Metastatic Breast Cancer Samples Research Articles

Prognosis and tumor-infiltrating lymphocytes (TILs) in estrogen receptor (ER)-low metastatic breast cancer (MBC): Analysis from a large multi-institutional cohort and the TONIC phase II trial with nivolumab.

1100 Background: Although 1% as ER cutoff to discriminate ER+/HER2- from triple-negative (TN) BC serves the purpose of maximizing access to endocrine therapy, it may be suboptimally informative in terms of prognosis and immune checkpoint inhibitor (ICI) benefit. In the early setting, we reported that ER-low BC (ER 1-9%/HER2-) is immunologically and prognostically similar to TN (ER 0%) [Massa, 2023]. Here we focus on MBC and aim to assess prognosis of ER-low BC, including the conversion from ER+(≥10%)/HER2- to ER-low at relapse. We also compared ER-low and TN in terms of outcome after ICI, and TILs. Methods: We included two cohorts of MBC patients (pts): a multicentric retrospective cohort and pts with ER<10%/HER2- MBC enrolled in the TONIC trial testing nivolumab +/- induction therapy. All pts had ER and HER2 status assessed on metastatic tumor lesion; in the retrospective cohort ER and HER2 status on primary tumor was also available. Survival endpoints in the retrospective cohort: overall survival (OS, from BC diagnosis), post-relapse survival (PRS, from BC relapse). Exploratory endpoints from the TONIC trial: clinical benefit rate (CBR), OS and PFS (both from randomization). TILs were assessed on MBC samples (both cohorts) and on matched primary tumor (retrospective cohort). Results: We included 1112 pts in the retrospective cohort: the prevalence of ER-low BC was 3.6% in primary tumor and 5.9% in MBC lesions. In the TONIC trial, 15/110 pts had ER-low MBC. In the retrospective cohort, ER-low and TN MBC showed similar outcome, and significantly unfavorable vs ER+/HER2- MBC (Table). Among pts with ER+/HER2- primary BC, 6.7% converted to ER-low and 14.7% to TN at relapse. ER+/HER2- BC pts converting to ER-low had similar outcome than those converted to TN, and significantly poorer than pts with stable ER+/HER2- (Table). In the TONIC trial, ER-low MBC pts, compared to TN, showed similar response to ICI (CBR: 20.0% vs 22.1%, p=1), similar PFS and numerically worse OS (Table). TIL levels on MBC samples were similar between ER-low and TN both in the retrospective (median: 6% vs 5%, p=0.83) and the TONIC cohorts (median: 5.5% vs 5.0%, p=0.56) and were higher than ER+/HER2- (median: 3%). Conclusions: We confirmed that ER-low and TN MBC show similar poor outcome and the shift from ER+/HER2- to ER-low has a comparable unfavorable prognostic impact compared to conversion to TN. Our results support the hypothesis that ER-low and TN are immunologically akin and similarly prone to respond to ICI. [Table: see text]

Abstract PO5-14-10: Dynamics and prognostic value of subtype specific TROP2 expression in matched pair samples of primary (PBC) and metastatic breast cancer (MBC) tissues

Abstract Background: The genotype and phenotype of breast cancer may change during disease progression. This is of particular interest in the advent of targeted treatment adressing extracellular targets such as TROP2, which serves as chemotherapy carrier rather than being required for tumor cell survival. In addition, technical issues may affect biomarker assessment when comparing primary breast cancer (PBC) tissues with biopsies of metastatic breast cancer (MBC) tissues at distant sites. Here we analyzed TROP2 expression on mRNA level by RT-qPCR in primary tumor and metastatic tissues on basis of molecular subtyping to determine subtype specificity and target gene stability/dynamics. Methods: The tumor bank of a single institution was screened for paraffin-embedded pairs of PBC and MBC tissue samples and a total of 34 matched PBC and MBC pairs were retrieved. RNA was extracted using a bead-based extraction method (RNXtract® IVD kits, Cerca Biotech). Multiplex RT-qPCR was performed using TaqMan® based primer probe sets for ESR1/PGR/ERBB2 and MKI67 (MammaTyper® IVD kits, Cerca Biotech) as well as TROP2 (TargetTyper RUO kits, STRATIFYER Molecular Pathology GmbH). Correlation analysis, Scatter Plots, Partitioning tests and Kaplan Meier analysis were performed using the SAS JMP® 9.0.0 software. Results: Samples from 34 patients with MBC and PBC were available. Positivity of PBC RT-qPCR for ESR1, PGR and HER2 was 78%, 70% and 3%. The overall agreement between matched primary and metastatic lesions 90%, 70% and 100% for RT-qPCR of ESR1, PGR and HER2. Median expression of TROP2 was 2 fold lower in metastatic tissues compared to matched primary tumor tissues, while the lower quartile of mRNA expression dropped 4 fold. In primary tumor tissues TROP2 expression was significantly associated with PGR and HER2 expression (Spearman r=0.5284 p=0.0013 and r=0.3950 p=0.0208; respectively), while no significant association was found for ESR1 and MKI67. In contrast, no significant association with neither PGR nor HER2 was found (Spearman r=0.0461 p=0.8041 and r=0.0461 p=0.7955; respectively), while TROP2 trended to be associated with MKI67 in metastatic lesions (Spearman r=0.3247 p=0.0610). In line with the strong positive association of TROP2 with PGR in primary tumor tissues, elevated TROP2 levels were associated with substantially longer median distant metastasis free survival of 72 months, while TROP2 negative tumors exhibited a median DDFS of only 24 months (p=0,0091). In contrast, no prognostic value for TROP2 mRNA level could be determined from metastatic lesions and determining the time from initial metastasis until death. Conclusion: In this selected matched pair, metastatic cohort, TROP2 mRNA in primary tumors is strongly associated with luminal type of breast cancer expressing higher levels of PGR mRNA, while no such correlation was found in matched metastatic tissues. Moreover, TROP2 is significantly downregulated in metastatic lesions. As TROP2 is expressed in luminal tumors, it may serve as a valuable target for luminal tumors of higher progression risk. However, TROP2 expression is unstable and requires careful decision making on actual biopsies rather than archival tissue samples. Citation Format: Thomas Deutsch, Ralph Wirtz, Stefan Stefanovic, Andreas Hartkopf, Hans-Peter Sinn, Andreas Schneeweiss, Markus Wallwiener. Dynamics and prognostic value of subtype specific TROP2 expression in matched pair samples of primary (PBC) and metastatic breast cancer (MBC) tissues [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-14-10.

Abstract PO5-15-08: Role of next-generation sequencing testing in metastatic breast cancer

Abstract Background: With recent advances in therapy, patients with metastatic breast cancer have been living longer. Treatment has previously largely depended on the subtypes of breast cancer (ER/PR positive, HER2 positive, triple negative). In recent years, testing metastatic breast cancer samples for somatic and germline mutations has revealed additional therapeutic targets which could help patients further than standard therapeutic options. Recent evidence has demonstrated that targeted therapy may offer an advantage in overall survival in patients with metastatic breast cancer. However, data regarding the use of targeted therapy is still sparse and its overall impact on metastatic breast cancer patients needs to be further investigated. We wanted to study genomic testing in such patients and see how often it leads to new therapy recommendations beyond standard of care as we move towards the era of precision medicine. Methods: Patients who were diagnosed with metastatic breast cancer between 2015-2020 were screened and a total of 193 patients were identified. Baseline characteristics, treatment/outcome and NGS testing information was collected. Univariate two group comparisons were performed using t-tests for continuous variables, and using chi-square, or Fisher’s tests if cell counts were < 5 for categorical variables. Survival analysis for progression free survival (PFS) and overall survival (OS) were done using log rank tests. Results: Out of 193 patients, the majority (189) were female. There were 121 (62.7%) White patients, 69 (35.8%) Black patients, and 3 (1.6%) patients that were another race. 30.6 % of patients received next-generation sequencing (NGS) testing, 68.4% of patients did not, and 1% were unknown. Patients that received NGS testing were on average younger than those that did not receive NGS testing (53.24 years old vs 65.17 years old, respectively). Patients that received NGS testing were more likely to be premenopausal (p < .0001). Patients without NGS testing were more likely to die than those with NGS testing (p=.0327). There were no statistically significant differences observed in percentage of patients getting NGS testing done and whether patients were triple negative, HER2 positive with hormone receptor positive or negative, and HER2 negative with hormone receptor positive. As the year of metastatic breast cancer diagnosis advanced from 2015-2020, a high percentage of patients received NGS testing (i.e. 20% diagnosed in 2015 received NGS testing, whereas 50% diagnosed in 2020 received NGS testing). As the number of years between diagnosis and last follow-up increased, the probability of progression decreased for patients that had NGS testing done. Patients with NGS testing did better than those without NGS testing, but patients with no treatment change had the lowest probability of progression. Conclusion: On average, only 30% of patients are receiving NGS testing, however it is being done more often in recent years than ever before. There is a clear progression free survival benefit seen in patients who received NGS testing. It is interesting to note that those who did not receive any changes in treatment based on NGS testing have the lowest probability of progression, but overall survival was not different for any of the different groups studied. This could be related to the low number of patients with NGS testing in our analysis. Further studies are warranted to understand this association. Table. Summary of NGS testing data in various demographic categories There was a statistically significant difference in whether NGS testing was obtained or not and age, menopausal status and current status. There was no statistically significant difference in whether NGS testing was obtained or not and gender or race. Citation Format: Kashmira Wani, Manasi Godbole, Brigid Jacob, Kylie Springer, Vrushali Dabak. Role of next-generation sequencing testing in metastatic breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-15-08.

Abstract 2767: Exploring ADAR1 dependencies in breast cancer brain-metastases

Abstract Background: Adenosine deaminase acting on double-stranded RNA (ADAR1) is a recognized driver of epitranscriptomic (post-transcriptional) remodeling and tumor progression. Changes in amino acid sequence, mRNA splicing, and/or polyadenylation sites are only some of the adenosine-to-inosine (A-to-I) RNA editing effects. Under physiological conditions, ADAR1 activity prevents autoinflammation by inhibiting the accumulation of endogenous immunostimulatory double-stranded RNA and by suppressing the Z-RNA sensor ZBP1. Such mechanisms are exploited by cancer cells to desensitize tumor response to therapies, therefore augmenting aggressiveness. Approximately 10 to 20% of patients diagnosed with breast cancer (BC) will develop metastatic disease, which remains the leading cause of death in individuals with BC. We have hypothesized that ADAR1 and its interferon-inducible p150 isoform, play a pivotal role in promoting BC metastases since high levels of ADAR1 are associated with a worse prognosis in patients with high grade BC, especially in the triple-negative BC subgroup (TNBC), which is the most likely to develop brain metastases. Methods: We established a humanized mouse model of breast cancer brain metastases (BC-BrM) using neonatal intracerebroventricular inoculation of MDA-MD-231 TNBC cells and primary patient derived metastatic cells in Rag2−/−γc−/− mice. Before implantation, MDA-MD-231 cells were transduced with a nanoluc-GFP reporter for tracing ADAR1 enzymatic activity in the brain metastatic niche. Lentiviral shRNA knockdown vectors targeting ADAR1, combined with over-expression vectors of full-length ADAR1 or the p150 deleted isoform were adopted to detect editing changes in the metastatic model through RNA-sequencing of BC-BrM. Results: BrM derived from MDA-MD-231 implants display upregulation of ADAR1 p150 and activation of the WNT/β-catenin pathway compared to the non-implanted cell lines. Upon shRNA knockdown of ADAR1, decreased expression of BC stem cell markers was detected via FACS in MDA-MD-231 ADAR1 knocked-down versus control BC-BrM isolated cells. We are now exploring molecular pathways affected by ADAR1 loss/overexpression in establishing BrM. Future Directions: We have developed a biorepository of primary patient-derived metastatic breast cancer samples and have begun the process of tracking metastatic kinetics and ADAR1 activation with the ADAR1 reporter in an orthotopic mouse model. Overall, this study will provide new insights into the molecular role of ADAR1 deaminase activity in establishing and maintaining metastatic niches. Citation Format: Teresa Sposito, Emma E. Klacking, Antonio W. Ruiz, Jessica Pham, Catriona Jamieson. Exploring ADAR1 dependencies in breast cancer brain-metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2767.

Transferrin receptor in primary and metastatic breast cancer: Evaluation of expression and experimental modulation to improve molecular targeting.

Conjugation of transferrin (Tf) to imaging or nanotherapeutic agents is a promising strategy to target breast cancer. Since the efficacy of these biomaterials often depends on the overexpression of the targeted receptor, we set out to survey expression of transferrin receptor (TfR) in primary and metastatic breast cancer samples, including metastases and relapse, and investigate its modulation in experimental models. Gene expression was investigated by datamining in twelve publicly-available datasets. Dedicated Tissue microarrays (TMAs) were generated to evaluate matched primary and bone metastases as well as and pre and post chemotherapy tumors from the same patient. TMA were stained with the FDA-approved MRQ-48 antibody against TfR and graded by staining intensity (H-score). Patient-derived xenografts (PDX) and isogenic metastatic mouse models were used to study in vivo TfR expression and uptake of transferrin. TFRC gene and protein expression were high in breast cancer of all subtypes and stages, and in 60-85% of bone metastases. TfR was detectable after neoadjuvant chemotherapy, albeit with some variability. Fluorophore-conjugated transferrin iron chelator deferoxamine (DFO) enhanced TfR uptake in human breast cancer cells in vitro and proved transferrin localization at metastatic sites and correlation of tumor burden relative to untreated tumor mice. TfR is expressed in breast cancer, primary, metastatic, and after neoadjuvant chemotherapy. Variability in expression of TfR suggests that evaluation of the expression of TfR in individual patients could identify the best candidates for targeting. Further, systemic iron chelation with DFO may upregulate receptor expression and improve uptake of therapeutics or tracers that use transferrin as a homing ligand.

HER2-low expression in patients with advanced or metastatic solid tumors

Human epidermal growth factor receptor 2 (HER2)-low is a newly defined category with HER2 1+ or 2+ expression by immunohistochemistry (IHC) and lack of HER2 gene amplification measured by in situ hybridization (ISH). Much remains unknown about the HER2-low status across tumor types and changes in HER2 status between primary and metastatic samples. HER2 expression by IHC was evaluated in 4701 patients with solid tumors. We have evaluated the HER2 expression by IHC and amplification by ISH in paired breast and gastric/gastroesophageal (GEJ) primary and metastatic samples. HER2 expression was correlated with ERBB2 genomic alterations evaluated by next-generation sequencing (NGS) in non-breast, non-gastric/GEJ samples. HER2 expression (HER2 IHC 1-3+) was found in half (49.8%) of the cancers, with HER2-low (1 or 2+) found in many tumor types: 47.1% in breast, 34.6% in gastric/GEJ, 50.0% in salivary gland, 46.9% in lung, 46.5% in endometrial, 46% in urothelial, and 45.5% of gallbladder cancers. The concordance evaluation of HER2 expression between primary and metastatic breast cancer samples showed that HER2 3+ remained unchanged in 87.1% with a strong agreement between primary and metastatic samples, with a weighted kappa (Κ) of 0.85 (95% confidence interval 0.79-0.91). ERBB2 alterations were identified in 117 (7.5%) patients with non-breast, non-gastric/GEJ solid tumors who had NGS testing. Of 1436 patients without ERBB2 alterations, 512 (35.7%) showed any level HER2 expression by IHC. Our results show that HER2-low expression is frequently found across tumor types. These findings suggest that many patients with HER2-low solid tumors might benefit from HER2-targeted therapies.

Concurrent predictors of an immune responsive tumor microenvironment within tumor mutational burden-high breast cancer.

Data supporting high tumor mutational burden (TMB-H) as a lone biomarker for an immune-responsive tumor microenvironment (TME) in metastatic breast cancer (MBC) are weak, yet tumor agnostic approval in TMB-H advanced tumors provides immune checkpoint inhibition (ICI) as a clinical option. We evaluated concurrent predictors of immune-responsive and non-responsive TME within MBC. Tumor samples from patients with MBC (N=5621) were analyzed by next-generation sequencing of DNA (592-gene panel or whole exome) and RNA (whole transcriptome) at Caris Life Sciences (Phoenix, AZ). TMB-H threshold was set to ≥ 10 muts/Mb. PDL-1 was evaluated using SP142 antibody. Gene expression profiling and RNA deconvolution were used to estimate immune and stromal cell population abundance in the TME, and transcriptomic signature of immunotherapy response (T cell-inflamed score). 461 (8.2%) TMB-H MBC samples were identified. Consistent with prior studies, TMB-H tumors exhibited significant dMMR/MSI-H enrichment (7 vs. 0%, p<0.0001) and PD-L1+ expression (36 vs. 28%, p<0.05) compared to TMB-L. Across all samples, T cell-inflamed scores were weakly correlated with TMB. TMB-H was not associated with significantly increased immune responsive cell types (CD8+ T-cells, NK cells, or B cells) or immune response gene signatures (e.g. antigen presentation), yet positive trends were observed, while immunosuppressive fibroblasts were significantly decreased in TMB-H tumors (0.84-fold change compared to TMB-L, P<0.05). HR+/HER2- breast cancer was the only subtype in which TMB-H tumors exhibited increased T cell-inflamed scores vs. TMB-L. Concurrent PD-L1+ or dMMR/MSI-H with TMB-H was associated with high T cell-inflamed scores in both HR+/HER2- and TNBC. Among several associated biomarkers, B2M mutations and CD274 amplifications were positively associated with T-cell inflamed scores in TMB-H tumors; CDH1 and ERBB2 mutations were negatively associated. High TMB alone does not strongly correlate with immune infiltrate or immune-related gene signatures in MBC. TMB-H predicts T-cell inflamed signature compared to TMB-L in HR+/HER2- tumors only. Along with MSI-H and PD-L1+, several biomarkers, including B2M mutation and CD274 amplification, may help predict ICI benefit amongst TMB-H tumors. Co-occurring biomarkers within TMB-H breast cancer warrant evaluation in larger cohorts for response or resistance to ICI to develop composite predictive biomarkers in MBC.

Abstract 5388: A unified computational pathology method to quantify HER2 expression from raw IHC and IF images in breast cancer

Abstract Background: The development of automated quantitative methods to measure biomarker expression such as HER2 aims at reducing the subjective variability of pathologist-performed biomarker assessment of immunohistochemically (IHC) stained tissue slides. As an example, the deep learning-based Quantitative Continuous Scoring (QCS) algorithm [1] enables the objective measurement of biomarker expression based on the detection of individual tumor cells in the tumor regions and - for each cell, on the instance segmentation of its nucleus, cytoplasm, and membrane compartments. Methods: In order to extend the QCS image analysis to similarly analyze tissue slides stained with immunofluorescence (IF), we re-trained the fully supervised deep-learning models, adjusted the normalization of images on tissue controls to account for variability between different staining batches, and finally used the normalized signal in IF instead of the Optical Density (OD) signal in IHC as a 8-bit grayscale image on which the biomarker expression is estimated. We performed QCS on HER2 IF images (HER2 clone 29D8 [CST], imaged with Vectra [Akoya] in parallel with HER2 IHC clone 4B5 [Roche Tissue Diagnostics]) performed on 26 primary and metastatic breast cancer samples representing the full range of HER2 expression, from null to highly overexpressed. Results: Our analysis demonstrated that the QCS-based scoring on IHC-HER2 images correlates with the QCS-based scoring on IF-HER2 images. We observed a Pearson correlation of R=0.92 between the median membrane OD in IHC and the median normalized membrane signal in IF. Defining a positive cell as having an estimated membrane expression higher than a given so-called positivity threshold, we found a median Pearson correlation of R=0.85 between the percentage of positive cells detected in IHC and the percentage of positive cells detected in IF for increasing values of positivity thresholds. Correlation of the QCS median normalized membrane signal in IF was R=0.91 with mRNA (ERBB2 transcript levels [Nano String]) and R=0.88 with IHC-based H-scores, against R=0.83 and R=0.87 respectively for the QCS median membrane OD signal in IHC. Conclusion: We describe the extension of a computational pathology-based approach for biomarker quantification in IHC to IF stained tissue slides. The consistency of the image analysis method translates into the consistency of the measurements in the two imaging methods. The use of IF could enable the improved quantification of expression, co-localization and spatial distribution of multiple proteins on the tissue sample.

Abstract P2-23-12: The Mutational Landscape of 1172 Patients with Hormone Receptor-Positive, HER2-negative Metastatic Breast Cancer Treated with CDK4/6 Inhibitors

Abstract Background: Recent studies suggest differences in outcomes among patients (pts) with metastatic breast cancer (MBC) treated with abemaciclib, ribociclib, or palbociclib, but whether these differences have a genomic basis is unknown. Here, we utilize a large real-world dataset to compare the mutational landscapes of HR+/HER2- MBC samples in which CDK4/6 inhibitor (CDK4/6i) treatment was initiated ≥6 months prior to biopsy to describe variations in tumor biology associated with exposure to each CDK4/6i. We also compare mutations detected by solid tumor sequencing and liquid biopsy to better understand each assay’s ability to identify relevant alterations in this population. Methods: De-identified data from a cohort of pts with HR+/HER2- MBC (n=1172) sequenced with the Tempus xT (DNA-seq of 595-648 genes, whole exome-capture RNA-seq) solid tumor and xF (105-gene panel focused on detecting oncogenic and resistance mutations from cell-free DNA) liquid biopsy assays were retrospectively analyzed. For pts with multiple samples sequenced, the most recent sample was analyzed. Pts were selected based on receipt of CDK4/6i between metastatic diagnosis date and biopsy collection and excluded if &amp;lt; 6 months elapsed between CDK4/6i initiation and biopsy collection. Demographics, clinical characteristics, and NGS findings were compared between groups by Chi-squared/Fisher’s Exact tests or Kruskal-Wallis tests, as applicable. The prevalence of individual gene alterations (consisting of pathogenic/likely pathogenic SNVs/indels and copy number alterations) were compared similarly with adjustment for false-discovery. Results: We compared the immune biomarker and DNA mutational landscapes of 1172 samples collected after a period of treatment with abemaciclib, ribociclib, or palbociclib. Across all pts, the most commonly altered genes were TP53, PIK3CA, ESR1, CDH1, and GATA3. Abemaciclib-treated pts had the highest median TMB and MSI-high frequency (Table). Palbociclib-treated pts were less likely to have a high TMB (≥10 mutations/megabase) or RB1 mutations, a known biomarker of resistance to CDK4/6i (Table). We note that the total N for pts positive for TMB high or MSI-high was very low across all groups. We also compared DNA mutational landscapes between pts tested with solid tumor sequencing and liquid biopsy; the lower prevalence of RB1 mutations in palbociclib-treated pts trended towards significance in both groups (Table). Conclusions: Results from our real-world dataset suggest that treatment with the different CDK4/6i drugs results in unique immune biomarkers and DNA mutational profiles. Detection of relevant alterations such as RB1 by both tissue testing and liquid biopsy supports a role for either assay in identifying mutations associated with CDK4/6i. Our findings raise the possibility that unique targeted treatment strategies and combination therapies may be warranted after progression on the different CDK4/6i drugs. Additional investigation into the differences in genomic alterations and outcomes among CDK4/6i drugs is necessary to further explore the hypotheses generated by this real-world study. Prevalence of immune biomarkers and DNA mutations in pts treated with each CDK4/6i drug 1Pearson’s Chi-squared test; Fisher’s exact test; Kruskal-Wallis rank sum test 2False discovery rate correction for multiple testing 3,4N=464; 708 pts with missing data 5N=1163; 9 pts with missing data Citation Format: Ami N. Shah, Bora Lim, Monica M. Mita, Elizabeth Mauer, Kayla V. Layng, Calvin Chao, Adam M. Brufsky. The Mutational Landscape of 1172 Patients with Hormone Receptor-Positive, HER2-negative Metastatic Breast Cancer Treated with CDK4/6 Inhibitors [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 P2-23-12.

Abstract P5-14-12: ESR1-alterations in HR+HER2- breast cancer patients

Abstract Introduction/Background Endocrine therapy remains the fundamental treatment for advanced HR+ breast cancer (BC). For those patients who become refractory to endocrine therapy, resistance may be associated with mutations, amplifications, and fusions in the ESR1-encoded estrogen receptor. Here we examine the frequency of ESR1 alterations and the associated genomic landscape. Methods HR+/HER2- BC samples were sequenced with the OncomapTM ExTra assay, which uses whole-exome DNA sequencing with germline subtraction to detect somatic single nucleotide substitutions, indels, and copy number alterations (CNAs), and uses RNA sequencing to detect gene fusions. Tumor mutational burden (TMB) and microsatellite instability (MSI) are also reported. For analysis, BC samples were grouped by site: local (primary breast or regional lymph node) versus metastatic. Prior treatment history was unknown. Testing for a possible association between ESR1 and other biomarkers (genes, MSI, and TMB) was done using Fisher’s Exact Test (p≤0.05). Results A total of 988 HR+HER2- breast cancer patient samples were included in the analysis. Of these, 821 (83.1%) were local samples and the remaining 167 were metastatic samples, with liver (63, 37.7%), bone (20, 12.0%), skin (16, 9.6%) and chest wall (15, 9.0%) being the most common locations. ESR1 alterations were present in 84 tumor samples, 37 local and 47 metastatic, representing 4.5% and 28.1% of samples, respectively. ESR1 alterations included missense mutations (54 samples), fusions (29 samples), and amplifications (8 samples). The most common missense mutations were Y537S (20 samples, 37.0%), D538Q (20 samples, 37.0%), and E380Q (6 samples, 11.1%), which were located in the ligand binding domain and included both clonal and subclonal events. There were 30 ESR1 fusions identified, 17 (2.1%) in local and 13 in metastatic (7.7%) samples. Most fusions (24 samples, 82.8%) involved the same partner, CCDC170, while the other 6 fusions had unique partners. Examination of the 143 other biomarkers altered among ESR1-altered samples revealed 15 genes and MSI-high status that appeared to be over-represented (Table 1). However, none of the associations were statistically significant after correcting for multiple comparisons. Further, there was no evidence that the prevalence of ERBB2, TP53, AKT1 and PIK3CA alterations differed by ESR1 status (Table 1). Conclusions ESR1 alterations were significantly more common in HR+/HER2- metastatic breast cancer samples compared to local samples. Comprehensive genomic profiling with RNA sequencing identified both common and rare ESR1 fusions, which were most frequent in the metastatic samples. No significant difference in the molecular profile of ESR1 altered vs ESR1 wildtype samples was found in this cohort. Clinical trials with novel selective ER degraders (SERDs) to target these ESR1 alterations are ongoing. Table 1. Biomarkers that showed the highest association with ESR1 and other notable breast cancer biomarkers. Citation Format: Gargi Basu, Sameer S. Udhane, Susan Dombrowski, Lenny Hong, Fadel Alyaqoub, Michelle Barbi de Moura, Thiruppavai Chandrasekaran, Turgut Dogruluk, David Driscoll, Aimee Jalkanen, Pawan Noel, Szabolcs Szelinger, Min Wang, David Hall, Jess Hoag, Janine Lobello, Frederick Baehner, Snehal Thakkar, Joyce O’Shaughnessy. ESR1-alterations in HR+HER2- breast cancer patients [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 P5-14-12.

Abstract P2-11-06: Plasma assay of methylated DNA markers (MDM) detects patients with metastatic breast cancer (MBC) compared to healthy controls and treated breast cancer patients with no evidence of disease

Abstract Objective: Aberrantly methylated DNA may be used to detect minimal residual disease or early recurrence in breast cancer. As a 1st step, we aimed to develop an MDM panel to delineate between healthy women, stage I-III breast cancer in remission with no evidence of disease (NED), and metastatic breast cancer (MBC). Methods: We prospectively enrolled patients into 3 groups: healthy controls (adult females with a normal mammogram in past 12 months with no history of breast cancer), NED [stage I-III breast cancer with no clinical evidence of recurrence 6 months - 3 years post-treatment (adjuvant endocrine therapy allowed)], and MBC (collected either at initial diagnosis of untreated metastatic disease or radiographic progression). DNA was extracted from 6 mL of plasma derived from blood collected in LBgard tubes (Exact Sciences Corp., San Diego CA), and was bisulfite-treated and assayed by target enrichment long-probe quantitative amplified signal (TELQASTM) method for a panel of 15 previously identified MDMs [Table], normalized by the control gene, B3GALT6. Areas under the receiver operating characteristic curve (AUC) were calculated for each MDM to assess discrimination of MBC from other groups. With 60 patients per group, we had greater than 80% power to detect a difference of 0.20 from the null AUC of 0.7. Results: We tested samples from 60 MBC (10 untreated, 50 recurrent), 60 NED, and 60 healthy women. The median age was 63 (IQR, 55-72) and was not different between groups. The NED group was all hormone-receptor (HR) positive, with 47 (78%) being human epidermal growth factor receptor 2 negative (HER2-) and 13 (22%) HER2+; 48 (80%) were stage I and 9 (15%) were N+. The MBC group had 35 (58%) patients with HR+/HER2- tumors, 11 (18%) HR+/HER2+, and 6 (10%) HR-/HER2-, 4 (7%) HR-/HER2+, with 4 (7%) unknown. Of the 41 MBC whose original stage and nodal status were known 9 (22%) were stage I and 22 (54%) were N+. The markers were able to discriminate between MBC and NED patient samples with AUCs from 0.97 to 0.72. AUCs for 10/15 MDMs (ITPRIPL1, EMX1, C17orf64, OSR2, TRIM67, CHST2, IFFO1, TRH, FAM59B, and MPZ) were &amp;gt;0.90. No difference in MDMs was observed between the healthy and NED groups. Conclusions: MDMs, assayed from plasma, appear highly discriminant for metastatic breast cancer cases in comparison to control patients with NED or healthy controls. Further clinical validation of this MDM panel in a larger cohort is warranted. Table 1. Plasma MDM discrimination of metastatic breast cancer (MBC) from healthy controls and previously treated breast cancer patients with no evidence of disease (NED) Citation Format: Karthik V. Giridhar, Fergus J. Couch, Jason P. Sinnwell, Seth W. Slettedahl, William R. Taylor, Douglas W. Mahoney, Patrick H. Foote, Maria C. O’Connell, Mariah J. Robran, Mary E. Devens, Anna M. Gonser, Nicole Larson, Karen A. Doering, Kelli N. Burger, Michael Kaiser, Hatim Allawi, Kathryn Ruddy, Janet Olson, John B. Kisiel. Plasma assay of methylated DNA markers (MDM) detects patients with metastatic breast cancer (MBC) compared to healthy controls and treated breast cancer patients with no evidence of disease [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 P2-11-06.

Abstract A005: Inhibition of ubiquitin receptor ADRM1 for the treatment of metastatic breast cancer

Abstract Adhesion-regulating molecule 1 (ADRM1) is a polyubiquitin receptor on the 26S proteasome. ADRM1 is upregulated in many cancers. In this study, we evaluated the potential prognostic and predictive value of ADRM1 in breast cancer patients. We determined the expression of ADRM1 and its relationship to breast cancer subtypes, using the Cancer Genome Atlas dataset that contained racial and clinical outcomes data totaling 1108 patients. The ADRM1 mRNA expression levels were divided into quartiles to designate the ADRM1 high versus low expression designation. Karanam et. al developed an orally available proteasome inhibitor bis-benzylidine piperidone (RA190), that binds to the ubiquitin receptor RPN13/ADRM1 on the 19S regulatory particle of the proteasome and directly kills cancer cells by triggering proteotoxic stress. RA190 binds to cysteine 88 of ADRM1/RPN13, triggering rapid accumulation of high-molecular-weight poly-ubiquitinated proteins resulting in apoptosis. Up284 is one of a second generation of small molecules that mimic RA190 activity. The objective of this study is to verify the role of ubiquitin receptor RPN13/ADRM1 in metastatic breast cancer samples of European American and African American patients and identify the safe combination of regimens of bortezomib in combination with Up289 to mitigate recurrence, metastasis and reduce mortality in AA TNBC/QNBC. Clinically, this will reveal a new, hitherto unknown targeted regimen for AA QNBC. From the biological perspective, it will provide insights into the underlying molecular changes that are associated with health disparities.Currently available treatments are unable to eradicate metastatic breast cancer specifically those classified as QNBC. Our preliminary analysis of Cancer Genome Atlas (TCGA) indicated that ADRM1 expression is highly expressed in AA versus EA breast cancer patients, resulting in a worse overall survival. Further analysis of ADRM1 in QNBC patients indicated that it was significantly elevated predominantly in African American patients with QNBC. Citation Format: Christopher B. Andrews Jr., Balasubramanyam Karanam, Clayton Yates. Inhibition of ubiquitin receptor ADRM1 for the treatment of metastatic breast cancer [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr A005.

Outcome of Breast Carcinoma between ER, PR with HER-2/Neu Positive Receptor Status

Background: The most frequent kind of cancer among women is breast cancer. Evidence shows that the receptor profile of primary and metastatic breast cancer tissue differs. Archival-paired pathology samples were evaluated to determine the level of hormone receptor discordance. Objective: To evaluate the efficacy of the most frequently used biological indicators in breast cancer for predicting how well a patient would respond to surgical management and their outcome. Materials and Methods: This comparative Study was conducted in the surgery department, Rajshahi Medical College, Bangladesh, with a Matricentred base Study from January 2019 to December 2021. They also included patients (n=100) for whom tissue from either the main or secondary metastatic location was detectable. Cancers were compared and analyzed for their ER, PR, and Her-2/neu status in both the primary and the metastatic. Results: The discordance rate for ER was 17.7% (2-sided p=0.0039), with 9.7% of tumors changing from ER-positive to ER-negative and 8.0% changing from ER-negative to ER-positive. The discordance rate for PR was 37.3% (2-sided p&lt;0.0001), with Each and every one of these tumors going through a transition from PR-positive to PR-negative. As far as Her-2/neu is concerned, no major discrepancies were discovered. Conclusions: Hormone receptor status is significantly different between primary and metastatic breast cancer samples, as suggested by this dataset. Common instances of PR decline were observed. More than half of the patients had a positive hormone status, and it was found that the illness had spread to other organs in most of these cases.

Ras suppressor 1 long form (RSU1L) silencing promotes apoptosis in invasive breast cancer cells

Ras Suppressor-1 (RSU1) is a cell-extracellular matrix (ECM) adhesion protein implicated in breast cancer (BC) cell metastasis. Nevertheless, its role in apoptosis is yet unknown. In the present study, we used bioinformatics tools to evaluate the association of RSU1 expression and BC patient survival, the expression of basic pro- and anti-apoptotic genes in metastatic BC samples and their correlation with the expression of RSU1. Then, we specifically depleted RSU1 long form (RSU1L) using a short hairpin RNA (shRNA) silencing approach in two BC cell lines, the non-invasive MCF-7 and the highly invasive MDA-MB-231-LM2 cells and assessed gene expression of pro-and anti-apoptotic genes, as well as cell survival and apoptosis. Our results showed that high RSU1 expression was correlated with poor survival and significant changes were found in the expression of apoptosis-related genes (PUMA, TP53, BCL-2 and BCL-XL) in metastatic BC. Moreover, silencing of the long and most common isoform of RSU1 (RSU1L) resulted in the upregulation of PUMA and TP53 and concomitant downregulation of anti-apoptotic BCL-2 and BCL-XL, with the effect being more prominent in invasive MDA-MB-231-LM2 cells. Finally, RSU1L depletion leads to a dramatic increase in apoptosis of MDA-MB-231-LM2 cells, while no change was observed in the apoptotic rate of MCF-7 cells. This is the first study linking RSU1L with apoptosis and provides evidence for its differential role in cell lines of different invasive potential. This indicates that RSU1L represses apoptosis in aggressive BC cells helping them evade cell death and survive.

Abstract 6211: Targeting the tumor microenvironment of metastasis to treat metastatic Ewing sarcoma

Abstract Introduction: Ewing sarcoma (EWS) is the second most common bone cancer in adolescents and young adults. Intensive multimodal treatment cures almost 75% of patients who present with localized disease. However, only 25% of patients who present with metastases become long term survivors, and those who suffer a metastatic relapse are almost never cured. Recently, a 3-cell assembly consisting of an invasive cancer cell, a Tie2-high expressing macrophage, and an endothelial cell (termed the Tumor Microenvironment of Metastasis, or TMEM), has been described as the doorway through which breast cancer cells enter the vasculature and disseminate to distant sites. We hypothesized that EWS cells use a similar mechanism for dissemination, and that targeting TMEM offers a novel therapeutic opportunity to prevent metastatic recurrence. Methods: Formalin-fixed, paraffin embedded tissue samples were obtained from 16 patients with EWS treated at our institution, and these were evaluated for the presence of TMEM structures by immunohistochemistry. We also evaluated samples obtained from our novel, clinically relevant murine model of spontaneous distant EWS metastasis. Fragments of EWS either from cell line-derived tumors or patient-derived xenografts (PDX) orthotopically or subcutaneously. After tumors grew, mice were injected with fluorescent dextran in the tail vein and tumors harvested 60 minutes later. Intravascular dextran remains inside blood vessels because the molecular weight is too large to allow diffusion between endothelial cells. As TMEM disrupts the endothelial barrier, dextran leaks out of blood vessels and can be detected and quantified using fluorescence microscopy. Tumors were evaluated for the presence of TMEM structures by immunohistochemistry (IHC), and for the presence of localized vascular leakiness, (the hallmark of functional TMEM), by fluorescence microscopy. Results: We found TMEM assemblies in all patient samples, at numbers well in excess of those seen in samples of metastatic breast cancer. Interestingly, although there was no difference in TMEM counts from patients who were survivors compared with those who died from metastatic disease, there was an increase in TMEM counts in samples from tumors that were exposed to chemotherapy compared to diagnostic biopsy samples, something also reported in breast cancer patients. We also identified TMEM assemblies and localized vascular leakiness in EWS PDX tumors implanted orthotopically. Discussion: TMEM assemblies are present in both EWS patient samples and PDX models, suggesting that this important mechanism of tumor intravasation into the vasculature may be contributing to distant metastasis. Future work will focus on identifying drugs that inhibit the function of TMEM, with the goal of translating this work into clinical trials aimed at diminishing the burden of metastasis in EWS patients. Citation Format: Rachel Offenbacher, Yu Lin, George Karagiannis, Maja Oktay, David Loeb. Targeting the tumor microenvironment of metastasis to treat metastatic Ewing sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6211.

Abstract 5124: Isolation of viable circulating tumor cells from peripheral and central venous blood using a rapid microfluidic biochip

Abstract Background: Thousands of circulating tumor cells (CTCs) may be released into the blood stream of a cancer patient each day. However, only viable CTCs can cause metastasis. These viable CTCs hold the promise of deciphering the tumor heterogeneity, uncovering the mechanism of resistances to therapies, and enabling personalized treatments. Despite the continuously mounting interest, isolation of these cells remains challenging due to the multitude of factors, including rarity of the CTCs in blood, their constant exposure to therapeutic agents, and the harsh environment in the circulation. To address this, we have developed a novel microfluidic biochip capable of CTC isolation from unprocessed whole blood. Herein, we compare isolation of CTCs from the central and peripheral blood samples of metastatic breast cancer (MBC) patients using our biochip to assess impact of blood collection location on CTC count and viability. Methods: We included 19 patients with MBC, of which 26% are white, 63% are African American, and 11% are Latino. The median age of the cohort is 58 (34-75y). All patients are undergoing therapy. A total of 36 samples (7.5 mL each) were collected from either an antecubital vein (peripheral vein) or the subcutaneous port catheter (central vein) at different time points. All samples were processed within 5 hours of blood drawn in our novel microfluidic biochip (only 40 minutes per sample, without pretreatment), followed by in situ immunostaining. CK+/EpCAM+, DAPI+ and CD45- cells were counted as CTCs. In situ live/dead assay using Calcein AM and propidium iodide was performed for some samples right after CTC isolation. Results: CTCs were detected in all the samples (36/36), with a median of 15 CTCs per sample. A &amp;gt;5 CTCs count was found in 86% of the samples (31/36). No correlation was found between CTC count and race/ethnicity. The CTC count in central venous samples was in the range of 6-105 (median 27), while the range was 1-45 (median 10) in the peripheral samples. The difference was found to be statistically significant (p&amp;lt;0.001 using ANOVA). While no correlation between CTC count and patient age was found for the overall samples, we noted a significantly higher CTC count in central venous blood of younger patients (&amp;lt;60y) than of senior patients (p&amp;lt;0.05). Live/dead assay immediately following the microfluidic isolation found live CTCs in patient samples. Conclusions: Viable CTCs were rapidly isolated and detected in MBC samples using our novel microfluidic biochip. Our results show that CTC count in blood drawn from central vein yields significantly higher numbers than from the peripheral vein, suggesting that central venous samples might be preferred for prognosis and monitoring to drug response in MBC patients. Viable CTCs may provide an opportunity to evaluate the mechanism of resistance to therapies. More studies with larger cohorts are needed to further confirm these findings. Citation Format: Jian Zhou, Qiyue Luan, Celine Macaraniag, Arielle Guzman, Maria Mantice, Oana Danciu, Kent Hoskins, Ian Papautsky. Isolation of viable circulating tumor cells from peripheral and central venous blood using a rapid microfluidic biochip [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5124.

Abstract 773: Inhibition of ubiquitin receptor ADRM1 for the treatment of metastatic breast cancer

Abstract Adhesion-regulating molecule 1 (ADRM1) is a polyubiquitin receptor on the 26S proteasome. ADRM1 is upregulated in many cancers. In this study, we evaluated the potential prognostic and predictive value of ADRM1 in breast cancer patients. We determined the expression of ADRM1 and its relationship to breast cancer subtypes, using the Cancer Genome Atlas dataset that contained racial and clinical outcomes data totaling 1108 patients. The ADRM1 mRNA expression levels were divided into quartiles to designate the ADRM1 high versus low expression designation. Karanam et. al developed an orally available proteasome inhibitor bis-benzylidine piperidone (RA190), that binds to the ubiquitin receptor RPN13/ADRM1 on the 19S regulatory particle of the proteasome and directly kills cancer cells by triggering proteotoxic stress. RA190 binds to cysteine 88 of ADRM1/RPN13, triggering rapid accumulation of high-molecular-weight poly-ubiquitinated proteins resulting in apoptosis. Up284 is one of a second generation of small molecules that mimic RA190 activity. The objective of this study is to verify the role of ubiquitin receptor RPN13/ADRM1 in metastatic breast cancer samples of European American and African American patients and identify the safe combination of regimens of bortezomib in combination with Up289 to mitigate recurrence, metastasis and reduce mortality in AA TNBC/QNBC. Clinically, this will reveal a new, hitherto unknown targeted regimen for AA QNBC. From the biological perspective, it will provide insights into the underlying molecular changes that are associated with health disparities. Currently available treatments are unable to eradicate metastatic breast cancer specifically those classified as QNBC. Our preliminary analysis of Cancer Genome Atlas (TCGA) indicated that ADRM1 expression is highly expressed in AA versus EA breast cancer patients, resulting in a worse overall survival. Further analysis of ADRM1 in QNBC patients indicated that it was significantly elevated predominantly in African American patients with QNBC. Citation Format: Christopher Andrews, Clayton Yates, Balasubramanyam Karanam. Inhibition of ubiquitin receptor ADRM1 for the treatment of metastatic breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 773.

Abstract 159: Thymidine kinase 1 and cell cycle control in breast cancer

Abstract Recent advances in cancer immunotherapy have transformed biomarkers into diagnostic and prognostic indicators and immunotherapeutic targets in clinical oncology. To ensure higher treatment success, it is critical to identify unique biomarkers to mitigate “off-target” effects. Therefore, the identification of novel biomarkers and appropriate target selection has never been more important to improve cancer immunotherapy. The DNA salvage pathway protein thymidine kinase 1 (TK1) plays an important role in DNA synthesis and repair. Normally, it is highly expressed during S phase and provides recycled nucleotides by phosphorylating thymidine to make thymidine monophosphate. Past studies have suggested that TK1 may influence cell cycle control and, therefore, provides a platform for the understanding of disease progression and possible means of mitigation. The purpose of our study was to verify elevated TK1 levels in breast cancer cells and further investigate TK1’s potential influence over cell cycle control. We hypothesized that TK1 may be important in regulating the cell cycle and other cell checkpoint proteins. Immunohistochemistry analysis was employed to quantify TK1 expression in ductal and lobular primary and matched metastatic breast cancer samples compared to normal tissue. Bioinformatics was then used to analyze RNA-seq data of cell cycle checkpoint factors and TK1 in BRCA patients from the Cancer Genome Atlas. To demonstrate TK1’s potential effect on the cell cycle checkpoint pathway, we utilized HCC1806 breast cancer cells and generated a CRISPR-Cas9 TK1 knockdown (L133) cell line for in vitro testing. These were validated by western blotting and qPCR. Propidium iodide staining and cell cycle analysis were performed via flow cytometry on both cell lines. Immunohistochemistry results indicated that TK1 levels increase as breast cancer progresses and, thus, may correlate with breast cancer aggressiveness. Bioinformatics analysis showed that strong positive correlations exist between cell cycle checkpoint factors and TK1 in BRCA patients, such as BRCA1 and CHEK2. Flow cytometry cell cycle analysis showed that mean differences of L133 cells in S phase were significantly higher than in G1 compared to HCC 1806 cells, suggesting that TK1 levels influence cell cycle arrest. Our preliminary results suggest that TK1 may affect cell cycle checkpoint pathways, which are essential to maintaining homeostasis in normal cells and preventing cancer progression. Further investigation to understand TK1’s potential interactions with important checkpoint factors, such as p53 or Gas6, may help elucidate other therapeutic targets for preventing disease progression. Citation Format: Eliza E. Bitter, Toni Mortimer, Rachel Morris, Kai Barlow, Abby Schekall, Michelle Townsend, Brett E. Pickett, Kim L. O'Neill. Thymidine kinase 1 and cell cycle control in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 159.

Development of an automated liquid biopsy assay for methylated markers in advanced breast cancer.

Current molecular liquid biopsy assays to detect recurrence or monitor response to treatment require sophisticated technology, highly trained personnel, and a turnaround time of weeks. We describe the development and technical validation of an automated Liquid Biopsy for Breast Cancer Methylation (LBx-BCM) prototype, a DNA methylation detection cartridge assay that is simple to perform and quantitatively detects nine methylated markers within 4.5 h. LBx-BCM demonstrated high interassay reproducibility when analyzing exogenous methylated DNA (75-300 DNA copies) spiked into plasma (Coefficient of Variation, CV = 7.1 - 10.9%) and serum (CV = 19.1 - 36.1%). It also demonstrated high interuser reproducibility (Spearman r = 0.887, P < 0.0001) when samples of metastatic breast cancer (MBC, N = 11) and normal control (N = 4) were evaluated independently by two users. Analyses of interplatform reproducibility indicated very high concordance between LBx-BCM and the reference assay, cMethDNA, among 66 paired plasma samples (MBC N = 40, controls N = 26; Spearman r = 0.891; 95% CI = 0.825 - 0.933, P< 0.0001). LBx-BCM achieved a ROC AUC = 0.909 (95% CI = 0.836 - 0.982), 83% sensitivity and 92% specificity; cMethDNA achieved a ROC AUC = 0.896 (95% CI = 0.817 - 0.974), 83% sensitivity and 92% specificity in test set samples. The automated LBx-BCM cartridge prototype is fast, with performance levels equivalent to the highly sensitive, manual cMethDNA method. Future prospective clinical studies will evaluate LBx-BCM detection sensitivity and its ability to monitor therapeutic response during treatment for advanced breast cancer.

Abstract P3-09-14: Whole exome sequencing of matched primary and metastatic triple-negative breast cancer samples

Abstract Background: Triple-negative breast cancer (TNBC) is a heterogeneous breast cancer subtype with distinct biological features and clinical behavior. TNBC is associated with an increased risk of metastasis and recurrence. In this whole exome study, we investigated the genetic profiles of primary TNBC tumors and paired metastases using next-generation sequencing (NGS). Methods: Genomic DNA extracted from 35 paraffin-embedded formalin-fixed (FFPE) tissues (15 primary tumors that did not metastasize, 11 primary tumors that metastasized, and nine paired metastatic tumors to the lymph nodes) was analyzed by whole exome sequencing (WES). Reads were trimmed using Trim-Galore and were aligned to the reference genome GRCh38 using Burrows-Wheeler Aligner (BWA). BAM files were preprocessed to optimize variant calling, and variant calling was carried out using the GATK pipeline. Variants were annotated using SnpEff. Tumors were analyzed for single nucleotide variants (SNV), point mutations, and insertions/deletions (indels). Results: Primary tumors that did not metastasize had a higher number of variants (~13,500) than primary tumors that metastasized (~12,900). However, the number of variants was similar between the primary tumors (~12,900 variants) and their matched metastases (~12,500 variants). MUC3A was the top mutated gene both in primary tumors that did not metastasize and in those that metastasized. MUC3A was also the top mutated gene in matched metastatic lesions. Moreover, we compared the mutational status of the most frequently mutated genes in TNBC samples from the TCGA and METABRIC datasets. We found that in our dataset, TP53, MAP3K1, and PTEN were mutated in 60%, 93%, and 7% of primary TNBC tumors without metastases and in 36%, 0%, and 36% of primary TNBC tumors that metastasized. Mutations in TP53 and PTEN were found in 2/9 and 1/9 of primary and metastases pairs, respectively. No mutations in PI3KCA were observed in any of the primary or matched metastatic tumors. Conclusions: We used WES to compare the genomic landscapes of primary TNBC tumors and matched metastatic tumors, as well as of primary TNBC tumors that metastasized and those that did not metastasize. We found very similar genomic alterations between the primary and paired metastatic tumors, indicating that genomic features may be retained during metastasis. Primary tumors that did not metastasize showed a greater extent of genomic alterations than primary tumors that metastasized. Citation Format: Jaspreet Kaur, Darshan S. Chandrashekar, Zsuzsanna Varga, Emiel Janssen, Khanjan Gandhi, Karuna Mittal, Umay Kiraz, Sooryanarayana Varambally, Ritu Aneja. Whole exome sequencing of matched primary and metastatic triple-negative breast cancer samples [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-09-14.