Abstract P4-02-09: Evaluation of the Automated Liquid Biopsy-Breast Cancer Methylation (LBx-BCM) Cartridge Assay for Predicting Early Disease Progression and Survival: TBCRC-005 Prospective Trial

Purpose: We previously demonstrated that high levels of circulating methylated DNA are associated with subsequent disease progression in women with metastatic breast cancer (MBC). In this study, we validated the clinical utility of a Liquid Biopsy-Breast Cancer Methylation (LBx-BCM) prototype assay using the GeneXpert® cartridge system for early assessment of disease progression in MBC. Study Design: The 9-marker, LBx-BCM prototype assay was evaluated in TBCRC-005, a prospective biomarker study, using plasma collected at baseline, week 4 and week 8 from 144 MBC patients. Results: At week 4 MBC patients with high cumulative methylation (CM) had a significantly shorter median PFS (2.88 months v 6.60 months, p = 0.001) and OS (14.52 months v 22.44 months, p=0.005) compared to those with low CM. In a multivariable model, high versus low CM was also associated with shorter PFS (HR = 1.90, 95%CI 1.20-3.01; p =0.006). Change in CM from baseline to week 4 (OR = 4.60, 95%CI 1.77, 11.93; p = 0.002) and high levels of CM at week 4 (OR = 2.78, 95%CI 1.29, 5.99; p = 0.009) were associated with progressive disease at the time of first restaging. A robust risk model (AUC = 0.733) based on week 4 circulating CM levels was developed to predict disease progression as early as 3 months after initiating a new treatment. Conclusion: The easy to perform and automated LBx-BCM prototype assay is a promising clinical tool for detecting disease progression early after initiating treatment in women with MBC. Further validation in larger clinical datasets is needed.

Citation Format: Kala Visvanathan, Leslie Cope, Mary Jo Fackler, Michael Considine, Lisa Carey, Andres Forero-Torres, James N. Ingle, Nancy U. Lin, Rita Nanda, Anna Maria Storniolo, Suzana Tulac, Natalie C. Wu, Sudhakar Marla, Neesha R. Venkatesan, Antonio C. Wolff, Saraswati Sukumar. Evaluation of the Automated Liquid Biopsy-Breast Cancer Methylation (LBx-BCM) Cartridge Assay for Predicting Early Disease Progression and Survival: TBCRC-005 Prospective Trial [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P4-02-09.

Evaluation of a Liquid Biopsy-Breast Cancer Methylation (LBx-BCM) Cartridge Assay for Predicting Early Disease Progression and Survival: TBCRC 005 Prospective Trial

PURPOSE

We previously demonstrated that high levels of circulating methylated DNA are associated with subsequent disease progression in women with metastatic breast cancer (MBC). In this study, we evaluated the clinical utility of a novel liquid biopsy-breast cancer methylation (LBx-BCM) prototype assay using the GeneXpert cartridge system for early assessment of disease progression in MBC.

EXPERIMENTAL DESIGN

The 9-marker LBx-BCM prototype assay was evaluated in TBCRC 005, a prospective biomarker study, using plasma collected at baseline, week 4, and week 8 from 144 patients with MBC.

RESULTS

At week 4, patients with MBC with high cumulative methylation (CM) had a significantly shorter median PFS (2.88 months vs. 6.60 months, P = 0.001) and OS (14.52 months vs. 22.44 months, P = 0.005) compared with those with low CM. In a multivariable model, high versus low CM was also associated with shorter PFS (HR, 1.90; 95% CI, 1.20-3.01; P = 0.006). Change in CM from baseline to week 4 (OR, 4.60; 95% CI, 1.77-11.93; P = 0.002) and high levels of CM at week 4 (OR, 2.78; 95% CI, 1.29-5.99; P = 0.009) were associated with progressive disease at the time of first restaging. A robust risk model based on week 4 circulating CM levels was developed to predict disease progression as early as 3 months after initiating a new treatment.

CONCLUSIONS

The automated LBx-BCM prototype assay is a promising clinical tool for detecting disease progression a month after initiating treatment in women with MBC undergoing routine care. The next step is to validate its clinical utility for specific treatments.

Genetic risk factors for endometriosis near estrogen receptor 1 and coexpression of genes in this region in endometrium

The etiology and pathogenesis of endometriosis are complex with both genetic and environmental factors contributing to disease risk. Genome-wide association studies (GWAS) have identified multiple signals in the estrogen receptor 1 (ESR1) region associated with endometriosis and other reproductive traits and diseases. In addition, candidate gene association studies identified signals in the ESR1 region associated with endometriosis risk suggesting genetic regulation of genes in this region may be important for reproductive health. This study aimed to investigate hormonal and genetic regulation of genes in the ESR1 region in human endometrium. Changes in serum oestradiol and progesterone concentrations and expression of hormone receptors ESR1 and progesterone receptor (PGR) were assessed in endometrial samples from 135 women collected at various stages of the menstrual cycle. Correlation between hormone concentrations, receptor expression and expression of genes in the ESR1 locus was investigated. The effect of endometriosis risk variants on expression of genes in the region was analyzed to identify gene targets. Hormone concentrations and receptor expression varied significantly across the menstrual cycle. Expression of genes in the ESR1 region correlated with progesterone concentration; however, they were more strongly correlated with expression of ESR1 and PGR suggesting coregulation of genes. There was no evidence that endometriosis risk variants directly regulated expression of genes in the region. Limited sample size and cellular heterogeneity in endometrial tissue may impact the ability to detect significant genetic effects on gene expression. Effects of these variants should be validated in a larger dataset and in relevant individual cell types.

Abstract P3-13-05: Multicentre observational study evaluating why mastectomies are advised by UK multi-disciplinary teams

Background: Marked variation in mastectomy rates exists across the UK. Identification of variation in practice is a key step towards standardisation of service. The rationale for advising mastectomy by multi-disciplinary teams (MDTs) has not been previously explored in the UK. The main aim of this multicentre observational study was to describe current practice in MDT decision-making for patients undergoing mastectomy. A secondary aim was to determine utilisation of neoadjuvant therapies.

Methods: A multicentre, protocol-driven, prospective cohort study, led by trainees of the West Midlands Research Collaborative was performed during July and September 2015. Data was collected securely using Research Electronic Data Capture. Inclusion criteria were: women >18 years undergoing mastectomy for in situ/invasive disease; presenting with symptomatic or screen detected disease; performed as a primary procedure or following failure of breast conserving surgery (BCS); with or without immediate breast reconstruction (IR).

Results: A total of 1776 patients (1823 mastectomies; 47 bilateral procedures) from 68 units were included. Median age was 63 years (range 20-99). In total 481 (26%) IRs were performed; median IR rate was 22% (range 0-67%).

Mastectomy was advised by the MDT in 1402 (77%) cases. Reasons for advising mastectomy are shown in Table 1.

Table 1. MDT rationale for advising mastectomyRationaleNumber of mastectomiesProportion (%)Large tumour to breast size ratio making BCS unsuitable53029.1Multi-centric disease on imaging37220.4Extensive malignant microcalcification1799.8Previous radiotherapy (Breast/Mantle)1638.9Requiring further surgery for positive margins following BCS1588.7Central tumour1136.2Large primary tumour, patient not suitable for neoadjuvant endocrine or chemotherapy treatment1126.1Neoadjuvant therapy failed to downsize tumour to allow BCS884.8Neoadjuvant therapy apparently successful but mastectomy advised anyway794.3Family History-High Risk512.8

In total 153 patients with oestrogen receptor positive (ER+) tumours were offered neoadjuvant endocrine treatment (NET); 131 (86%) received treatment. A total of 293 post-menopausal women with uni-focal, ER+ tumours, >20mm were not offered NET; mastectomy was advised by MDTs in 202 patients and the rationale for advising mastectomy in 173 patients (86%) was large tumour to breast size ratio.

In total 104 patients with Human Epidermal Growth Factor Receptor 2 over-expressing (HER2+) tumours were offered neoadjuvant chemotherapy and trastuzumab (NACT); 89 (86%) received treatment. A total of 88 women <70 years old with HER2+ tumours, >20mm were not offered NACT; mastectomy was advised by MDTs in 75 patients and rationale for advising mastectomy in 45 women (60%) was large tumour to breast size ratio.

Conclusions: Although most mastectomies are advised for large tumour to breast size ratio, there is inconsistency in the utilisation of neoadjuvant therapies with many potentially eligible patients with large tumours not being given the opportunity to be downsized. Application of standardised recommendations for neoadjuvant treatment resulting in increased and appropriate use of neoadjuvant therapies could reduce the number of mastectomies advised by MDTs.

Citation Format: Singh JK, McEvoy K, Marla S, Wilcox M, Rea D, Hallissey MT, Francis A, West Midlands Research Collaborative. Multicentre observational study evaluating why mastectomies are advised by UK multi-disciplinary teams [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-13-05.

Multiplexed, rapid detection of H5N1 using a PCR-free nanoparticle-based genomic microarray assay

BACKGROUND

For more than a decade there has been increasing interest in the use of nanotechnology and microarray platforms for diagnostic applications. In this report, we describe a rapid and simple gold nanoparticle (NP)-based genomic microarray assay for specific identification of avian influenza virus H5N1 and its discrimination from other major influenza A virus strains (H1N1, H3N2).

RESULTS

Capture and intermediate oligonucleotides were designed based on the consensus sequences of the matrix (M) gene of H1N1, H3N2 and H5N1 viruses, and sequences specific for the hemaglutinin (HA) and neuraminidase (NA) genes of the H5N1 virus. Viral RNA was detected within 2.5 hours using capture-target-intermediate oligonucleotide hybridization and gold NP-mediated silver staining in the absence of RNA fragmentation, target amplification, and enzymatic reactions. The lower limit of detection (LOD) of the assay was less than 100 fM for purified PCR fragments and 103 TCID50 units for H5N1 viral RNA.

CONCLUSIONS

The NP-based microarray assay was able to detect and distinguish H5N1 sequences from those of major influenza A viruses (H1N1, H3N2). The new method described here may be useful for simultaneous detection and subtyping of major influenza A viruses.

HER2 positive early breast cancers: tumour demographics and trastuzumab therapy in the real-world

Abstract #3159

Background: Various trials have shown substantial benefits of addition of Trastuzumab (Herceptin®) to adjuvant chemotherapy in Early Breast Cancer (EBC). We analysed our breast cancer population to determine the incidence of HER2 positive Early Breast Cancers, the tumour demographics and the number of patients eligible for and receiving trastuzumab therapy in this group.
 Methods: Data for all patients diagnosed with EBC in 2006 was recorded prospectively in a database. Case notes were consulted where the HER2 positive patients, determined by a combination of IHC and FISH, had not received trastuzumab, to ascertain the reasons.
 Results: A total of 951 patients were diagnosed with Breast Cancer in 2006. 417 (43.9%) of these were screen-detected cancers.
 There were 123 (12.9%) HER2 positive newly diagnosed Breast Cancers of whom 117 were EBCs. The HER2 positivity rate in the screen detected cancers (n=417) was 9% and 17% in the symptomatic cancers (n=433).
 1. Demographics of the HER2 positive Early Breast Cancer Population:
 The median age at diagnosis was 61 yrs (range: 30-92).
 
 2. Fifty nine (50.4%) of the HER2 positive EBCs received trastuzumab therapy.
 
 Conclusions: The HER2 positivity rate is lower than that previously reported suggestive of changing demographics secondary to a high screen detected cancer population. A third of the HER2 positive tumours are screen detected. The percentage of ER positive, node negative and low grade tumours was higher than anticipated.
 Only 50% of HER 2 positive EBC patients received trastuzumab therapy. Of those who did not receive trastuzumab, the commonest reason was low risk status or age and co-morbidities precluded chemotherapy.
 HER 2 positivity alone confers high risk irrespective of pathological stage. Further trials are required to evaluate whether the substantial number of patients who are at present not eligible for trastuzumab therapy might also benefit.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 3159.

NEEDLY, a Pinus radiata ortholog of FLORICAULA/LEAFY genes, expressed in both reproductive and vegetative meristems

The LEAFY/FLORICAULA genes from Arabidopsis and Antirrhinum are necessary for normal flower development and play a key role in diverse angiosperm species. A homologue of these flower meristem-identity genes, NEEDLY (NLY), has been identified in Pinus radiata. Although the NLY protein shares extensive sequence similarity with its angiosperm counterparts, it is lacking the proline-rich and acidic motifs thought to function as transcriptional activation domains. NLY already is expressed during vegetative development at least 5 years before the transition to the reproductive phase. Expression of NLY in transgenic Arabidopsis promotes floral fate, demonstrating that, despite its sequence divergence, NLY encodes a functional ortholog of the FLORICAULA/LEAFY genes of angiosperms. Expression of the LFY::NLY transgene can largely complement the defects in flower development caused by a severe lfy allele.