M. Guidry Auvil, Richard Gorlick, Malcolm A. Smith, Daniela Gerhard, Ching C. Lau. Translational and mechanistic implications of osteosarcoma genomics: A TARGET report [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-307.

Abstract LB-306: Long non-coding RNA NEAT1 promotes lung metastasis of soft tissue sarcoma by regulating RNA splicing pathways

Soft tissue sarcomas (STS) are malignant tumors from diverse mesenchymal tissues. About 40% STS patients develop fatal lung metastasis with a median survival of 15 months. The mechanisms driving the development of lung metastasis in sarcoma patients are poorly understood. Therefore, our lab has developed a genetically engineered mouse model (GEMM) of high-grade primary STS with conditional mutations in Kras and Trp53 (KP) where 40% of mice tumors develop lung metastasis. This KP model recapitulates human patients with Undifferentiated Pleomorphic Sarcoma (UPS), one of the most common subtypes of STS diagnosed in adults. RNA sequencing (RNA-Seq) was performed on paired primary and lung metastases in KP mouse sarcomas and determined that the expression of the long non-coding RNA (lncRNA) Neat1 is increased in lung metastases compared to paired primary tumors. Real time PCR (qPCR) in 22 paired KP mouse primary sarcomas and lung metastases further confirmed that Neat1 is significantly upregulated in some lung metastases. In addition, RNA-Seq and qPCR data from 10 pairs of human primary sarcomas and matched lung metastases also showed that NEAT1 levels are increased in lung metastases. Furthermore, NEAT1 RNA in situ hybridization (ISH) on tissue microarrays (TMAs) of human primary UPS and lung metastases determined that the expression of NEAT1 is upregulated in lung metastases. Next, CRISPR/Cas9 technology was applied to delete Neat1 in primary mouse sarcoma cells and loss of expression of Neat1 was confirmed by qPCR and northern blot in knockout (KO) clones. In addition, loss of Neat1 significantly reduced lung metastasis in vivo following tail vein injection of these modified cells into nude mice. Furthermore, RNA pull down assay with mass spectrometry analysis determined Neat1 interacting proteins, such as Khsrp, were mainly involved in RNA splicing pathways which was also shown to be dysregulated in lung metastases and Neat1 KO cells. Finally, CRISPR/Cas9 mediated knockout of Khsrp significantly reduced lung metastasis in vivo following tail vein injection of these modified cells into nude mice. Overall, these results suggest that upregulation of Neat1 promotes lung metastasis of soft tissue sarcoma through regulating RNA splicing pathways and NEAT1 is a potential target to prevent or treat lung metastasis in sarcoma patients.

Citation Format: Jianguo Huang, Eric Xu, Mohit Sachdeva, Timothy Robinson, Xiaodi Qin, Dadong Zhang, Kouros Owzar, Nalan Gokgoz, Andrew Seto, Irene Andrulis, Jay Wunder, Tomoyo Okada, Simuel Singer, Alexander Lazar, Brian Rubin, David G. Kirsch. Long non-coding RNA NEAT1 promotes lung metastasis of soft tissue sarcoma by regulating RNA splicing pathways [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-306.

Abstract 516: Long noncoding RNA NEAT1 promotes lung metastasis of soft tissue sarcoma

Soft tissue sarcomas (STS) are malignant tumors from diverse mesenchymal tissues. About 40% STS patients develop fatal lung metastasis with a median survival of 15 months. The mechanisms driving the development of lung metastasis in sarcoma patients are poorly understood. Therefore, our lab has developed a genetically engineered mouse model (GEMM) of high-grade primary STS with conditional mutations in Kras and Trp53 (KP) where 40% of mice tumors develop lung metastasis. This KP model recapitulates human patients with Undifferentiated Pleomorphic Sarcoma (UPS), one of the most common subtypes of STS diagnosed in adults. RNA sequencing (RNA-Seq) was performed on paired primary and lung metastases in KP mouse sarcomas and determined that the expression of the long non-coding RNA (lncRNA) Neat1 is increased in lung metastases compared to paired primary tumors. Real time PCR (qPCR) in 22 paired KP mouse primary sarcomas and lung metastases further confirmed that Neat1 is significantly upregulated in lung metastases. In addition, RNA-Seq data from 5 pairs of human primary sarcomas and matched lung metastases also showed that NEAT1 levels are increased in lung metastases. Furthermore, NEAT1 RNA in situ hybridization (ISH) on tissue microarrays (TMAs) of human primary UPS and lung metastases determined that the expression of NEAT1 is upregulated in lung metastases. Next, CRISPR/Cas9 technology was applied to delete Neat1 in primary mouse sarcoma cells and loss of expression of Neat1 was confirmed by qPCR and northern blot in knockout (KO) clones. In addition, loss of Neat1 significantly reduced lung metastasis in vivo following tail vein injection of these modified cells into nude mice. To further test that loss of Neat1 reduces lung metastasis in primary sarcoma mouse model, primary tumors with Neat1 deletion are generated in GEMMs using in vivo CRISPR/Cas9 technology and KrasLSL-G12D/+; Trp53Flox/Flox; Neat1-/- (KPN) mouse model. Finally, RNA-Seq and capture hybridization analysis of RNA targets (CHART) are performed to determine mechanisms by which Neat1 regulates lung metastasis. Overall, these results suggest that upregulation of Neat1 promotes lung metastasis of soft tissue sarcoma and NEAT1 is a potential target to prevent or treat lung metastasis in sarcoma patients.

Citation Format: Jianguo Huang, Eric Xu, Mohit Sachdeva, Timothy Robinson, Xiaodi Qin, Dadong Zhang, Kouros Owzar, Nalan Gokgoz, Andrew Seto, Irene Andrulis, Jay Wunder, Tomoyo Okada, Samuel Singer, Alexander Lazar, Brian Rubin, David G. Kirsch. Long noncoding RNA NEAT1 promotes lung metastasis of soft tissue sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 516.

Abstract PR12: Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape

Several types of bone/cartilage tumors reportedly contain high-frequency missense mutations in histone H3, yet the underlying oncogenic mechanism remains poorly characterized. We find that the H3 lysine 36 to methionine (H3K36M) mutation, identified in &gt;90% of chondroblastomas, impairs the differentiation of mesenchymal progenitor cells and generates undifferentiated sarcoma in vivo. H3K36M mutant nucleosomes inhibit the enzymatic activities of several H3K36 methyltransferases, resulting in globally diminished H3K36 methylation. Depletion of H3K36 methyltransferases, or expressing an H3K36I mutant that similarly inhibits H3K36 methylation, is sufficient to phenocopy H3K36M mutation. Following the loss of H3K36 methylation, a genome-wide gain in H3K27 methylation leads to a redistribution of polycomb repressive complex 1 and de-repression of polycomb target genes known to block mesenchymal differentiation. Our findings are mirrored in human undifferentiated sarcomas where novel K36M/I mutations in H3.1 are identified in rare pediatric cases.

This abstract is also being presented as Poster A12.

Citation Format: Chao Lu, Siddhant Jain, Dominik Hoelper, Denise Bechet, Leili Ran, Irene Andrulis, Brendan Dickson, Jacek Majewski, Craig Thompson, Ping Chi, Benjamin Garcia, Nada Jabado, Peter Lewis, C. David Allis. Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape [abstract]. In: Proceedings of the AACR Conference on Advances in Sarcomas: From Basic Science to Clinical Translation; May 16-19, 2017; Philadelphia, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(2_Suppl):Abstract nr PR12.

Abstract 4741: Biomarker significance of plasma and tumor miR-21, miR-221, and miR-106a in pediatric osteosarcoma

Osteosarcoma is the most common malignant bone tumor in children and young adults. Despite the use of surgery and multi-agent chemotherapy, osteosarcoma patients who respond poorly towards chemotherapy or develop relapses have a dismal outcome. Identification of biomarkers for active disease may help to monitor tumor burden, detect early relapses, and predict prognosis in these patients, so that they can be treated as early as possible to improve their survival. In this study, we examined if circulating microRNAs (miRNAs) can be used as biomarkers in osteosarcoma patients. We performed genome-wide miRNA profiling on a discovery cohort of OS plasma samples (n=32) collected from the Texas Children’s Hospital. A total of 56 miRNAs were upregulated and 164 miRNAs were downregulated in osteosarcoma samples when compared to normal plasma samples (n=8). miRNA-21, miR-221 and miRNA-106a were selected for further validation based on their known biological importance. We showed that all three circulating miRNAs were expressed significantly higher in OS samples (n=29) than normal samples (n=17) in an independent cohort obtained from the Children’s Oncology Group. Furthermore, we demonstrated that miR-21 was expressed significantly higher in osteosarcoma tumors (n=89) compared with normal bone controls. More importantly, lower expressions of miR-21 and miR-221, but not miR-106a, significantly correlated with a poor outcome. In conclusion, our results indicate that miR-21, miR-221 and miR-106a are elevated in the circulation of osteosarcoma patients, whereas tumor expressions of miR-21 and miR-221 are prognostically significant. Further investigation of the miRNAs may lead to a better prognostic method and potential miRNA therapeutics for osteosarcoma.

Citation Format: Manjula Nakka, Wendy Allen-Rhoades, Yiting Li, Aaron Kelly, Jianhe Shen, Aaron Taylor, Donald A. Barkauskas, Jason Yustein, Irene Andrulis, Jay Wunder, Richard Gorlick, Paul Meltzer, Ching Lau, Tsz-Kwong Man. Biomarker significance of plasma and tumor miR-21, miR-221, and miR-106a in pediatric osteosarcoma [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 4741. doi:10.1158/1538-7445.AM2017-4741

BRCA2 Hypomorphic Missense Variants Confer Moderate Risks of Breast Cancer

Breast cancer risks conferred by many germline missense variants in the BRCA1 and BRCA2 genes, often referred to as variants of uncertain significance (VUS), have not been established. In this study, associations between 19 BRCA1 and 33 BRCA2 missense substitution variants and breast cancer risk were investigated through a breast cancer case-control study using genotyping data from 38 studies of predominantly European ancestry (41,890 cases and 41,607 controls) and nine studies of Asian ancestry (6,269 cases and 6,624 controls). The BRCA2 c.9104A>C, p.Tyr3035Ser (OR = 2.52; P = 0.04), and BRCA1 c.5096G>A, p.Arg1699Gln (OR = 4.29; P = 0.009) variant were associated with moderately increased risks of breast cancer among Europeans, whereas BRCA2 c.7522G>A, p.Gly2508Ser (OR = 2.68; P = 0.004), and c.8187G>T, p.Lys2729Asn (OR = 1.4; P = 0.004) were associated with moderate and low risks of breast cancer among Asians. Functional characterization of the BRCA2 variants using four quantitative assays showed reduced BRCA2 activity for p.Tyr3035Ser compared with wild-type. Overall, our results show how BRCA2 missense variants that influence protein function can confer clinically relevant, moderately increased risks of breast cancer, with potential implications for risk management guidelines in women with these specific variants. Cancer Res; 77(11); 2789-99. ©2017 AACR.

PALB2, CHEK2 and ATM rare variants and cancer risk: data from COGS

BACKGROUND

The rarity of mutations in PALB2, CHEK2 and ATM make it difficult to estimate precisely associated cancer risks. Population-based family studies have provided evidence that at least some of these mutations are associated with breast cancer risk as high as those associated with rare BRCA2 mutations. We aimed to estimate the relative risks associated with specific rare variants in PALB2, CHEK2 and ATM via a multicentre case-control study.

METHODS

We genotyped 10 rare mutations using the custom iCOGS array: PALB2 c.1592delT, c.2816T>G and c.3113G>A, CHEK2 c.349A>G, c.538C>T, c.715G>A, c.1036C>T, c.1312G>T, and c.1343T>G and ATM c.7271T>G. We assessed associations with breast cancer risk (42 671 cases and 42 164 controls), as well as prostate (22 301 cases and 22 320 controls) and ovarian (14 542 cases and 23 491 controls) cancer risk, for each variant.

RESULTS

For European women, strong evidence of association with breast cancer risk was observed for PALB2 c.1592delT OR 3.44 (95% CI 1.39 to 8.52, p=7.1×10-5), PALB2 c.3113G>A OR 4.21 (95% CI 1.84 to 9.60, p=6.9×10-8) and ATM c.7271T>G OR 11.0 (95% CI 1.42 to 85.7, p=0.0012). We also found evidence of association with breast cancer risk for three variants in CHEK2, c.349A>G OR 2.26 (95% CI 1.29 to 3.95), c.1036C>T OR 5.06 (95% CI 1.09 to 23.5) and c.538C>T OR 1.33 (95% CI 1.05 to 1.67) (p≤0.017). Evidence for prostate cancer risk was observed for CHEK2 c.1343T>G OR 3.03 (95% CI 1.53 to 6.03, p=0.0006) for African men and CHEK2 c.1312G>T OR 2.21 (95% CI 1.06 to 4.63, p=0.030) for European men. No evidence of association with ovarian cancer was found for any of these variants.

CONCLUSIONS

This report adds to accumulating evidence that at least some variants in these genes are associated with an increased risk of breast cancer that is clinically important.

Abstract A18: Investigating the differential expressions of miRNAs and programmed-death-ligand-1 related to the T-bet positive tumor-infiltrating lymphocytes in axillary-node-negative breast cancer

Axillary lymph node-negative (ANN) breast cancer (BC) patients generally have a good prognosis; however, 20-30% of ANN patients will experience recurrence. To identify biomarkers that distinguish ANN patients who may benefit from systemic therapy we have been studying characteristics of the breast tumor cells and the tumor microenvironment. We have found that tumor-infiltrating lymphocytes (TILs) that express T-bet (T-box transcription factor) are associated with poor prognosis features such as high grade, hormone receptor negativity and basal subtype. Despite these adverse clinical-pathologic characteristics, T-bet+ TILs cells are associated with a favorable outcome. T-bet is essential for Th1 development and IFN-γ production. To investigate how T-bet+ TILs influence the BC suppression, we are examining molecular differences in T-bet+/high and T-bet-/low tumors including expression of tumor miRNA expression profiles and expression of Programmed-Death-Ligand-1 (PD-L1). Tumors expressing PD-L1 inhibit Programmed-Death-receptor-1-(PD-1)-expressing TILs and evade immune surveillance. Interestingly, PD-L1 is induced by IFNγ, the hallmark cytokine of the T-bet+ TILs, which suggests a potential relationship between the tumor PD-L1 and T-bet+ TILs. Microdissected, formalin-fixed, paraffin-embedded (FFPE) samples of 35 T-bet+/high and 35 T-bet-/low ANN BC tumors are being used to identify the differentially-expressed miRNAs via miRNA sequencing. The sufficiency of the FFPE samples as the miRNA source was confirmed by quantifying miRNA expressions in the 3-5 paired frozen and FFPE samples, and observing the expressions to be highly correlated with both qPCR (r=0.81) and miRNA sequencing (rs=0.73). After identifying the differentially-expressed miRNAs via miRNA sequencing, these miRNAs will be validated via qPCR in both the original and independent BC tumor set. Based on the genes and molecular pathways the validated miRNA(s) may regulate, appropriate in vitro functional assays will be conducted to examine their roles in cellular proliferation, migration and invasion. Furthermore, PD-L1 mRNA expression has been evaluated in 107 ANN tumors and correlations with clinico-pathological characteristics will be determined. Identifying the tumor miRNA(s) associated with T-bet+ TILs and studying their functions may indicate differences between T-bet+/high and T-bet-/low tumors that can be used to improve the prognosis of ANN BC. Characterizing the tumor PD-L1 expression based on T-bet+ TILs and the clinical data may distinguish a subset of ANN BC patients who may benefit from the PD-L1 blockade therapy.

Citation Format: Minji Lee, Anna-Marie Mulligan, Shelley Bull, Dushanti Pinnaduwage, Irene Andrulis. Investigating the differential expressions of miRNAs and programmed-death-ligand-1 related to the T-bet positive tumor-infiltrating lymphocytes in axillary-node-negative breast cancer. [abstract]. In: Proceedings of the AACR Special Conference: Function of Tumor Microenvironment in Cancer Progression; 2016 Jan 7–10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2016;76(15 Suppl):Abstract nr A18.

Abstract 2787: Exon sequencing of candidate genes for early onset ER negative breast cancer risk reveals novel gene-level associations

Purpose: To test whether genes located in GWAS-identified regions contain exonic variants that show novel gene-level associations with early-onset ER negative breast cancer risk.

Background: Only a small portion of the expected genetic contribution to breast cancer risk has been identified by examining the effect of common variants using single-variant analyses. In contrast to single-variant analyses, sequencing studies combined with gene-based tests evaluate the collective effect of all variants in a gene. In regions identified as associated with disease in GWAS, sequencing combined with gene-based tests can potentially provide evidence whether exonic variation contributes to disease risk independently of the common variants already. However, these studies have not yet been widely implemented in breast cancer research.

Methods: We selected 19 genes in 11 genomic regions in which previous GWA studies found associations between common variants and breast cancer. We sequenced the exons of each of these genes in 210 cases (women diagnosed with breast cancer before age 45 who did not carry a known BRCA-1 or BRCA-2 mutation and whose tumors were ER-), and 169 age-matched controls. We analyzed these exons using the variance-based SKAT-O test to determine if exonic variation in any of these 19 genes was associated with risk of developing breast cancer. To examine whether any association was driven by the known GWAS variant, we repeated the analysis, controlling for the common variant that single-variant association tests indicated was most strongly associated with breast cancer. To examine whether the association was driven by putative “functional” variants, we also repeated both analyses, including only non-synonymous variants that alter the amino acid sequence.

Results: Exonic variants in three genes were collectively associated with breast cancer risk in our population of early-onset cases: ZMIZ1 (p = 2.07•10-4), FGF3 (p = 1.30•10-3), and ANKLE1 (p = 2.80•10-5). In all of these three genes, the associations persisted or even strengthened after adjusting for the top variant identified by GWAS in the region (ZMIZ1 p = 2.41•10-5; FGF3 p = 1.41•10-3; ANKLE1 p = 7.63•10-6). Functional variants in these three genes (restricted only to non-synonomous variants) also were collectively associated with risk (ZMIZ1 p = 2.65•10-5; FGF3 p = 4.52•10-5; ANKLE1 p = 6.52•10-5). These associations are similar after adjusting for the strongest single variant association identified by GWAS in the region (ZMIZ1 p = 5.10•10-4; FGF3 p = 7.74•10-5; ANKLE1 p = 9.42•10-5).

Conclusions: Our results are consistent with the hypothesis that the exons of genomic regions identified through GWAS contain additional variants that contribute to ER- breast cancer risk. These results, that need to be independently validated in a larger study, contribute to our understanding of the genetic determinants that influence the risk of ER- early onset breast cancer.

Citation Format: Molly Scannell Bryan, Muhammad G. Kibirya, Irene Andrulis, Jenny Chang-Claude, Habibul Ahsan, Brandon Pierce. Exon sequencing of candidate genes for early onset ER negative breast cancer risk reveals novel gene-level associations. [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 2787. doi:10.1158/1538-7445.AM2015-2787

Abstract P6-10-17: Psychosocial adjustment, cancer worry and perceived risk in 6-13 year old girls from breast cancer families

Background: Many parents discuss familial and genetic risk of breast cancer (BC) with offspring. What girls know and perceive of BC risk and its psychosocial impact is unknown.

Methods: In the multisite LEGACY Girls Study, 6-13 YO daughters and their parents/guardians from BC families (FH+) and families without BC (FH-) were recruited to examine early determinants of, and responses to BC risk. Parents/guardians completed surveys reporting on their daughters’ psychosocial adjustment (PSA). Mothers and daughters 10-13 YO completed surveys reporting their PSA and perceptions of breast cancer risk. We used linear and logistic regressions with variable selection.

Results: 731 parents/guardians reported on their own and the PSA of 898 daughters (450 FH+, 448 FH-), and 447 girls (10-13 YO) completed surveys (227 FH+, 220 FH-). FH+ girls have lower somatization and internalizing behaviors by parent/guardian report than FH- girls (Table 1). Intrusive BC (IBC) worry, and avoidant BC (ABC) worry were significantly higher in FH+ girls. IBC worry (coef=0.8, p=0.04) and ABC worry (coef 1.8, p=0.007) were higher in daughters whose mother had BC. Daughter perceived stress (PS), anxiety, depression, somatization, and internalizing did not differ by mother BC history. In multivariable models, daughter-anxiety was associated with mother-anxiety (Coef 1.4, p&lt;0.0001) and BRCA+ family (coef -13.5, p=0.040). Daughter-depression was associated with mother-anxiety (coef 1.0, p=0.009). Daughter-IBC worry was associated with mother-IBC worry (coef 0.2, p&lt;0.001). Daughter-ABC worry was associated with mother-IBC worry (coef 0.2, p=0.002) and being FH+ (coef 1.3, p=0.02). Daughter-PS was associated with mother-depression (coef 0.2, p=0.003). Somatization was not associated with any variables in multivariable models. FH+ girls were more likely to report themselves at higher risk for BC, although many reported uncertainty about their own BC risk.

Table 1Daughter Psychosocial AdjustmentFH+ Mean(SD)FH-Mean(SD)By parent/guardian reportn=437n=431Anxiety46.7 (30.3)49.1 (29.1)Depression51.2 (27.2)52.8 (27.3)Somatization43.9 (30.7)**50.3 (30.7)**Internalizing46.1 (29.6)*50.8 (29.1)*Daughter reportedn=228n=222Anxiety40.2 (28.5)42.4 (29.5)Depression32.4 (26.2)32.4 (27.7)Somatization36.5 (25.5)44.0 (27.7)Internalizing33.1 (25.5)34.0 (26.7)IBC Worry2.0 (3.4)**1.2 (2.4)**ABC Worry3.8 (5.8)**2.0 (4.3)**Perceived Stress4.8 (2.8)4.6 (2.8)Daughter Perceived BC Riskn=219n=209Higher risk for BC than peers85 (39%)**27 (13%)**Same risk as peers57 (26%)54 (26%)Lower risk than peers19 (9%)35 (17%)Responded 'not sure'58 (26)93 (45)* p&lt;0.05, ** p&lt;0.01

Conclusions: Pre-adolescent girls from BC families have lower somatization and internalizing behaviors by parent report, but higher self-reported BC worry. Daughter general anxiety, depression and BC worry are associated with corresponding mother affect. Some girls from BC families are aware of their increased risk and related research suggests this may increase with age. Understanding how PSA and BC worry changes over time and the impact on health and risk behaviors can inform interventions to optimize responses to growing up in families at familial and genetic risk for breast cancer.

Citation Format: Angela R Bradbury, Linda Patrick-Miller, Brian Egleston, Lisa Schwartz, Colleen B Sands, Wendy Chung, Gord Glendon, Lisa Tuchman, Cindy Moore, Paula Rauch, Irene Andrulis, Saundra Buys, Caren J Frost, Esther M John, Theresa Keegan, Julia Knight, Mary Beth Terry, Mary Daly. Psychosocial adjustment, cancer worry and perceived risk in 6-13 year old girls from breast cancer families [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P6-10-17.

Abstract P3-08-04: Aspirin and breast cancer risk for BRCA1 and BRCA2 mutation carriers

Background : Although epidemiologic studies have found evidence that aspirin use may be inversely associated with breast cancer (BC) risk, little is known about whether this applies to BRCA1 and BRCA2 mutation carriers.

Methods : We compared aspirin use in 613 women with BRCA1 or BRCA2 mutations from the six centers of the Breast Cancer Family Registry (BCFR) who were recruited at baseline and completed a questionnaire at 10 year follow-up. We defined cases as carriers with BC (n = 215 with BRCA1 mutations and 137 with BRCA2 mutations) and controls as carriers unaffected with BC (n = 141 with BRCA1 mutations and 120 with BRCA2 mutations). We used logistic regression to estimate odds ratios and 95% confidence intervals separately by gene mutation type.

Results : Three cases (1.4%) and 27 controls (19.1%) among the BRCA1 carriers and 3 cases (2.2%) and 25 controls (20.8%) among the BRCA2 carriers reported ever use of aspirin-based medications before diagnosis. Aspirin use before diagnosis was inversely associated with BC risk for both BRCA1 (OR, 0.13; 95% CI, 0.04-0.46 for ever vs. never use) and BRCA2 (OR, 0.12; 95% CI, 0.03-0.41 for ever vs. never use) carriers, after adjusting for age and center for BRCA1 carriers and age for BRCA2 carriers.

Conclusion : If replicated by larger, prospective studies, aspirin use could become an inexpensive and acceptable risk-reducing measure for BRCA1 and BRCA2 mutation carriers.

Citation Format: Naomi Kornhauser, Mary Beth Terry, Linda T Vahdat, Irene Andrulis, Saundra Buys, Mary Daly, Esther John, John L Hopper, Tessa Cigler. Aspirin and breast cancer risk for BRCA1 and BRCA2 mutation carriers [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P3-08-04.

Association of type and location of BRCA1 and BRCA2 mutations with risk of breast and ovarian cancer

IMPORTANCE

Limited information about the relationship between specific mutations in BRCA1 or BRCA2 (BRCA1/2) and cancer risk exists.

OBJECTIVE

To identify mutation-specific cancer risks for carriers of BRCA1/2.

DESIGN, SETTING, AND PARTICIPANTS

Observational study of women who were ascertained between 1937 and 2011 (median, 1999) and found to carry disease-associated BRCA1 or BRCA2 mutations. The international sample comprised 19,581 carriers of BRCA1 mutations and 11,900 carriers of BRCA2 mutations from 55 centers in 33 countries on 6 continents. We estimated hazard ratios for breast and ovarian cancer based on mutation type, function, and nucleotide position. We also estimated RHR, the ratio of breast vs ovarian cancer hazard ratios. A value of RHR greater than 1 indicated elevated breast cancer risk; a value of RHR less than 1 indicated elevated ovarian cancer risk.

EXPOSURES

Mutations of BRCA1 or BRCA2.

MAIN OUTCOMES AND MEASURES

Breast and ovarian cancer risks.

RESULTS

Among BRCA1 mutation carriers, 9052 women (46%) were diagnosed with breast cancer, 2317 (12%) with ovarian cancer, 1041 (5%) with breast and ovarian cancer, and 7171 (37%) without cancer. Among BRCA2 mutation carriers, 6180 women (52%) were diagnosed with breast cancer, 682 (6%) with ovarian cancer, 272 (2%) with breast and ovarian cancer, and 4766 (40%) without cancer. In BRCA1, we identified 3 breast cancer cluster regions (BCCRs) located at c.179 to c.505 (BCCR1; RHR = 1.46; 95% CI, 1.22-1.74; P = 2 × 10(-6)), c.4328 to c.4945 (BCCR2; RHR = 1.34; 95% CI, 1.01-1.78; P = .04), and c. 5261 to c.5563 (BCCR2', RHR = 1.38; 95% CI, 1.22-1.55; P = 6 × 10(-9)). We also identified an ovarian cancer cluster region (OCCR) from c.1380 to c.4062 (approximately exon 11) with RHR = 0.62 (95% CI, 0.56-0.70; P = 9 × 10(-17)). In BRCA2, we observed multiple BCCRs spanning c.1 to c.596 (BCCR1; RHR = 1.71; 95% CI, 1.06-2.78; P = .03), c.772 to c.1806 (BCCR1'; RHR = 1.63; 95% CI, 1.10-2.40; P = .01), and c.7394 to c.8904 (BCCR2; RHR = 2.31; 95% CI, 1.69-3.16; P = .00002). We also identified 3 OCCRs: the first (OCCR1) spanned c.3249 to c.5681 that was adjacent to c.5946delT (6174delT; RHR = 0.51; 95% CI, 0.44-0.60; P = 6 × 10(-17)). The second OCCR spanned c.6645 to c.7471 (OCCR2; RHR = 0.57; 95% CI, 0.41-0.80; P = .001). Mutations conferring nonsense-mediated decay were associated with differential breast or ovarian cancer risks and an earlier age of breast cancer diagnosis for both BRCA1 and BRCA2 mutation carriers.

CONCLUSIONS AND RELEVANCE

Breast and ovarian cancer risks varied by type and location of BRCA1/2 mutations. With appropriate validation, these data may have implications for risk assessment and cancer prevention decision making for carriers of BRCA1 and BRCA2 mutations.

Germline mutation in BRCA1 or BRCA2 and ten-year survival for women diagnosed with epithelial ovarian cancer

PURPOSE

To analyze the effect of germline mutations in BRCA1 and BRCA2 on mortality in patients with ovarian cancer up to 10 years after diagnosis.

EXPERIMENTAL DESIGN

We used unpublished survival time data for 2,242 patients from two case-control studies and extended survival time data for 4,314 patients from previously reported studies. All participants had been screened for deleterious germline mutations in BRCA1 and BRCA2. Survival time was analyzed for the combined data using Cox proportional hazard models with BRCA1 and BRCA2 as time-varying covariates. Competing risks were analyzed using Fine and Gray model.

RESULTS

The combined 10-year overall survival rate was 30% [95% confidence interval (CI), 28%-31%] for non-carriers, 25% (95% CI, 22%-28%) for BRCA1 carriers, and 35% (95% CI, 30%-41%) for BRCA2 carriers. The HR for BRCA1 was 0.53 at time zero and increased over time becoming greater than one at 4.8 years. For BRCA2, the HR was 0.42 at time zero and increased over time (predicted to become greater than 1 at 10.5 years). The results were similar when restricted to 3,202 patients with high-grade serous tumors and to ovarian cancer-specific mortality.

CONCLUSIONS

BRCA1/2 mutations are associated with better short-term survival, but this advantage decreases over time and in BRCA1 carriers is eventually reversed. This may have important implications for therapy of both primary and relapsed disease and for analysis of long-term survival in clinical trials of new agents, particularly those that are effective in BRCA1/2 mutation carriers.

Germline mutation in BRCA1 or BRCA2 and ten-year survival for women diagnosed with epithelial ovarian cancer

PURPOSE

To analyze the effect of germline mutations in BRCA1 and BRCA2 on mortality in patients with ovarian cancer up to 10 years after diagnosis.

EXPERIMENTAL DESIGN

We used unpublished survival time data for 2,242 patients from two case-control studies and extended survival time data for 4,314 patients from previously reported studies. All participants had been screened for deleterious germline mutations in BRCA1 and BRCA2. Survival time was analyzed for the combined data using Cox proportional hazard models with BRCA1 and BRCA2 as time-varying covariates. Competing risks were analyzed using Fine and Gray model.

RESULTS

The combined 10-year overall survival rate was 30% [95% confidence interval (CI), 28%-31%] for non-carriers, 25% (95% CI, 22%-28%) for BRCA1 carriers, and 35% (95% CI, 30%-41%) for BRCA2 carriers. The HR for BRCA1 was 0.53 at time zero and increased over time becoming greater than one at 4.8 years. For BRCA2, the HR was 0.42 at time zero and increased over time (predicted to become greater than 1 at 10.5 years). The results were similar when restricted to 3,202 patients with high-grade serous tumors and to ovarian cancer-specific mortality.

CONCLUSIONS

BRCA1/2 mutations are associated with better short-term survival, but this advantage decreases over time and in BRCA1 carriers is eventually reversed. This may have important implications for therapy of both primary and relapsed disease and for analysis of long-term survival in clinical trials of new agents, particularly those that are effective in BRCA1/2 mutation carriers.

A genome-wide association study of early-onset breast cancer identifies PFKM as a novel breast cancer gene and supports a common genetic spectrum for breast cancer at any age

Early-onset breast cancer (EOBC) causes substantial loss of life and productivity, creating a major burden among women worldwide. We analyzed 1,265,548 Hapmap3 single-nucleotide polymorphisms (SNP) among a discovery set of 3,523 EOBC incident cases and 2,702 population control women ages ≤ 51 years. The SNPs with smallest P values were examined in a replication set of 3,470 EOBC cases and 5,475 control women. We also tested EOBC association with 19,684 genes by annotating each gene with putative functional SNPs, and then combining their P values to obtain a gene-based P value. We examined the gene with smallest P value for replication in 1,145 breast cancer cases and 1,142 control women. The combined discovery and replication sets identified 72 new SNPs associated with EOBC (P < 4 × 10(-8)) located in six genomic regions previously reported to contain SNPs associated largely with later-onset breast cancer (LOBC). SNP rs2229882 and 10 other SNPs on chromosome 5q11.2 remained associated (P < 6 × 10(-4)) after adjustment for the strongest published SNPs in the region. Thirty-two of the 82 currently known LOBC SNPs were associated with EOBC (P < 0.05). Low power is likely responsible for the remaining 50 unassociated known LOBC SNPs. The gene-based analysis identified an association between breast cancer and the phosphofructokinase-muscle (PFKM) gene on chromosome 12q13.11 that met the genome-wide gene-based threshold of 2.5 × 10(-6). In conclusion, EOBC and LOBC seem to have similar genetic etiologies; the 5q11.2 region may contain multiple distinct breast cancer loci; and the PFKM gene region is worthy of further investigation. These findings should enhance our understanding of the etiology of breast cancer.

DNA glycosylases involved in base excision repair may be associated with cancer risk in BRCA1 and BRCA2 mutation carriers

Single Nucleotide Polymorphisms (SNPs) in genes involved in the DNA Base Excision Repair (BER) pathway could be associated with cancer risk in carriers of mutations in the high-penetrance susceptibility genes BRCA1 and BRCA2, given the relation of synthetic lethality that exists between one of the components of the BER pathway, PARP1 (poly ADP ribose polymerase), and both BRCA1 and BRCA2. In the present study, we have performed a comprehensive analysis of 18 genes involved in BER using a tagging SNP approach in a large series of BRCA1 and BRCA2 mutation carriers. 144 SNPs were analyzed in a two stage study involving 23,463 carriers from the CIMBA consortium (the Consortium of Investigators of Modifiers of BRCA1 and BRCA2). Eleven SNPs showed evidence of association with breast and/or ovarian cancer at p<0.05 in the combined analysis. Four of the five genes for which strongest evidence of association was observed were DNA glycosylases. The strongest evidence was for rs1466785 in the NEIL2 (endonuclease VIII-like 2) gene (HR: 1.09, 95% CI (1.03-1.16), p = 2.7 × 10(-3)) for association with breast cancer risk in BRCA2 mutation carriers, and rs2304277 in the OGG1 (8-guanine DNA glycosylase) gene, with ovarian cancer risk in BRCA1 mutation carriers (HR: 1.12 95%CI: 1.03-1.21, p = 4.8 × 10(-3)). DNA glycosylases involved in the first steps of the BER pathway may be associated with cancer risk in BRCA1/2 mutation carriers and should be more comprehensively studied.

Identification of new genetic susceptibility loci for breast cancer through consideration of gene-environment interactions

Genes that alter disease risk only in combination with certain environmental exposures may not be detected in genetic association analysis. By using methods accounting for gene-environment (G × E) interaction, we aimed to identify novel genetic loci associated with breast cancer risk. Up to 34,475 cases and 34,786 controls of European ancestry from up to 23 studies in the Breast Cancer Association Consortium were included. Overall, 71,527 single nucleotide polymorphisms (SNPs), enriched for association with breast cancer, were tested for interaction with 10 environmental risk factors using three recently proposed hybrid methods and a joint test of association and interaction. Analyses were adjusted for age, study, population stratification, and confounding factors as applicable. Three SNPs in two independent loci showed statistically significant association: SNPs rs10483028 and rs2242714 in perfect linkage disequilibrium on chromosome 21 and rs12197388 in ARID1B on chromosome 6. While rs12197388 was identified using the joint test with parity and with age at menarche (P-values = 3 × 10(-07)), the variants on chromosome 21 q22.12, which showed interaction with adult body mass index (BMI) in 8,891 postmenopausal women, were identified by all methods applied. SNP rs10483028 was associated with breast cancer in women with a BMI below 25 kg/m(2) (OR = 1.26, 95% CI 1.15-1.38) but not in women with a BMI of 30 kg/m(2) or higher (OR = 0.89, 95% CI 0.72-1.11, P for interaction = 3.2 × 10(-05)). Our findings confirm comparable power of the recent methods for detecting G × E interaction and the utility of using G × E interaction analyses to identify new susceptibility loci.

Identification of fifteen novel germline variants in the BRCA1 3'UTR reveals a variant in a breast cancer case that introduces a functional miR-103 target site

Mutations in the BRCA1 gene confer a substantial increase in breast cancer risk, yet routine clinical genetic screening is limited to the coding regions and intron-exon boundaries, precluding the identification of mutations in noncoding and untranslated regions (UTR). As 3'UTR mutations can influence cancer susceptibility by altering protein and microRNA (miRNA) binding regions, we screened the BRCA1 3'UTR for mutations in a large series of BRCA-mutation negative, population and clinic-based breast cancer cases, and controls. Fifteen novel BRCA1 3'UTR variants were identified, the majority of which were unique to either cases or controls. Using luciferase reporter assays, three variants found in cases, c.* 528G>C, c.* 718A>G, and c.* 1271T>C and four found in controls, c.* 309T>C, c.* 379G>A, c.* 823C>T, and c.* 264C>T, reduced 3'UTR activity (P < 0.02), whereas two variants found in cases, c.* 291C>T and c.* 1139G>T, increased 3'UTR activity (P < 0.01). Three case variants, c.* 718A>G, c.* 800T>C, and c.* 1340_1342delTGT, were predicted to create new miRNA binding sites and c.* 1340_1342delTGT caused a reduction (25%, P = 0.0007) in 3'UTR reporter activity when coexpressed with the predicted targeting miRNA, miR-103. This is the most comprehensive identification and analysis of BRCA1 3'UTR variants published to date.

Abstract 1447: Investigating susceptibility to sporadic osteosarcoma by genome-wide copy number analysis

Constitutional copy-number variants (CNVs) frequently overlap genomic regions that contain genes associated with cancer. In addition, copy number alterations (CNAs) in tumors often coincide with sites of CNVs and may arise through progression of CNVs. Osteosarcoma (OS), the most common human bone malignancy, can arise in familial or sporadic forms. While germline mutations of tumor suppressor genes have been implicated in a minority of OS cases, little is known about genetic changes that contribute to the etiology of sporadic OS. Using high-resolution SNP/CNV arrays, we observed a higher global germline CNV frequency in patients with sporadic OS compared to healthy controls. Given the early age of onset and the extensive constitutional CNVs, we hypothesize that these genomic alterations are linked to susceptibility to OS. Here we investigate whether specific constitutional CNVs are related to susceptibility to sporadic OS and whether OS tumor CNAs arise via progression of constitutional CNVs in these patients. Blood derived DNA samples from patients with sporadic OS with wild-type germline p53 sequence and gene dosage were selected for analysis on Affymetrix GW6.0 arrays with paired pre-therapy tumor biopsies. Initial results from a discovery set of samples (n=43 pairs) reveal a copy number loss at 1q43, in a region that overlaps several genes that have a role in bone formation, microtubules and cytoskeletal organization. This loss was present in 43% of the blood-derived DNA samples and 44% of the tumor-derived samples, whereas this variant was noted in only 1.2% of controls. Furthermore, the germline 1q43 deletion correlates with poor survival of the OS patients (p=0.04, Long Rank). Analysis of an independent validation set (n=32 pairs) is currently underway to confirm the initial finding and further characterize specific constitutional CNVs among sporadic OS patients. The findings of this study will open new avenues for the discovery of novel loci implicated in susceptibility to OS with potential for improved diagnostic and prognostic options as well as further insight into disease pathogenesis.

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 1447. doi:1538-7445.AM2012-1447

Associations of common variants at 1p11.2 and 14q24.1 (RAD51L1) with breast cancer risk and heterogeneity by tumor subtype: findings from the Breast Cancer Association Consortium

A genome-wide association study (GWAS) identified single-nucleotide polymorphisms (SNPs) at 1p11.2 and 14q24.1 (RAD51L1) as breast cancer susceptibility loci. The initial GWAS suggested stronger effects for both loci for estrogen receptor (ER)-positive tumors. Using data from the Breast Cancer Association Consortium (BCAC), we sought to determine whether risks differ by ER, progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2), grade, node status, tumor size, and ductal or lobular morphology. We genotyped rs11249433 at 1p.11.2, and two highly correlated SNPs rs999737 and rs10483813 (r(2)= 0.98) at 14q24.1 (RAD51L1), for up to 46 036 invasive breast cancer cases and 46 930 controls from 39 studies. Analyses by tumor characteristics focused on subjects reporting to be white women of European ancestry and were based on 25 458 cases, of which 87% had ER data. The SNP at 1p11.2 showed significantly stronger associations with ER-positive tumors [per-allele odds ratio (OR) for ER-positive tumors was 1.13, 95% CI = 1.10-1.16 and, for ER-negative tumors, OR was 1.03, 95% CI = 0.98-1.07, case-only P-heterogeneity = 7.6 × 10(-5)]. The association with ER-positive tumors was stronger for tumors of lower grade (case-only P= 6.7 × 10(-3)) and lobular histology (case-only P= 0.01). SNPs at 14q24.1 were associated with risk for most tumor subtypes evaluated, including triple-negative breast cancers, which has not been described previously. Our results underscore the need for large pooling efforts with tumor pathology data to help refine risk estimates for SNP associations with susceptibility to different subtypes of breast cancer.

Rare variants in the ATM gene and risk of breast cancer

Introduction

The ataxia-telangiectasia mutated (ATM) gene (MIM ID 208900) encodes a protein kinase that plays a significant role in the activation of cellular responses to DNA double-strand breaks through subsequent phosphorylation of central players in the DNA damage-response pathway. Recent studies have confirmed that some specific variants in the ATM gene are associated with increased breast cancer (BC) risk. However, the magnitude of risk and the subset of variants that are pathogenic for breast cancer remain unresolved.

Methods

To investigate the role of ATM in BC susceptibility, we studied 76 rare sequence variants in the ATM gene in a case-control family study of 2,570 cases of breast cancer and 1,448 controls. The variants were grouped into three categories based on their likely pathogenicity, as determined by in silico analysis and analyzed by conditional logistic regression. Likely pathogenic sequence variants were genotyped in 129 family members of 27 carrier probands (15 of which carried c.7271T > G), and modified segregation analysis was used to estimate the BC penetrance associated with these rare ATM variants.

Results

In the case-control analysis, we observed an odds ratio of 2.55 and 95% confidence interval (CI, 0.54 to 12.0) for the most likely deleterious variants. In the family-based analyses, the maximum-likelihood estimate of the increased risk associated with these variants was hazard ratio (HR) = 6.88 (95% CI, 2.33 to 20.3; P = 0.00008), corresponding to a 60% cumulative risk of BC by age 80 years. Analysis of loss of heterozygosity (LOH) in 18 breast tumors from women carrying likely pathogenic rare sequence variants revealed no consistent pattern of loss of the ATM variant.

Conclusions

The risk estimates from this study suggest that women carrying the pathogenic variant, ATM c.7271T > G, or truncating mutations demonstrate a significantly increased risk of breast cancer with a penetrance that appears similar to that conferred by germline mutations in BRCA2.

Abstract 5334: Genome-wide copy number analysis reveals two novel loci for susceptibility to sporadic osteosarcoma

Copy-number variants (CNVs) frequently overlap genomic regions that contain genes associated with cancer. In addition, copy number alterations (CNAs) often coincide with sites of CNVs and may arise through progression of CNVs. Osteosarcoma (OS), the most common human bone malignancy, can arise in familial or sporadic forms. While germline mutations of tumor suppressor genes have been implicated in some hereditary forms of OS, little is known about genetic changes that contribute to the etiology of sporadic OS. Using high-resolutation SNP/CNV arrays, we have observed a high global CNV frequency in patients with sporadic osteosarcoma. We hypothesized that these genomic alterations are linked to susceptibility to OS. Here we investigate whether CNAs in OS tumor DNA reflect extensive constitutional CNVs in OS patients and whether OS tumor CNAs arise by progression of constitutional CNVs in these patients.

Paired samples from blood and pre-therapy tumor biopsies of 44 OS patients were hybridized to Affymetrix GW 6.0 arrays and analyzed using Partek Genomics Suite and Nexus Copy Number™ software. Analysis focused on CNVs which fulfilled the following criteria: 1) absent from normal controls, 2) recurrent, 3) previously unreported, 4) mapped within or nearby known genes and 5) overlapped with paired tumour CNA. Regions identified in this analysis were validated as candidate regions by quantitative PCR.

Two candidate CNVs have been identified: a copy-number loss at 1q43 and a copy-number gain at 2p11.2. The copy number loss at 1q43 was present in DNA of 43% of the blood and 40% of tumor samples. 38% of the 1q43 deletions in the tumors were de novo events. This CNV is upstream of the centrosomal protein 170kDa gene (CEP170) which has been shown to maintain microtubule organization and cell morphology. As microtubule function is critical for proper chromosome segregation during cell division, copy-number change-driven dysregulation of CEP170 might be related to the characteristic genomic instability in OS. We are currently exploring this possibility via expression profiling. The copy-number gain at 2p11.2 was identified in 45% of the OS blood derived DNA and in 65% of those, the gain was also seen in matched tumor DNA. This CNV is in proximity to FLJ40330, a non-coding RNA, and to ribose 5-phosphate isomerase (RPI). A custom CGH array platform is currently being used to further characterize these loci on paired blood and tumor DNA samples from an additional cohort of OS patients.

These findings support the premise that excessive constitutional CNV is a hallmark of sporadic OS and may open new avenues for the discovery of novel specific CNVs and genes implicated in susceptibility to OS which may be of diagnostic and/or prognostic relevance.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5334. doi:10.1158/1538-7445.AM2011-5334

Abstract 3940: Identifying novel susceptibility genes in genomic aberrant regions in early-onset breast cancer

Several genes have been implicated in hereditary breast cancer, but account for a fraction of all hereditary cases. We hypothesize that other genes are involved in susceptibility and progression of breast cancer and will be represented as chromosomal losses and gains that can be detected in tumors from breast cancer patients who are at high risk of carrying mutations in breast cancer susceptibility genes other than BRCA1 and BRCA2.

We have focused on women with personal (diagnosis &lt; 40 years) and family (at least one affected sister) histories of breast cancer and are not carriers of mutations in known cancer susceptibility genes. Blocks of formalin fixed and paraffin embedded (FFPE) tumor tissue from early age of onset breast cancer patients have been retrieved from the Ontario site of the Breast Cancer Family Registry. Each case is reviewed by a pathologist and tumor material is selected for micro-dissection. We have been using Illumina's high resolution genomic single nucleotide polymophism (SNP) microarrays to identify and characterize changes in germline and tumor DNA from women with early-onset breast cancer. By using SNPs to determine DNA copy numbers of the tumor and germline DNA from each case, we will differentiate changes in the genomes that are specific to the tumors.

I have modified and optimized the protocols for which DNA is extracted and prepared from microdissected FFPE tumor cases prior to hybridization onto microarrays which improves the SNP call rate of FFPE. In a comparison of SNP microarray copy number analysis in cases for which we have archival and matching fresh frozen tumor DNAs, 80% deleted and amplified regions delineated in FFPE samples were detected in the matching fresh frozen reference. These results lead us to be confident that FFPE treated tumor tissues used in our study are a viable resource of for which novel genes involved in breast cancer can be discovered.

On SNP microarrays, we have so far evaluated 25 early-onset cases for which both tumor and germline DNA have been hybridized. Recurrent regions of aberration include gains in 6p21.1 and 8q24 in 24% of cases and losses in 11q22.3 and 9q21.13 in 44% and 24% of cases, respectively. Interesting, our initial analysis shows gains in CCND1 and CCND3 in 14% and 24% of cases, implicating cell cycle regulation genes as frequently aberrant in copy number.

With access to the germline DNA, normal variation can be accounted for, while regions of LOH can be found in the tumors. Validated recurrently amplified and deleted regions in tumor samples containing candidate genes, onco- and tumor suppressing genes will be further studied for their role in breast cancer through functional analysis. This study is very likely to have significance, not only for our understanding of hereditary breast cancer, but also for the more common non-hereditary form of breast cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3940. doi:10.1158/1538-7445.AM2011-3940

Global DNA methylation levels in girls with and without a family history of breast cancer

Lower levels of global DNA methylation in white blood cell (WBC) DNA have been associated with adult cancers. It is unknown whether individuals with a family history of cancer also have lower levels of global DNA methylation early in life. We examined global DNA methylation in WBC (measured in three repetitive elements, LINE1, Sat2 and Alu, by MethyLight and in LINE1 by pyrosequencing) in 51 girls ages 6-17. Compared to girls without a family history of breast cancer, methylation levels were lower for all assays in girls with a family history of breast cancer, and statistically significantly lower for Alu and LINE1 pyrosequencing. After adjusting for age, body mass index (BMI), and Tanner stage, only methylation in Alu was associated with family history of breast cancer. If these findings are replicated in larger studies, they suggest that lower levels of global WBC DNA methylation observed later in life in adults with cancer may also be present early in life in children with a family history of cancer.

Abstract P2-11-01: Molecular Profiling Identifies Differentially Expressed Genes between Normal Breast Tissue from BRCA Carriers and Women at Population Risk

Background: Women found to carry a BRCA1 or BRCA2 gene mutation are at significant risk of future breast cancer (BC). Prophylactic mastectomy (PM) remains the most effective risk reducing strategy in that setting. Thus far, there are no data available identifying changes in gene expression profiles prior to the onset of BC in these women using microarray technology.

Material and methods : In this pilot study, we prospectively collected PM specimens from BRCA1/2 mutation carriers (n=21), and reduction mammoplasty (RM) specimens from healthy controls at population risk of breast cancer (n=13). Samples were collected from all 4 quadrants (fresh frozen) and careful histological examination was conducted. Selected samples (most dense parenchymal tissue) were sent for microarray analyses (19K chip, http://www.uhnres.utoronto.ca/facilities/index.htm). We compared the molecular profiles of breast tissue obtained from these two groups using two approaches: 1) microarray analysis for a global assessment of gene expression, and 2) gene set analysis to identify differences based on cellular function and biologic themes. Results: Women in each group were of similar age (p=NS). No invasive cancer was identified. In histologically normal breast tissue, class comparison identified differential gene expression between RM and PM tissues. Gene set analysis of five collections including MSigDB C2, C4, cytobands, Stanford 5Mb chromosomal tiles and KEGG database identified 22 significant gene sets. Nine sets were overexpressed and 13 sets were underexpressed in PM tissues (FDR &lt; 0.2; p &lt; 0.012). We found overexpression of genes relating to proliferation and transcription specifically in the PM tissues enriched for Gene Ontology annotations. The top 200 genes ranked by SAM were also examined by pathway analysis that showed high enrichment for cancer related pathways. All three approaches implicated T cell receptor signaling and a TSG101-stathmin breast cancer related pathway as contributing to the differential molecular profiles between RM and PM tissues.

Discussion: We have shown differential expression of single genes as well as cancer related biologic pathways (using microarray and gene set analyses) between normal breast tissue from BRCA1/2 mutation carriers (at high risk of BC) and healthy controls (at population risk of BC). These differences may represent early molecular defects of genetic pathways potentially involved in the early stages of breast carcinogenesis in women at hereditary high risk or may represent the result of BRCA1/2 haploinsufficiency. These results support the hypothesis that molecular pathways leading to BC formation are unique to BRCA1/2 carriers. This information may help the development of innovative preventive strategies for BRCA carriers in the future.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P2-11-01.

A Genomic Biomarker for Breast Cancer Development in High-Risk Women

BackgroundFamily history is an important factor contributing to a woman's risk of breast cancer development. This increased risk reflects the participation of inherited genetic components such as breast cancer susceptibility genes. However, many of the genetic components contributing to breast cancer remain unknown, and a number of women with a family history of breast cancer never develop breast cancer despite their high-risk status, while other high-risk woman go on to develop breast cancer. Thus, it is clear that we lack crucial pieces of information to help define a person's true risk of developing breast cancer.Methods and FindingsWe hypothesize that there are many undiscovered germline variations in genes that lead to altered gene expression patterns predictive of breast cancer development in high-risk women. We have developed a genomic model capable of predicting which high-risk women, both BRCA1/2 mutation carriers and BRCAX women, will actually develop breast cancer. Specifically, we use exon-level genome-wide expression profiling of peripheral blood mononuclear cells (PBMCs) to develop a model of disease risk (n=118 samples of either control or high-risk women). From this data, we generate a biomarker consisting of genes that most correlate to cancer development in women with strong family histories of breast cancer. Using an internal independent dataset, our biomarker can predict the high-risk women who will or will not develop cancer with over 85% accuracy. Further, we have validated this model on an independent external cohort (n=36) which was obtained and processed at sites unique to our training dataset. Our genomic biomarker can accurately predict breast cancer development in high-risk women with over 78% accuracy using this external dataset. Therefore, from our analyses, we can calculate with high accuracy an individual woman's true risk of developing breast cancer. This method provides a personalized approach to hereditary breast cancer risk assessment that is not currently available. This personalized risk assessment will aide clinicians in counseling their patients regarding specific management options based on a patient's individual risk of breast cancer. Lastly, these studies have also identified novel genes associated with breast cancer risk, which may provide a basis for targeted therapies that may help modify the risk of breast cancer development in high risk patients.ConclusionsTogether, these studies deliver both a non-invasive biomarker for hereditary breast cancer risk and a characterization of genes that contribute to breast cancer development. Overall, we expect these experiments to identify the genetic changes that underlie breast cancer predisposition, and assist clinicians and patients in determining the appropriate preventative measures based on their personal risk of developing breast cancer.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 4059.

Aberrant methylation of RASSF1A in plasma DNA before breast cancer diagnosis in the Breast Cancer Family Registry

In addition to classic genetic mechanisms such as deletions and mutations, growth regulatory genes can be inactivated via methylation of cytosine-residues in their promoter regions. Hypermethylation of promoter CpG islands is now recognized as an important and early event in carcinogenesis. Detection of methylated DNA in serum or plasma has been suggested to be a marker for early cancer development. We examined methylation changes in RASSF1A, a growth regulatory gene in plasma DNA from blood collected before diagnosis from women with breast cancer and from controls. Samples were from two sets of subjects, 28 women with breast cancer and 10 of their unaffected siblings, and 33 women with breast cancer and 29 age- and ethnicity-matched population-based controls. Using methylation specific PCR, we found 11 of 61 (18%) cases were positive for methylation of RASSF1A in their plasma DNA collected before diagnosis. Two of 10 healthy high-risk sibling controls (20%) had plasma DNA positive for RASSF1A methylation in their plasma DNA compared with 0 of 29 (0%) population-based controls. Tumor tissue was available for 12 cases and all were positive for RASSF1A methylation. These results, if replicated, suggest that aberrant promoter hypermethylation in serum/plasma DNA may be common among high-risk women and may be present years before cancer diagnosis.

Prognosis in BRCA1, BRCA2 associated breast cancer (BC): a prospective Breast Cancer Family Registry (BCFR) international population-based cohort study

Abstract #2072

Hereditary BC occurs at a younger age and is associated with more adverse tumor-related features than sporadic breast cancer (BC) (defined here as BC in those with no 1st or 2nd degree family history of breast or ovarian cancer). Using pre-specified criteria, we assembled a population-based cohort of newly diagnosed BC at 3 centers: Ontario, Canada (1996-98), San Francisco Bay area, USA (1995-2000), Melbourne/Sydney, Australia (1991-1998). Medical information was obtained from medical records; women were followed prospectively for recurrence, new cancers and death. Pathology data were obtained from central review or pathology reports. BRCA1 and BRCA2 mutation testing was performed on 77% and 70% of cases, respectively (sporadic BC cases were not tested at 2 centers). Hereditary and sporadic BC cases were compared using Cox proportional hazards (stratified by center). 3215 eligible cases were enrolled in the BCFR, with a mean age at diagnosis of 46.9 years. Median follow-up was 7.61 years; 565 women had distant recurrences and 547 died. There were 92 cases with BRCA1 and 72 with BRCA2 mutations; 1549 (48.2%) had sporadic BC; the remainder had familial BC as defined above. BRCA1 mutations were associated with young age, estrogen and progesterone receptor (ER and PgR) negativity and high grade; BRCA2 mutations were associated with node positivity and high grade. Distant disease-free survival (DDFS) and overall survival (OS) did not differ significantly between BRCA1 carriers and sporadic cases in univariate or multivariate analyses. DDFS and OS were worse in BRCA2 carriers than in sporadic cases (HR 1.6, p=0.04 and HR 1.8, p=0.01, respectively) in univariate analyses but not in multivariate analyses (DDFS HR 1.0, p=0.98; OS HR 1.13, p=0.61). The small group of BRCA2 carriers who did not receive adjuvant chemotherapy had a significantly worse OS (multivariate HR 3.63, p = 0.005). Furthermore, BRCA2 carriers who received adjuvant tamoxifen had significantly worse OS than women with sporadic BC (HR=2.0, p=0.03). We conclude that BRCA1 and BRCA2 mutations do not independently impact DDFS or OS. Significantly worse outcomes were seen in BRCA2 carrier subgroups defined by adjuvant treatment; this requires further investigation and may have implications for clinical practice.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2072.

HER2 testing in a population-based study of patients with metastatic breast cancer treated with trastuzumab

CONTEXT

The development of trastuzumab has led to new therapeutic strategies for patients with breast cancer. Trastuzumab has been shown to only be effective in those patients whose cancers are HER2 positive by either immunohistochemistry (IHC) or fluorescence in situ hybridization (FISH).

OBJECTIVE

To determine the accuracy of HER2 testing in 2 provinces in Canada.

DESIGN

Patients with metastatic breast cancer diagnosed between 1999 and 2002 who were HER2 positive in the local laboratories were included in this study. All cases were retested centrally, by IHC (using 4 methods) and FISH. In addition, 205 locally reported HER2-negative metastatic breast cancer cases were retested centrally.

RESULTS

Concordance between the 505 local IHC-positive cases with central IHC testing varied between 79.3% and 89.6% depending on the IHC method and scoring method used. HER2 gene amplification by FISH was present in 86.1% of local IHC-positive cases. Concordance between the 205 local IHC-negative tumors with central testing ranged between 94.8% and 100% for IHC and was 98.5% for FISH.

CONCLUSIONS

This study demonstrated that locally reported HER2-negative results were highly accurate, but less accuracy was demonstrated with local HER2-positive results. These results emphasize the need for participation in a quality assurance program.

Application of reliability coefficients in cDNA microarray data analysis

Gene expression microarray technology has been widely used in areas such as human cancer research to identify molecular characteristics of sample specimens. The microarray study, however, is a very complicated procedure which involves numerous sources of variability that may be either systematic or random. Systematic variation is often eliminated by applying normalization procedures, but at present there are no standard criteria available to evaluate the performance of a particular normalization approach. In this paper, we propose a reliability-type coefficient as a criterion to assess the effectiveness of normalization procedures in eliminating systematic variation. Simulation studies show that this criterion performs reasonably well in a range of settings. The proposed method is illustrated using a subset of an ongoing microarray study of soft-tissue sarcoma.

Invasive lobular carcinoma: to grade or not to grade

Grading of invasive ductal carcinoma of no special type using the Nottingham combined histologic grading system provides independent prognostic information. The prognostic utility of grading invasive lobular carcinomas, however, has not been fully elucidated. In addition, the relationship between grade in invasive lobular carcinomas and expression of predictive biomarkers is less certain. The purpose of this study was to correlate histologic grade in invasive lobular carcinoma with known prognostic and predictive markers. All primary resections for invasive mammary carcinomas diagnosed in Mount Sinai Hospital, Toronto, between the years 1996 and 2002 were reviewed (n=1053). Of these cases, 50 were pure invasive lobular carcinoma (incidence 4.7%). The median age at diagnosis was 64 years. These tumors were graded using the Nottingham combined histologic grading system and analyzed for estrogen receptor, progesterone receptor, HER2/neu and E-cadherin expression. Tumor grade was correlated with tumor size (P=0.03), and the American Joint Committee on Cancer nodal status (P=0.05). Assessment of the individual components of grade showed that the mitotic score was highly correlated with tumor size (P=0.02), lymph node positivity (P=0.02) and overall American Joint Committee on Cancer stage (P=0.01). Estrogen receptor and progesterone receptor were highly expressed irrespective of the grade of tumor. HER2/neu protein overexpression and E-cadherin protein expression was absent in all invasive lobular carcinomas studied. We conclude that pure invasive lobular carcinoma is uncommon and occurs predominantly in postmenopausal women. Increasing tumor grade is correlated with median tumor size and the American Joint Committee on Cancer nodal stage, but not correlated with the expression of estrogen receptor, progesterone receptor, E-cadherin or HER2/neu protein overexpression.

Prognostic factors affecting the natural history of node-negative breast cancer

PURPOSE

We undertook a natural history investigation of a broad selection of prognostic factors in a cohort of women with node-negative breast cancer.

PATIENTS AND METHODS

The cohort consisted of 415 consecutive histologic node-negative (T1-3, M0) patients, operated on for primary breast cancer at Women's College Hospital, Toronto, Canada, between 1977 and 1986. Only 7% of these patients were given adjuvant systemic therapy; further, for the 48% of women who underwent lumpectomy, only 29% received adjuvant radiotherapy to the breast. Paraffin-embedded tumour tissue was available for the majority of patients. The following factors were examined for their univariate and multivariate effects on time to recurrence outside the breast (DFI) and survival from breast cancer (DSS): age, weight, tumour size, estrogen receptor, progesterone receptor, histologic type, tumour grade, nuclear grade, lymphovascular invasion, overexpression of neu oncoprotein, DNA ploidy, % cells in S-phase, and adjuvant therapy. Multivariate analyses utilized a Cox model with a step-wise factor selection for the 260 patients with complete information.

RESULTS

A worse prognosis was indicated when there was lymphovascular invasion (for DFI, p < 0.001; for DSS, p = 0.0046), high %S-phase (for DFI, p = 0.08; for DSS, p = 0.02), high tumour grade (for DFI, p = 0.02; for DSS, p = 0.03), and overexpression of neu oncoprotein (for DSS, p = 0.07).

CONCLUSIONS

In our natural history investigation, two factors, lymphovascular invasion and tumour grade, are of particular interest since they may be readily incorporated into clinical practice. Overexpression of neu oncoprotein may also play a role in determining prognosis for women administered adjuvant systemic therapy.

Oral contraceptive use and ovarian cancer risk among carriers of BRCA1 or BRCA2 mutations

Women with mutations of the genes BRCA1 or BRCA2 are at increased risk of ovarian cancer. Oral contraceptives protect against ovarian cancer in general, but it is not known whether they protect against the disease in carriers of these mutations. We obtained self-reported lifetime histories of oral contraceptive use from 451 women who carried mutations of BRCA1 or BRCA2. We used conditional logistic regression to estimate the odds ratios associated with oral contraceptive use, comparing the histories of 147 women with ovarian cancer (cases) to those of 304 women without ovarian cancer (controls) who were matched to cases on year of birth, country of residence and gene (BRCA1 vs BRCA2). Reference ages for controls had to exceed the ages at diagnosis of their matched cases. After adjusting for parity, the odds-ratio for ovarian cancer associated with use of oral contraceptives for at least 1 year was 0.85 (95 percent confidence interval, 0.53–1.36). The risk decreased by 5% (1–9%) with each year of use (P for trend=0.01). Use for 6 or more years was associated with an odds-ratio of 0.62 (0.35–1.09). These data support the hypothesis that long-term oral contraceptive use reduces the risk of ovarian cancer among women who carry mutations of BRCA1 or BRCA2.

Amplification of the TOP2A gene does not predict high levels of topoisomerase II alpha protein in human breast tumor samples

Recent clinical trials have suggested that patients whose breast tumors overexpress HER2 may derive particular benefit from anthracycline-containing chemotherapy compared to that without anthracycline. It has been proposed that the HER2 gene amplification reported in these tumors might mask an underlying TOP2A gene amplification that occurs frequently and concurrently with HER2 amplification. Topoisomerase II alpha, encoded by TOP2A, is a direct molecular target of anthracycline drug action and is potentially useful as a predictive marker of response to anthracycline therapy for breast cancer. In this study, we examined whether TOP2A gene amplification is an appropriate marker for identifying breast tumors expressing high levels of topoisomerase II alpha. We determined topoisomerase II alpha protein expression by immunohistochemistry in 81 human breast tumors in relation to HER2 and TOP2A gene copy numbers analyzed by fluorescence in situ hybridization, histologic grade, cell proliferation fraction measured by MIB-1 expression, and HER2 protein expression determined by immunohistochemistry. The results showed no correlation between TOP2A gene copy number and topoisomerase II alpha protein expression levels in breast tumors, in contrast to the analogous situation for HER2 gene amplification and HER2 immunohistochemistry. Our results suggest that TOP2A gene amplification in breast tumors does not predict high expression of topoisomerase II alpha protein.

Ethnicity, but not cancer family history, is related to response to a population-based mailed questionnaire

PURPOSE

To determine if family history and ethnic background are factors affecting response to a mailed cancer family history questionnaire from the Ontario Familial Breast Cancer Registry.

METHODS

Individuals diagnosed with primary invasive breast carcinomas (probands) were mailed a family history questionnaire, the first contact in a multi-stage process. This questionnaire obtained cancer family history and ethnicity data. After one month, a follow up telephone call was made to those who did not return this questionnaire and attempts were made to ask similar questions by telephone interview. Characteristics of those responding to the mailed questionnaire were compared to those who responded to the telephone interview only.

RESULTS

339 probands were included in this study: 242 returned a mailed version of the questionnaire; 57 completed the questionnaire over the phone. Cancer family history/genetic risk criteria was not significantly related to type of response. Probands identifying themselves as visible minorities were significantly less likely to respond to the mailed questionnaire than the telephone interview (11.6% vs. 22.8%, P=0.03).

CONCLUSIONS

Having a family history of cancer did not appear to influence response to a mailed questionnaire, but those reporting an ethnic/racial background other than White were more likely to respond to a telephone interview.

Biology of childhood osteogenic sarcoma and potential targets for therapeutic development: meeting summary

Childhood osteogenic sarcoma (OS) is a rare bone cancer occurring primarily in adolescents. The North American pediatric cooperative groups have performed a series of clinical treatment trials in this disease over the past several decades, and biology studies of tumor tissue have been an important study component. A meeting was held in Bethesda, Maryland on November 29-30, 2001, sponsored by the NIH Office of Rare Diseases, the Children's Oncology Group, and the National Cancer Institute-Cancer Therapy Evaluation Program with the general objectives: (a) to review the current state of knowledge regarding OS biology; (b) to identify, prioritize, and support the development of biology studies of potential clinical relevance in OS; and (c) to discuss the available tissue resources and the appropriate methods for analysis of OS samples for the conduct of biology studies. This report summarizes the information presented and discussed by the meeting participants.

Reduced growth of human sarcoma xenografts in hosts homozygous for the lit mutation

BACKGROUND AND OBJECTIVES

Prior studies have shown that sarcoma growth can be stimulated by insulin-like growth factor-I (IGF-I). To extend this line of research, we carried out in vivo growth studies of primary human sarcoma in immunosuppressed control and IGF-I-deficient mice.

METHODS

Human sarcoma specimens (one osteosarcoma and seven soft tissue sarcomas) were harvested in the operating room and implanted in immunosuppressed mice. Second-generation sarcomas were transplanted to control (GH replete lit/+ mice) and to experimental (GH/IGF-I-deficient lit/lit) animals. When tumors reached 1,000 mm(3) in one group, average tumor size was compared in the two groups. IGF-I receptor expression was measured by RT-PCR and IGF-I receptor binding sites were assayed by radiolabeled IGF-I.

RESULTS

Five of eight sarcomas demonstrated reduced growth in the GH/IGF-I-deficient lit/lit animals. In four of the five sarcomas that demonstrated growth inhibition, IGF-R was elevated relative to placenta or a positive control cell line (MCF-7, which is known to be responsive to IGF-I in vitro and in vivo). In three of the five sarcomas that demonstrated growth suppression, IGF-R was elevated twofold after implantation in the experimental IGF-I-deficient animals.

CONCLUSIONS

The GH-IGF axis may be an important stimulator of tumor growth in sarcomas. These experiments suggest that IGF suppression may inhibit sarcoma growth in vivo.

Comparison of HER2/neu status assessed by quantitative polymerase chain reaction and immunohistochemistry

We prospectively evaluated a series of 254 breast cancers by quantitative polymerase chain reaction (PCR) and immunohistochemistry using 3 antibodies: HercepTest, CB11, and TAB250. DNA was extracted from a 10-micron tumor section for PCR, and 4-micron serial sections were taken from the same block for immunohistochemistry. The immunohistochemical results were scored using a semiquantitative immunohistochemical system. A positive tumor by immunohistochemistry had a score of 5 or more. The manufacturer's recommended scoring system was used for the HercepTest. Tumors were positive for gene amplification if the ratio of the HER2/neu gene to control gene after normalization was 2 or more. Of 254 cases, 61 showed gene amplification. For immunohistochemistry, 23% of tumors were positive with CB11, 27% with TAB250, and 37% with the HercepTest. Results for each antibody were compared with PCR results. The overall concordance for the HercepTest was 82%, which was significantly lower than that for CB11 (88%) or TAB250 (87%). The specificity for the HercepTest was 80% compared with 90% for TAB250 and 93% for CB11, while the positive predictive value for the HercepTest was 57% compared with 71% and 76% for TAB250 and CB11, respectively.

Methylation of the BRCA1 promoter is associated with decreased BRCA1 mRNA levels in clinical breast cancer specimens

Functional inactivation of BRCA1 is an important mechanism involved in breast cancer pathogenesis. Mutation is often responsible for BRCA1 inactivation in familial breast cancer, but is not responsible for the decreased levels of BRCA1 seen in a subset of sporadic breast cancer patients. To determine if aberrant cytosine methylation of the BRCA1 promoter is associated with decreased BRCA1 gene expression in human breast cancer, high resolution bisulfite sequence analysis was used to analyze the cytosine methylation status of the BRCA1 promoter in 21 axillary node negative breast cancer patients with known levels of BRCA1 expression. Aberrant cytosine methylation of the BRCA1 promoter was detected in three of 21 patient specimens. These three specimens also expressed the lowest levels of BRCA1. Results from this analysis show that aberrant cytosine methylation of the BRCA1 promoter is directly correlated with decreased levels of BRCA1 expression in human breast cancer, and suggest that epigenetic silencing may be one mechanism of transcriptional inactivation of BRCA1 in sporadic mammary carcinogenesis.

Molecular alterations in bone and soft-tissue sarcoma

Understanding the molecular alterations evident in human cancer offers the potential for more meaningful diagnosis and more accurate prediction of cancer risk as well as the hope of developing novel therapies. In this review, several of the molecular abnormalities identified in both bone and soft-tissue sarcoma are outlined. Some sarcomas exhibit consistent gene translocations, which produce a unique oncoprotein that can serve as a molecular fingerprint for the sarcoma subtype. Mutations in tumour suppressor genes result in cell proliferation that is not regulated by normal cell cycle control genes. Amplification (multiple copies) of genes that act as positive controls on cell division have a similar effect on increasing cell proliferation. Finally, the understanding of drug resistance and sarcoma response to signalling systems such as IGF ligand and receptors may help in designing new therapies based on molecular changes in the cancer.

Phase II study of dexverapamil plus anthracycline in patients with metastatic breast cancer who have progressed on the same anthracycline regimen

The purpose of this study is to evaluate whether metastatic breast cancer that has progressed on an anthracycline-containing drug regimen will subsequently respond to that identical regimen if dexverapamil, a modulator of P-glycoprotein-mediated drug resistance, is given concomitantly. Eligible patients received 180 mg/m2 dexverapamil every 6 h for 15 doses with the anthracycline administered 30 min after the seventh dose. Blood for dexverapamil levels was drawn before and 30 min after this dose. When possible, biopsies were obtained to measure mdr-1 expression by reverse transcription-PCR and by image cytometry. Of the 21 patients entered onto the trial, 20 were evaluable for response. There were two partial responses (10%) that both lasted for 6 months, and two additional patients had stable disease. Seven patients had asymptomatic cardiotoxicity consisting of hypotension (24%), bradycardia (5%), or prolongation of the P-R interval (14%). Two patients developed acute congestive heart failure, one on dexverapamil and one 10 days after stopping it. Dexverapamil did not seem to increase anthracycline toxicity. The median trough dexverapamil plus norverapamil level on day 3 was 1110 ng/ml (range, 186-3385 ng/ml), and the median peak level was 2164 ng/ml (range, 964-8382 ng/ml). There was poor correlation between reverse transcription-PCR and image cytometry for the level of mdr-1 expression. Because dexverapamil has been shown to affect doxorubicin pharmacokinetics subsequent to the initiation of this trial, it cannot be concluded that the responses seen were necessarily due to P-glycoprotein inhibition. Additional studies are necessary to determine whether mdr-1 modulators can reverse clinical drug resistance in breast cancer patients. The intrinsic cardiotoxicity of dexverapamil makes it less suitable for such studies than several other available agents.

EWS-FLI1 fusion transcript structure is an independent determinant of prognosis in Ewing's sarcoma

PURPOSE

More than 90% of Ewing's sarcomas (ES) contain a fusion of the EWS and FLI1 genes, due to the t(11;22)(q24;q12) translocation. At the molecular level, the EWS-FLI1 rearrangements show great diversity. Specifically, many different combinations of exons from EWS and FLI1 encode in-frame fusion transcripts and result in differences in the length and composition of the chimeric protein, which functions as an oncogenic aberrant transcription factor. In the most common fusion type (type 1), EWS exon 7 is linked in frame with exon 6 of FLI1. As the fundamental pathogenetic lesion in ES, the molecular heterogeneity of these fusion transcripts may have functional and clinical significance.

PATIENTS AND METHODS

We performed a clinical and pathologic analysis of 112 patients with ES in which EWS-FLI1 fusion transcripts were identified by reverse-transcriptase polymerase chain reaction (RT-PCR). Adequate treatment and follow-up data were available in 99 patients treated with curative intent. Median follow-up in these 99 patients was 26 months (range, 1 to 140 months). Univariate and multivariate survival analyses were performed that included other prognostic factors, such as age, tumor location, size, and stage.

RESULTS

Among the 99 patients suitable for survival analysis, the tumors in 64 patients contained the type 1 fusion and in 35 patients contained less common fusion types. Stage at presentation was localized in 74 patients and metastatic in 25. Metastases (relative risk [RR] = 2.6; P = .008), and type 1 EWS-FLI1 fusion (RR = 0.37; P = .014) were, respectively, independent negative and positive prognostic factors for overall survival by multivariate analysis. Among 74 patients with localized tumors, the type 1 EWS-FLI1 fusion was also a significant positive predictor of overall survival (RR = 0.32; P = .034) by multivariate analysis.

CONCLUSION

EWS-FLI1 fusion type appears to be prognostically relevant in ES, independent of tumor site, stage, and size. Further studies are needed to clarify the biologic basis of this phenomenon.

Metastatic behavior of the RIF-1 murine fibrosarcoma: inhibited by hypophysectomy and partially restored by growth hormone replacement

BACKGROUND

We recently demonstrated that hypophysectomy profoundly inhibits metastatic behavior in the MGH-OGS murine osteosarcoma model and speculated that this effect is related at least in part to ablation of the growth hormone (GH)-insulin-like growth factor I (IGF-I) axis.

PURPOSE

In this study, we determined whether the administration of GH to animals rendered GH and IGF-I deficient by hypophysectomy attenuates the inhibitory effects of hypophysectomy on metastatic behavior.

METHODS

Metastatic behavior was assayed by counting visible metastases in lungs 3 weeks after tail vein injection of RIF-I fibrosarcoma cells to control mice (n = 29), hypophysectomized mice (n = 19), and hypophysectomized mice administered 0.05 microgram/g body weight recombinant human GH twice daily (n = 21).

RESULTS

Twenty of 21 hypophysectomized mice receiving GH, eight of 19 hypophysectomized mice not receiving GH, and 26 of 29 controls had grossly visible pulmonary metastases 3 weeks after intravenous injection of 5 x 10(5) cells; mean numbers +/- SD of gross metastases were 38.4 +/- 11.3, 6.4 +/- 2.2, and 13.1 +/- 2.8 in the three groups, respectively. The presence (P < .005, chi-square test) and number (P = .0003, Mann-Whitney U test) of metastases were significantly reduced in hypophysectomized hosts compared with control hosts and were significantly higher in hypophysectomized, GH-replaced hosts compared with hypophysectomized hosts (P < .001, chi-square test; P = .011, Mann-Whitney U test), while the difference in presence and extent of metastases between control and hypophysectomized, GH-replaced hosts was not statistically significant.

CONCLUSIONS

These data support the hypothesis that the status of the host with respect to GH and/or GH-dependent factors such as IGF-I influences the metastatic behavior of certain neoplasms.

IMPLICATIONS

Our results raise the possibility that compounds that reduce GH output or interfere with GH action, such as somatostatin analogues, GH antagonists, IGF antagonists, and GH-releasing hormone antagonists, may suppress metastatic behavior of certain neoplasms.