Abstract P3-09-02: CRISPR-Cas9 mediated BRCA1 mutation in primary cells: Mutation efficiency and effects

Background: Germline mutations in Breast Cancer Associated (BRCA) 1 or 2 genes confer an increased risk of the development of breast and ovarian cancer. Germline mutation is followed by somatic loss of heterozygosity (LOH) resulting in biallelic inactivation. BRCA1 is involved in multiple homeostatic functions including control of chromatin organization, gene transcription, protein stability and cell division. Recent studies have demonstrated heterogeneity in LOH within and between premalignant and malignant breast tissues of BRCA1 mutation carriers. We hypothesize that LOH does not have a unitary effect on phenotype but differs by the function that is abrogated.

Methods: To test our hypothesis, we adopted CRISPR-Cas9 gene editing technology. The guide RNAs for targeting the exon sequence in the RING finger, nuclear export signal (NES), nuclear localization signal (NLS) and BRCA1 C Terminus (BRCT) domain/motif of BRCA1 were designed and synthesized. MCF10A cells were transfected with a complex of guide RNA and Cas9 protein (RNP) to cause in/del mutation. The mutation was analyzed by both T7E1 assay, and an innovative and more precise method developed in our lab that utilizes linked nucleic acids (LNA) and qPCR. Proliferation and apoptosis assays were performed using the transfected cells. Organoids prepared from BRCA1 mutation carriers also were transfected with RNPs and the mutation burden determined.

Results: Since single cell clones of the transfected MCF10A cells could not be selected and expanded, a pool of transfected cells was used for the analyses. T7E1 assay and qPCR analysis using LNAs demonstrated the presence of the mutations. A standard curve was created to enable the calculation of the mutation burden. IncuCyte analysis revealed increased proliferation and apoptosis, induced by irradiation, in cells with the mutation in Exon 10, where the extent of increase varied from 11% to 48% depending on the degree of mutation. In contrast, cells with the mutation in Exon 5 displayed diminished proliferation with no change in apoptosis. That mutations in exon10 and 5 have distinct biological effects when compared to the mutations in other exons is intriguing, and modification of binding proteins will be investigated. Organoids generated from BRCA1 mutation carriers (primary and nonmalignant cells) were able to be successfully transfected using the NEON electroporation system. Mutations were introduced by the CRISPR-Cas9 system and their extent quantified by our LNA-mediated qPCR method.

Conclusions: CRISPR-Cas9-mediated gene editing of BRCA1 in MCF10A resulted in a change in the proliferation rate and the extent of apoptosis that is dependent on the location of the de novo mutation within the gene. The development of a novel method, LNA-mediated qPCR, provides quantitative information regarding the mutations that may be used to correlate mutation burden with biological functional change. Successful establishment of this BRCA1 tumorigenesis model has provided us with a method to test other putative tumor suppressors.

Citation Format: Choi MR, Yadav S, Shidfar A, Khan SA, Clare SE. CRISPR-Cas9 mediated BRCA1 mutation in primary cells: Mutation efficiency and effects [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-09-02.

Abstract P5-04-02: Progesterone receptor (PR) antagonism by telapristone acetate (TPA): A randomized, placebo-controlled phase IIB pre-surgical window trial in women with stage 0-II breast cancer

Background: In vitro and preclinical data indicate that TPA, a selective PR modulator, has activity against hormone-sensitive early breast cancer. We conducted a pre-surgical window trial of oral TPA in Stage 0-II breast cancer to assess the effect of TPA on suppression of cell proliferation (Ki67), and on differential gene expression in responsive and non-responsive tumors.

Methods: We enrolled 70 pre and postmenopausal women into a 1:1 randomized, double-blind, placebo-controlled trial of oral TPA 12mg (Repros Therapeutics Inc.) for 2-10 weeks. The primary endpoint was Ki67 labelling, comparing diagnostic core needle biopsy to post-therapy surgical specimens. Ki67 changes were quantitated by dual immunohistochemistry (Ki67/pan-cytokeratin) and image analysis (Aperio ImageScope and Definiens Tissue Studio®). RNA-sequencing (using RNA extracted from the paraffin blocks) was performed with Illumina TruSeq RNA Coding Access method. Differential gene expression pre-post therapy was assessed, followed by Gene Set Enrichment Analysis for pathway analysis. Ki67 changes from baseline were tested with Paired signed-rank test. For gene expression analysis, p values were calculated by Wald test and adjusted for multiple comparisons by Benjamini-Hochberg method (adjusted p <0.05 and 2-fold gene expression cut-off).

Results: Among 61 evaluable women, (29 placebo and 32 TPA) 97% of tumors were ER or PR positive and 91% were ER and PR positive (balanced across arms). A significant 6% decrease in mean %Ki67 was seen in the TPA arm (p= 0.003). When stratified by menopause, the significance held in premenopausal women (n= 22, p= 0.03) but not in postmenopausal women (n=10, p= 0.08). However, a Ki67 decrease (4%) was also observed in placebo group (p = 0.04); this was non-significant after pre- postmenopausal stratification. Overall, differential gene expression analysis showed no significant modulation of genes in either group. Using a pre-specified response parameter (50% relative reduction in Ki67), we identified 12/32 (38%) “responders” in the TPA, and 9/29 (31%) in the placebo arm. In sub-group analysis of these responders, we found 103 genes to be significantly modulated by treatment in the TPA “responders”, but saw no significant change in any gene expression in placebo “responders”. Gene set enrichment analysis for the 103 genes showed that TPA blocked the progression of cell cycle genes (PTTG1, PLK1, UBE2C, HIST1H3F, PSMD3, and etc.) and suppressed PGR and ERBB2 expression. In a pre-planned pooled analysis, these results will be combined with NCT02314156, reported in SABCS abstract 851790.

Conclusions: An anti-proliferative (Ki67) signal of TPA was observed in early stage breast cancer patients, but interpretation was limited by placebo group changes. The TPA group demonstrated differential suppression of proliferation-related genes among Ki67 responders, but the placebo group did not. Ongoing analysis will examine signatures related to stemness, metastasis, and immune suppression (potentially better endpoints in trials targeting P signaling). These analyses may help us select the right population and the right biomarkers for future trials.

Citation Format: Lee O, Sullivan ME, Xu Y, Shidfar A, Ivancic D, Zeng Z, Singhal H, Helenowski I, Jovanovic B, Hansen N, Bethke K, Gann P, Gradishar WJ, Clare SE, Khan SA. Progesterone receptor (PR) antagonism by telapristone acetate (TPA): A randomized, placebo-controlled phase IIB pre-surgical window trial in women with stage 0-II breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-04-02.

Abstract P4-11-02: Mammary tumor formation induced by N-methyl-N-nitrosourea (MNU) is accelerated by natural and synthetic progesterone but suppressed by an anti-progesterone CDB4124

Background: CDB4124, anti-progesterone suppresses the development of carcinogen-induced ER+/PR+ mammary tumors in rats, and may have implications for prevention and treatment of human breast cancer. We hypothesize that progesterone (P4) and medroxyprogesterone acetate (MPA) will accelerate mammary carcinogenesis induced by MNU, however CDB4124 will efficiently suppress tumor formation stimulated by progesterone.

Methods: ovary intact female Sprague Dawley rats received a single intraperitoneal injection of 50mg/kg MNU at 4-5 weeks of age. 30mg of CDB4124 and 25mg of P4 or MPA (90 release pellets, Innovative research of America, Inc) were implanted in dorsal area at 3 weeks and 4 weeks after MNU injection, respectively. 10-11 rats were used for each treatment group. Tumor incidence, latency, multiplicity, and burden were recorded weekly. 9 weeks after MNU injection all the mice were euthanized and mammary tumors and glands were fixed in 10% (v/v) neutral buffered formalin. Plasma concentrations of CDB4124 and its metabolite CDB4453 were determined by LC-MS/MS.

Results: The first tumor appeared in the control group at 5 weeks, and in the P4 and MPA treated groups at 6 weeks after MNU injection. 7 weeks after MNU injection, mammary tumor incidence of MPA and P4 treated groups were 80% and 50%, respectively compared to 30% in the control group. 9 weeks after MNU injection all MPA treated mice, 80% of P4 treated mice, and 60% of control mice developed tumors. Tumor incidence, latency, multiplicity, and tumor weight were summarized as mean ± SD in Table 1.

[Table 1] Tumor latency, incidence, multiplicity, and burden in mammary tumorsTreatmentsLatency (days)Incidence(%)MultiplicityBurden (g)Control53.7 ± 12.9602.34.25 ± 7.02P453.6 ± 9.6802.64.11 ± 5.32MPA50.8 ± 7.71002.56.02 ± 4.85P4 + CDB412459.3 ± 11.53621.38 ± 0.61MPA + CDB412454.3 ± 10.7732.84.19 ± 4.39

Tumor latency of CDB4124 treated groups was increased; tumor incidence and burden (g) of CDB4124 treated groups were decreased compared to P4 and MPA treated groups. In particular, tumor incidence and burden of CDB4124 + P4 treated group were significantly lower than those of the control group. Plasma CDB4124 and CDB4453 were 11.6 ±5.88 ng/mL and 3.4±1.68 ng/mL, respectively. Histopathology of tumors and mammary glands and immuno-histochemical evaluations of Ki67, activated caspase-3, CD34, ER, and PR are currently underway.

Conclusions: Our results indicated that natural progesterone promotes MNU- induced mammary tumor formation similar to synthetic progesterone, MPA in rats. Under this tumor permissive environment, CDB4124 provided excellent prevention efficacy, suggesting good potential as breast cancer prevention agent.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-11-02.

Abstract P3-04-08: Expression of hormone-responsive genes in benign breast tissue varies with menstrual cycle phase and menopausal status

Background: The expression of many genes is known to be regulated by ambient hormone levels. In a preliminary study of random fine-needle aspirate (rFNA) samples from benign breast tissue, we found several genes that were highly correlated with the serum levels of progesterone (P4) and estradiol (E2). We now present data to further validate these genes as markers of menstrual cycle phase (MCP) and menopausal status (MPS) in benign breast tissue which may allow retrospective classification of archived breast samples with respect to MCP and MPS at the time of sampling.

Methods: 240 rFNA samples from healthy women with recorded hormonal data at the time of sampling were analyzed. We divided these subjects by menstrual cycle phase (MCP) and menopausal status (MPS): 41 early follicular: (low circulating E2 and P4); 48 mid-cycle (high E2 and low P4); 31 luteal (moderate E2 and high P4). 120 post-menopausal (low E2 and low P4). 100 ng of RNA from rFNA samples of the breast was reverse transcribed. Amplicons of interest were linearly amplified to 14 cycles for 35 genes related to hormone responsiveness. qPCR reactions were carried out using the TaqMan OpenArray (Applied Biosystems). For each gene of interest, expression levels were normalized to the average expression of GAPDH. Gene expression difference between groups were conducted using the Mann-Whitney Test. P-values from gene expression difference were adjusted via the Benjamini-Hochberg (1995) approach.

Results: The mean value of TNFSF11 expression level was 13.19 fold higher in luteal phase subjects than in post-menopausal subjects (p = 0.0003) where there was also the biggest difference of serum P4 level between groups. The expression of DIO2 and MYBPC1 was also significantly higher in luteal phase group than in the post-menopausal group (p = 0.005, p = 0.02, respectively). These 3 genes also demonstrated a higher expression pattern in luteal phase than mid-cycle and follicular phase but analysis is still ongoing. All comparisons between these groups will be presented at the meeting.

Conclusion: The expression levels of TNFSF11, DIO2 and MYBPC1 vary with MCP and MPS. These hormone-responsive genes are candidate MCP classifiers which could be applied to archived breast samples to assess whether biomarkers of breast cancer risk are stable across the menstrual cycle, since MCP and MPS variation is likely an important source of biological noise in studies of archived breast biopsy material.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P3-04-08.

P4-11-09: Polymorphisms Related to Steroid Hormone Concentrations in Nipple Aspirate Fluid (NAF)

Background

The steroid hormone concentrations in NAF are variable, and differ significantly from systemic levels. Single nucleotide polymorphisms (SNPs) in genes associated with the metabolism of estradiol (E2) to 4-hydroxyestradiol (CYP1B1) and a transporter of steroid sulfate uptake (SLCO2B1) may partially determine the steroid hormone level in NAF, and thereby contribute to breast cancer risk. We determined the relationship between SNPs of interest and the measured concentrations of sex steroids in NAF.

Methods: Blood samples of 263 women at high risk of breast cancer who produced NAF were extracted for gDNA, and 40 ng of gDNA was used to determine the presence of the selected SNPs or their wild type genes in all subjects by the Taqman Drug Metabolism genotyping assays (Applied Biosystems). The concentrations of six steroid hormones, estradiol(E2), estrone (E1), progesterone (P4), testosterone (T), androstenedione (A4), and dehydroepiandrosterone (DHEA), from NAF were measured by immunoassay procedures after extraction and purification by High Pressure Liquid Chromatography. Comparisons of NAF steroid hormone concentrations were made for the polymorphism and wild type groups using the nonparametric Mann-Whitney tests (significance p < 0.05, two-tailed).

Results: 46% of the subjects carried the V432K polymorphism of CYP1B1 (rs 1056836, C>G), and 45% of the subjects carried the S486F polymorphism of SLCO2B1 (rs 2851069, C>T). All NAF hormone concentrations are represented as a median with the quartile range (25%, 75%). The NAF P4 levels of the V432K mutation carriers of CYP1B1 were significantly lower than those of subjects with the wild type alleles: 3.54(1.62, 8.79) ng/mL and 7.65(2.13, 27.77) ng/mL, respectively (p = 0.002). Those with the S486F polymorphism of SLCO2B1 had significantly higher E1 levels than the wild type subjects: 0.35(0.14, 1.12) ng/mL and 0.25(0.11, 0.59) ng/mL, respectively (p = 0.026) and significantly lower P4 levels: 3.77(1.71, 11.53) ng/mL and 6.65 (2.34, 22.24) ng/mL, respectively (p=0.021). In addition, we found that the women carrying both the V432K and S486F mutations had significantly lower P4 levels than the women carrying only the S486F mutation: 2.43(1.45, 6.67) ng/mL and 6.94(2.13, 26.64) ng/mL (p=0.013). No associations were found between the other hormones and these polymorphisms.

Conclusions: The anticipated effects of CYP1B1 in increasing clearance of E2 and E1 were not observed. Instead, NAF E1 concentrations were significantly increased. In subjects with the S486F polymorphism of SLCO2B1 the expected decrease in E1 and E2 in NAF was not observed; nor was the DHEA concentration decreased. These expectations were based on the reported lower activity of the S486F gene product. The decreased concentrations of NAF P4 associated with both polymorphisms are difficult to explain. Additional studies are required to understand the observed associations, but these findings raise the possibility that low P4 levels in NAF may be genetically determined, and suggest the hypothesis that this polymorphism may be related to a decreased risk of breast cancer.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P4-11-09.

Prognostic classification of ipsilateral breast tumor recurrence (IBTR)

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Background: IBTR after breast conservation encompasses true recurrence (TR) and new primary cancer (NP). No clear criteria distinguish TR from NP, but there is agreement that NP tumors have better outcomes than TR. Prior studies have used distance of IBTR from index cancer (IC), time to IBTR, histological, immunohistochemical (IHC) and genetic differences, but all data are not often available. We have examined IBTR patterns with the goal of identifying the simplest, most robust determinants of outcomes following IBTR.

Methods: We reviewed records of breast cancer patients diagnosed with IBTR at the Lynn Sage Breast Center from 8/1992 to 6/2010. Data for the IBTR and IC were reviewed for histology, IHC, location, time between IC and IBTR, follow-up status, and cause of death. Parameters were scored as 1 if IBTR and IC were similar, and 0 if different (location=1 if ≤3cm; IHC=1 if hormone receptors and HER2 similar; interval=1 if ≤ 4 years). Univariate and multivariate proportional hazard models were used to determine impact on overall survival (OS), disease-specific survival (DSS), recurrence-free survival (RFS), distant recurrence free survival (DRFS) and local recurrence (LR). The multivariate model included significant univariate parameters.

Results: We identified 161 patients with IBTR and complete data on ≥3 parameters; post-IBTR median follow up was 25 months. Data were missing on location in 13%, histology in 9%, IHC in 26%, and time interval in 0%. In univariate analysis, short interval to IBTR significantly decreased OS (HR 2.56, p=0.04), DSS (HR 4.31, p=0.009), RFS (HR 2.25, p=0.01), DRFS (HR 2.53, p=0.02), LR (HR 2.28, p=0.02); close location of IBTR decreased OS (HR 2.68, p=0.04). Histology and receptor status had no significant impact on the outcomes. Multivariate analysis included time and location, time ≤ 4 years was shown to decrease DSS (HR 4.00, p= 0.04), RFS (HR 2.32, p=0.03) and LR (HR 2.41, p=0.03).

Conclusions: A short time interval between IC and IBTR is the most important prognostic parameter; location of IBTR within 3 cm of the IC also increases HR of subsequent events. These are the most easily available parameters when evaluating patients with IBTR, and therefore the most useful for distinction of TR versus new primary.