Landscape Of Metastatic Breast Cancer Research Articles

Activating HR+/HER2- and triple-negative breast cancer care teams and their patients in shared decision-making.

1547 Background: In the rapidly evolving treatment landscape of metastatic breast cancer (MBC), shared decision-making (SDM) is critical to individualize care and improve patient outcomes. To help facilitate improved SDM, we developed an educational toolkit for health care providers (HCPs) to use with HR+/HER2- and triple negative breast cancer (TNBC) patients (pts) and evaluated the implementation of this toolkit at 5 community oncology clinics. Methods: In May-June 2022, pts (N=94) and HCPs (N=18) completed surveys assessing attitudes, confidence, goals, and barriers to SDM in MBC care. HCPs then led collaborative learning sessions with their pts using the SDM toolkit to provide education regarding treatment options and side effects, and to better align on shared goals and treatment plans. Results: In surveys, only 50% of pts reported that they decide on a treatment plan together with their HCPs , 38% reported being asked about treatment preferences, and 34% reported discussing supportive care, such as mental health care or pain relief. Additionally, very few pts reported high knowledge of BC treatments and side effects. HCPs and pts were misaligned on patient goals and barriers to SDM. For example, 56% of HCPs thought pts were too overwhelmed/anxious/fatigued to make treatment decisions, but only 21% of pts agreed that was a top challenge. While pts and HCPs were aligned on top treatment decision factors of effectiveness and quality-of-life, HCPs underestimated the importance of concerns about side effects (HCPs 11% vs pts 32%), and the cost and duration of treatment (17% vs 30%, and 22% vs 30%, respectively). HCPs correctly identified survival (56%) as a top goal for pts but were less likely to identify progression/recurrence as important to pts (39%). Additionally, 28% of pts reported their top challenge was worrying about being unable to work or meet responsibilities at home; however, only 19% of HCPs recognized this as a top challenge. Following pt-HCPs collaborative education sessions, in which HCPs used the SDM toolkit to facilitate pt education and SDM, HCPs and pts reported improved confidence in pt-HCP communication. Additionally, 46% of pts reported discussing treatment goals with their HCPs and 46% reported taking a more active role in their care following the learning session. Conclusions: These findings reveal misalignments between HCPs and patients with BC regarding treatment decision-making. The gaps identified are critical to address as they are pre-requisites for SDM. The downloadable shared decision-making toolkit developed as part of this implementation science initiative can be adopted by breast cancer clinical teams to help facilitate patient education and SDM, empowering patients to be active participants in their care.

Comprehensive molecular profiling from liquid and tissue for analysing the somatic mutational landscape in an Indian breast cancer cohort.

e13080 Background: Breast cancer is a genetically and clinically heterogeneous entity, with high prevalence in the Indian population. The primary objective of this study was to characterize the somatic mutational landscape of metastatic breast cancer in Indian patients from tumor and liquid specimens. Methods: We performed molecular profiling of 341 tumor tissue specimens and 901 blood specimens from individual breast cancer patients, with paired tissue and blood processing in a sub cohort (n=101). Targeted NGS evaluating single nucleotide alterations, copy number alterations, and fusions was performed on these specimens. Results: In the cohort with tissue-based sequencing (n = 341), TP53 was the prevalently altered gene (55%). PIK3CA and ESR1 mutations were detected in 32% and 9%, respectively. BRCA1/2 alterations were detected in 10.8%, ARID1A in 7%, KEAP1 in 6%, NF1 in 6%, and ATR in 6%. ERBB2 amplification was observed in 10% of the cases. ESR1 gene fusions were detected in 3.7%. This is clinically relevant as along with other ESR1 resistance mutations, ESR1 fusions are also known as recurrent drivers of endocrine therapy resistance and are impervious to ER-targeted therapies. In a sub cohort comprising 255 specimens, TMB analysis showed a median TMB of 5 mut/Mb (range 1 - 88 mut/Mb), and 15.3% specimens with TMB-High (≥10 mut/mb). The ctDNA analysis (n = 901) revealed TP53 being the most altered (41%) gene, followed by PIK3CA (23%), ESR1(11%), EGFR (6%) and GNAS (4%). Acquired resistance mutations in ERBB2 were identified in ctDNA analysis liquid biopsy from two patients treated with HER2-targeted therapy and were absent in corresponding tissue samples. Mutations in ESR1 were more commonly seen in liquid biopsy than paired tissue, indicating this acquired resistance alteration being better captured in ctDNA than tissue due to tumor heterogeneity and tumor evolution. This indicates causative role for ESR1 mutations in endocrine resistance but not in disease pathogenesis. Conclusions: We report the largest liquid biopsy study reporting the genomic landscape from breast cancer cases of Indian origin along with tissue based molecular landscape. High concordance of liquid for PIK3CA alteration and higher sensitivity for detection of resistance conferring alterations like ESR1 and ERBB2 shows utility of liquid biopsy profiling. It reinforces the utility of liquid biopsy as effective tool that reveal clinically relevant information including mutational status and therapeutic options and seem more relevant in acquired resistance settings. [Table: see text]

NCCN Guidelines® Insights: Breast Cancer, Version 4.2023.

The NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines) for Breast Cancer address all aspects of management for breast cancer. The treatment landscape of metastatic breast cancer is evolving constantly. The therapeutic strategy takes into consideration tumor biology, biomarkers, and other clinical factors. Due to the growing number of treatment options, if one option fails, there is usually another line of therapy available, providing meaningful improvements in survival. This NCCN Guidelines Insights report focuses on recent updates specific to systemic therapy recommendations for patients with stage IV (M1) disease.

Abstract 5923: The genetic landscape of metastatic breast cancer reflected in circulating tumor DNA

Abstract Tissue biopsies of breast tumors only provide a snapshot of the evolution of the disease and may miss potential therapeutic targets, especially in the metastatic setting. Plasma-derived cell-free tumor DNA constitutes a potential surrogate for tumor DNA obtained from tissue biopsies to potentially capture inter-and intra-tumoral heterogeneity present in metastatic breast cancer. We aimed to investigate to what extent variants identified in the primary tumor and metastases are reflected in plasma. We performed whole-exome sequencing on tumor DNA from primary and metastatic lesions and plasma-derived circulating tumor DNA of eight patients with metastatic breast cancer. Our results show that metastases most often follow parallel evolution, given the low levels of stem mutations detected between primary tumors and matched metastases and mutational events private to the primary tumor. Furthermore, we demonstrated that ctDNA mainly reflected old stem mutations shared between primary tumor and metastasis, and less often, genetic alterations found solely in primary tumor or metastasis. Lastly, clinically relevant variants, e.g., resistance mutations detected in primary tumor and metastasis, were to some extent reflected in ctDNA, including affected genes MET, MTOR, CDK6, PIK3CA, and GATA3. However, mutations in MED1, NCOR1, and NCOR2 were only found in tumor tissues. These findings support the importance of a metastatic deposit biopsy to guide treatment decisions. Together, our results have implications for future ctDNA studies. For monitoring tumor burden using ctDNA, our results suggest that truncal mutations are the best candidates, as they are highest in circulating levels. For confident tracking of subclonal mutations in ctDNA, liquid biopsies are not yet to substitute metastatic tissue biopsies and instead demonstrate support to the current gold standard. Citation Format: Stephanie Kavan. The genetic landscape of metastatic breast cancer reflected in circulating tumor DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5923.

Genomic landscape of metastatic breast cancer (MBC) patients with methylthioadenosine phosphorylase (MTAP) loss

Homozygous deletion of MTAP upregulates de novo synthesis of purine (DNSP) and increases the proliferation of neoplastic cells. This increases the sensitivity of breast cancer cells to DNSP inhibitors such as methotrexate, L-alanosine and pemetrexed. 7,301 cases of MBC underwent hybrid-capture based comprehensive genomic profiling (CGP). Tumor mutational burden (TMB) was determined on up to 1.1 Mb of sequenced DNA and microsatellite instability (MSI) was determined on 114 loci. Tumor cell PD-L1 expression was determined by IHC (Dako 22C3). 208 (2.84%) of MBC featured MTAP loss. MTAP loss patients were younger (p = 0.002) and were more frequently ER- (30% vs. 50%; p < 0.0001), triple negative (TNBC) (47% vs. 27%; p < 0.0001) and less frequently HER2+ (2% vs. 8%; p = 0.0001) than MTAP intact MBC. Lobular histology and CDH1 mutations were more frequent in MTAP intact (14%) than MTAP loss MBC (p < 0.0001). CDKN2A (100%) and CDKN2B (97%) loss (9p21 co-deletion) were significantly associated with MTAP loss (p < 0.0001). Likely associated with the increased TNBC cases, BRCA1 mutation was also more frequent in MTAP loss MBC (10% vs. 4%; p < 0.0001). As for immune checkpoint inhibitors biomarkers, higher TMB >20 mut/Mb levels in the MTAP intact MBC (p < 0.0001) and higher PD-L1 low expression (1-49% TPS) in the MTAP loss MTAP (p = 0.002) were observed. MTAP loss in MBC has distinct clinical features with genomic alterations (GA) affecting both targeted and immunotherapies. Further efforts are necessary to identify alternative means of targeting PRMT5 and MTA2 in MTAP-ve cancers to benefit from the high-MTA environment of MTAP-deficient cancers.

Abstract P3-01-04: A real-world evidence study of everolimus plus endocrine therapy beyond CDK4/6 inhibitors for HR+/HER2- advanced breast cancer

Abstract Introduction Since the approval a decade ago of everolimus in combination with endocrine therapy (ET), the treatment landscape of metastatic breast cancer (mBC) has changed dramatically. Endocrine monotherapy after progression to CDK4/6 inhibitors has shown a limited progression-free survival (PFS) below 3 months. Evidence of the efficacy of everolimus plus ET after CDK4/6 inhibitors is scarce. Methods We performed a retrospective observational study of patients with mBC treated with everolimus between September 2011 and April 2022 in 4 Spanish hospitals. Clinical and demographic data were collected from medical records. Our main objective was to estimate the median progression-free survival (mPFS) for everolimus + ET in patients previously treated with a CDK4/6 inhibitor. We also collected the adverse events (AE) related to everolimus. Quantitative variables were summarized with medians (range), and qualitative variables with proportions. We used the Kaplan-Meier method for survival estimates. Results We identified a total of 297 mBC patients treated with everolimus plus ET. The median follow-up time was 20 months (interquartile range: 1 – 97 months). In this cohort, the median age at diagnosis was 49 years (26 – 84 years). At the moment of starting everolimus, the median number of previous lines of treatment was 2 (0 – 12), 22% of patients were ‘de novo’ metastatic, 67% presented visceral involvement, 40% had received previous chemotherapy for advanced disease, and 51% (n=152) had received a previous CDK4/6 inhibitor. The ET combined with everolimus was exemestane (77%), fulvestrant (18%), and tamoxifen (5%). 45% of patients were alive at data cut-off. In patients previously treated with a CDK4/6 inhibitor, the estimated median PFS (mPFS) was 5.9 months (95%CI: 5.0 – 7.8 months). In patients without visceral involvement (n=52), mPFS was 7.2 months (95%CI: 5.5 – 11.0 months), and 5.6 months (95%CI: 3.9 – 7.8 months) in the presence of visceral metastasis (n=100). In patients without previous chemotherapy in the metastatic setting (n=109), mPFS was 7.2 months (95%CI: 5.9 – 8.4 months), and 4.6 months (95%CI: 3.1 – 5.7 months) for patients who had received previous chemotherapy (n=43). For patients without a previous CDK4/6 inhibitor (n=145), the median PFS was 8.3 months (95%CI: 6.4 – 10.3 months). Everolimus starting doses were 10 mg (83%), 5 mg (15%), and 7.5 mg (2%). Dexamethasone mouthwash was used by 44% of patients. The most frequent AE were mucositis (51%; 3% grade 3), anemia (41%; 3% grade 3), hyperglycemia (34%; 2% grade 3), rash (28%; 2% grade 3), neumonitis (21%; 2% grade 3), and diarrhea (17%; 1% grade 3). There were no grade 4-5 adverse events. Dose reduction was made in 35% of patients, and in 16% of patients the treatment was discontinued due to toxicity. Conclusions In our cohort, the use of everolimus plus ET in mBC patients previously treated with a CDK4/6 inhibitor showed a clinically significant benefit in terms of PFS, especially in patients without visceral metastasis, and no previous chemotherapy for advanced disease. In this real-world study, the toxicity profile of everolimus was manageable. Citation Format: Rodrigo Sánchez-Bayona, Manuel Alva, Alfonso López de sa, Yolanda Jerez Gilarranz, Ana Sánchez de torre, Pablo Tolosa, Alicia de luna, Sara López-Tarruella, Laura Lema, Fernando Moreno, Isabel Echavarria, Ainhoa Madariaga, Javier Benítez, Blanca Herrero, Macarena Rey, Justo Ortega, Salvador Gámez, Andrea Modrego, Rocío Martín Lozano, Luis Figuero-Pérez, Roberto Jiménez, Marta González Sevilla, Irene González, Marianela Bringas Beranek, María de toro, Tatiana Massarrah, María del Monte-Millán, Marina Pinardo, Luis Manso, Coralia Bueno-Muiño, José Ángel García-Sáenz, Miguel Martín, Eva Ciruelos. A real-world evidence study of everolimus plus endocrine therapy beyond CDK4/6 inhibitors for HR+/HER2- advanced breast cancer. [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 P3-01-04.

The Molecular Predictive and Prognostic Biomarkers in Metastatic Breast Cancer: The Contribution of Molecular Profiling.

Simple SummaryWe propose in this article to review the state of knowledge about predictive and prognosis biomarkers in metastatic breast cancer through the prism of molecular profiling studies.The past decade was marked by several important studies deciphering the molecular landscape of metastatic breast cancer. Although the initial goal of these studies was to find driver oncogenic events to explain cancer progression and metastatic spreading, they have also permitted the identification of several molecular alterations associated with treatment response or resistance. Herein, we review validated (PI3KCA, ESR1, MSI, NTRK translocation) and emergent molecular biomarkers (ERBB2, AKT, PTEN, HRR gene, CD274 amplification RB1, NF1, mutational process) in metastatic breast cancer, on the bases of the largest molecular profiling studies. These biomarkers will be classed according the level of evidence and, if possible, the ESCAT (ESMO) classification. Finally, we will provide some perspective on development in clinical practice for the main biomarkers.

Abstract OT1-19-01: The metastatic breast cancer project: Generating the clinical and genomic landscape of metastatic breast cancer through patient-partnered research

Abstract The Metastatic Breast Cancer Project (MBCproject) is an ongoing research study that directly engages patients (pts) through social media and advocacy groups, and empowers them to share their samples, clinical information, and experiences. The goal is to create a publicly available dataset of linked genomic, clinical, and pt-reported data to enable research. In collaboration with pts, advocates, and advocacy groups, a website (MBCproject.org) was developed that allows pts with metastatic breast cancer (MBC) anywhere in the US or Canada to register. From 10/20/15-6/1/21, 6100 patients with MBC registered for the MBCproject. Registered pts are sent an online consent form that asks for permission to obtain and analyze their medical records and samples. Consented pts are sent a saliva and/or blood kit and asked to mail back a saliva sample, which is used to extract germline DNA, and/or a blood sample, which is used to extract germline DNA and cell free DNA (cfDNA). We contact participants’ medical providers to obtain medical records and a portion of their stored tumor biopsies. 3456 pts receiving care at over 1700 different institutions have consented to share medical records and tumor/saliva/blood samples and to have genomic analysis performed. Whole exome sequencing (WES) is performed on tumor DNA, germline DNA, and cfDNA; transcriptome sequencing (RNA-seq) is performed on tumor RNA. Medical records and pt-reported data are abstracted to create a detailed clinical record for each pt. Table 1 highlights clinical data collection, biospecimen acquisition, and genomic data generation to date. Examples of clinicogenomic analyses are shown in Table 2. De-identified linked genomic, clinical, and pt-reported data is shared regularly via public databases (mbcproject.org, cBioPortal, dbGaP, NCI Genomic Data Commons). To date, this data has been cited in over 40 publications. Study updates are shared with participants regularly. The MBCproject continues to enroll new patients, generate additional data, and perform integrated clinical and genomic analyses with the goal of building a dataset that is representative of patients with MBC. We have partnered with over 30 non-profit breast cancer advocacy groups. We also have several community engagement efforts underway to more directly reach patients in underrepresented communities, including partnerships with faith-based organizations and colleges/universities, as well as targeted engagement with the African American community. In addition, in partnership with Latinx patients, advocates, and researchers, a Spanish-language version of the MBCproject was launched in June 2021. Partnering directly with pts rapidly enables thousands of pts to remotely share tumors, blood, saliva, and medical records to accelerate research. The resulting publicly shared clinically annotated dataset is a resource that allows researchers to identify patients with specific phenotypes, who have often been challenging to identify with traditional approaches. Clinical data collection, biospecimen acquisition, and genomic data generation:NumberConsent signed (US &amp; CA)3456 ptsPatient-reported data collected (demographics, diagnosis details, receptor status, clinical experiences, pathology details, sites of metastasis, treatments with start and stop dates3456 ptsMedical record received from clinical institution1365 ptsSaliva sample received from pt2124 ptsBlood sample received from pt1114 ptsTumor samples received from clinical institution631 tumor samples from 398 ptsWES from germline complete505 germline samplesWES from tumor (primary and metastatic) samples complete429 tumor samplesRNA-seq from tumor (primary and metastatic) samples complete351 tumor samplesULP-WGS from cfDNA (taken in metastatic setting) complete953 blood samplesWES from circulating tumor DNA (taken in metastatic setting) complete144 blood samples CohortConsented (US &amp; CA)Tumor WES completeTumor RNA-seq completePts diagnosed &amp;lt; 40 yrs of age114615292De novo MBC1207158109Late recurrence (&amp;gt;5 years after dx)9099141Long term survivors (MBC &amp;gt; 10yrs)163138Resistance to CDK4/6 inhibitors70914839NED at time of f/u survey4305445Triple Negative Breast Cancer3304632Patients with 2 or more tumor biopsies/cfDNA samples collected by the MBCproject29810882 Citation Format: Nikhil Wagle, Corrie Painter, Elana Anastasio, Mary McGillicuddy, Esha Jain, Tania G. Hernandez, Brett N. Tomson, Beena Thomas, Daniel Abravanel, Dewey Kim, Sara Balch, Alyssa L. Damon, Shahrayz Shah, Rafael Ramos, Delia Sosa, Ilan Small, Colleen Nguyen, Sarah Winnicki, Taylor Cusher, Parker Chastain, Michael Dunphy, Jorge Gomez Tejeda Zanudo, Netsanet Tsegai, Lauren Sterlin, Ulcha F. Ulysse, Imani Boykin, Oyin Alao, Todd R. Golub. The metastatic breast cancer project: Generating the clinical and genomic landscape of metastatic breast cancer through patient-partnered research [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 OT1-19-01.

Abstract PD6-02: The metastatic breast cancer project - Expanding the clinical, genomic, and transcriptomic landscape of metastatic breast cancer through patient-partnered research

Abstract Background: The Metastatic Breast Cancer Project (MBCproject) is an ongoing research study that directly engages patients (pts) through social media and advocacy groups, and empowers them to share their biospecimens, clinical history, and experiences. The goal is to create a publicly available dataset of linked clinicogenomic and pt-reported data to enable research. From 2015-10-20 to 2020-3-31, 3,245 MBC pts who received treatment at &amp;gt;1,700 institutions, consented to share medical records, pt-reported data, and tumor/saliva/blood samples and to have genomic analysis performed. Here, we describe an analysis of the clinical and genomic features in this initial MBCproject cohort. Methods: We performed whole exome sequencing (WES) on 379 tumors (with matched germline) from 301 pts, 377 germline samples and RNA sequencing (RNA-seq) from 200 tumors from 141 pts. In 14 pts, we characterized 2 or more serial tumor biopsies. WES data was analyzed for mutations and copy number variants. RNA-seq data was used to call fusions, research-grade PAM50, and gene set enrichment scores. Medical records and pt-reported data were abstracted to create detailed clinical record for each pt. Results: WES of 249 metastatic tumors identified 34 cancer genes (e.g., TP53, PIK3CA, CDH1, PTEN, AKT1, NF1, ESR1) that were significantly recurrently altered. Potential clinically actionable alterations were identified in 39% of metastatic tumors. 45 tumors (22.5%) had fusions with known functional effects and 24 (12%) had in-frame fusions in key cancer genes like FANCD2 (3), FGFR3 (2), ESR1 (1), BRAF (1), and NCOR1 (1). PAM50 classification suggested depletion of Luminal A subtype in this cohort compared to TCGA breast cancer cohort (p-value &amp;lt;0.05). Of 29 pts with paired RNA-seq biopsies, 10 pts showed a PAM50 subtype switch [LumB to Basal = 1, Her2 to Basal =1, Basal to LumA = 1, Her2 to LumA = 2, LumA/B to Her2 = 3, LumA to LumB = 2]. Germline analysis showed that 30.2% (114/377) of pts had at least one pathogenic variant in a cancer predisposition gene, including BRCA1/BRCA2 (5%), NF1 (5.8%), ATM (1.06%) and PALB2 (1.59%). In 10.9% pts (33/301), pathogenic variants in a cancer predisposition gene was accompanied by an apparent somatic loss of function event in the same gene. There was ~ 90% concordance between abstracted features (e.g., receptor status, histology, diagnosis dates, metastatic sites) and pt-reported data, enabling the use of both data types for integrated analyses. The utility of integrated analyses is illustrated by a case study of a pt who had an initial diagnosis of ductal carcinoma in situ and developed metastatic disease 5.5 yrs later. Analysis of 3 metastatic tumors (WES and RNA-seq) and a circulating tumor DNA sample (WES only) from this pt collected over the course of therapy revealed evidence of tumor evolution and multiple mechanisms of resistance to endocrine therapies and CDK4/6 inhibitors, including 2 distinct acquired ESR1 mutations, an activating BRAF fusion, and estrogen receptor (ER) loss by immunohistochemistry with concomitant development of ESR1-PLEKHG1 in-frame fusion. RNA-seq data also showed a PAM50 luminal phenotype and a persistent ER. signature throughout despite the apparent ER loss, suggesting compensation by the ESR1 fusion. Analyses of 13 additional pts with serial biopsies will be presented. Integrated analyses of several additional cohorts of interest, such as de novo MBC (91 pts), resistance to CDK4/6 inhibitors (39 pts), and pts diagnosed with breast cancer &amp;lt;40 yrs, will also be presented. Conclusion: This clinicogenomic dataset generated by partnering directly with pts was uniquely built with pt-reported data, medical record data, and multi-omic characterization, and serves as a powerful tool for researchers to harness to accelerate discoveries in MBC. Citation Format: Esha Jain, Dewey Kim, Jorge Gomez Tejeda Zanudo, Sara Balch, Mary McGillicuddy, Brett N. Tomson, Tania G. Hernandez, Beena S. Thomas, Daniel L. Abravanel, Shahrayz Shah, Rafael Ramos, Delia Sosa, Ilan Small, Lauren Sterlin, Sarah Winnicki, Colleen Nguyen, Micheal Dunphy, Elana Anastasio, Todd R. Golub, Corrie A. Painter, Nikhil Wagle. The metastatic breast cancer project - Expanding the clinical, genomic, and transcriptomic landscape of metastatic breast cancer through patient-partnered research [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 PD6-02.

Molecular features of untreated breast cancer and initial metastatic event inform clinical decision-making and predict outcome: long-term results of ESOPE, a single-arm prospective multicenter study

BackgroundPrognosis evaluation of advanced breast cancer and therapeutic strategy are mostly based on clinical features of advanced disease and molecular profiling of the primary tumor. Very few studies have evaluated the impact of metastatic subtyping during the initial metastatic event in a prospective study. The genomic landscape of metastatic breast cancer has mostly been described in very advanced, pretreated disease, limiting the findings transferability to clinical use.MethodsWe developed a multicenter, single-arm, prospective clinical trial in order to address these issues. Between November 2010 and September 2013, 123 eligible patients were included. Patients at the first, untreated metastatic event were eligible. All matched primary tumors and metastatic samples were centrally reviewed for pathological typing. Targeted and whole-exome sequencing was applied to matched pairs of frozen tissue. A multivariate overall survival analysis was performed (median follow-up 64 months).ResultsPer central review in 84 patients (out of 130), we show that luminal A breast tumors are more prone to subtype switching. By combining targeted sequencing of a 91 gene panel (n = 67) and whole-exome sequencing (n = 30), a slight excess of mutations is observed in the metastases. Luminal A breast cancer has the most heterogeneous mutational profile and the highest number of mutational signatures, when comparing primary tumor and the matched metastatic tissue. Tumors with a subtype change have more mutations that are private. The metastasis-specific mutation load is significantly higher in late than in de novo metastases. The most frequently mutated genes were TP53 and PIK3CA. The most frequent metastasis-specific druggable genes were PIK3CA, PTEN, KDR, ALK, CDKN2A, NOTCH4, POLE, SETD2, SF3B1, and TSC2. Long-term outcome is driven by a combination of tumor load and metastasis biology.ConclusionsProfiling of the first, untreated, metastatic event of breast cancer reveals a profound heterogeneity mostly in luminal A tumors and in late metastases. Based on this profiling, we can derive information relevant to prognosis and therapeutic intervention, which support current guidelines recommending a biopsy at the first metastatic relapse.Trial registrationThe trial was registered at ClinicalTrials.gov (NCT01956552).

Abstract PD9-07: Genomic landscape of metastatic breast cancer (MBC): Comprehensive cell-free DNA analysis from over 10,000 patients and comparison with primary breast cancer

Abstract Background: Current tissue-based genomic sequencing datasets typically reflect early stage, mostly treatment-naïve cohorts, and fail to capture the genomic landscape of advanced disease, including mutations conferring acquired resistance to therapy. Plasma cell-free DNA (cfDNA) can provide information on somatic alterations non-invasively and can capture spatial tumor heterogeneity. Here, we studied cfDNA from 15,564 blood samples from 12, 827 patients (11.5% of patients had serial samples) with MBC, and analyzed the differences in mutational landscape between cohorts of heavily pre-treated and primary untreated breast cancers. Materials and methods: Deidentified aggregate genomic data from stage III/IV breast cancer clinical samples submitted for cfDNA next-generation sequencing (NGS) analysis with Guardant360 (Guardant Health, Inc; Redwood City, CA, USA) assay between 11/25/16 and 5/26/20. This clinical assay detects somatic single nucleotide variants (SNVs), indels, copy number gains, and fusions in either all or a subset of exons in up to 74 genes. We compare the observed alterations to events detected from whole-exome sequencing data representing ~1,000 untreated primary breast cancers from The Cancer Genome Atlas (TCGA) project. Results: In the overall cohort (N = 12, 827), the average patient age was 61 (range 18-100); 99% were female. Of the 11,290 pts with at least one samples with a non-synonymous alteration, the most frequently mutated genes were TP53 (53%), PIK3CA (38%), ESR1 (28%), ATM (13%), GATA3 (10%), and ARID1A (10%) at varying allelic frequencies with dynamic changes over time (in pts with serial specimens) highlighting clonal heterogeneity and temporal evolution. Copy-number gains were most frequent in FGFR1 (13%), CCND1 (11%), EGFR (9%) and PIK3CA (9%), but fusions were infrequent (below 1%), with fusions involving FGFR3 (n=22), FGFR2 (n=12), ALK (n=7), NTRK1 (n=6), RET (n=4), and ROS1 (n=1). Overall, patients had significantly higher frequency of actionable alterations based on ctDNA analysis, as compared to that observed in TCGA. Similarly, non-synonymous mutations were identified in genes associated with acquired resistance, including ESR1 (28%), ERBB2 (9%), PTEN (8.1%), RB1 (7.7%), NF1 (6.2%), and AKT1 (4%), mutated at frequencies significantly exceeding those observed in TCGA. Finally, we developed a novel classifier to identify the breast cancer receptor subtypes based on differential genomic profile, which was further validated in an independent genomic dataset. Conclusions: In the largest dataset to date, we provide the comparative genomic landscape of the various SNVs, indels, copy-number gains, and fusions identified by next generation sequencing of cfDNA in patients with MBC, compared to primary breast cancer. Interestingly, both targetable genomic alterations and resistance mutations occur at frequencies much higher than observed in primary breast cancer, highlighting the genomic complexity of MBC and potential need for combinatorial therapy. Finally, we describe a novel classifier for detection of HR+ and HER2+ tumors, which could be particularly valuable clinically given the receptor switch with tumor evolution and practical difficulty with serial tissue biopsies in MBC. Comparison of genomic signature profiles between MBC and primary breast cancer will be presented at the meeting. Citation Format: Aditya Bardia, Massimo Cristofanilli, Justin Cha, Lesli Kiedrowski, Dejan Juric, Ben H Park, Adam Brufsky, Joyce O’Shaughnessy, Becky Nagy, Leif Ellisen, Ignaty Leshchiner, Gaddy Getz. Genomic landscape of metastatic breast cancer (MBC): Comprehensive cell-free DNA analysis from over 10,000 patients and comparison with primary breast cancer [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD9-07.

Abstract OT-18-01: The metastatic breast cancer project: Generating the clinical and genomic landscape of metastatic breast cancer through patient-partnered research

Abstract The Metastatic Breast Cancer Project (MBCproject) is an ongoing research study that directly engages patients (pts) through social media and advocacy groups, and empowers them to share their samples, clinical information, and experiences. The goal is to create a publicly available dataset of linked genomic, clinical, and pt-reported data to enable research. In collaboration with pts, advocates, and advocacy groups, a website (MBCproject.org) was developed that allows pts with metastatic breast cancer (MBC) anywhere in the US or Canada to register. From 10/20/15-3/31/20, 5708 women and men with MBC registered for the MBCproject. Registered pts are sent an online consent form that asks for permission to obtain and analyze their medical records and samples. Consented pts are sent a saliva and/or blood kit and asked to mail back a saliva sample, which is used to extract germline DNA, and/or a blood sample, which is used to extract germline DNA and cell free DNA (cfDNA). We contact participants’ medical providers to obtain medical records and a portion of their stored tumor biopsies. 3245 pts receiving care at over 1700 different institutions have consented to share medical records and tumor/saliva/blood samples and to have genomic analysis performed. Whole exome sequencing (WES) is performed on tumor DNA, germline DNA, and cfDNA; transcriptome sequencing (RNA-seq) is performed on tumor RNA. Medical records and pt-reported data are abstracted to create a detailed clinical record for each pt. Table 1 highlights clinical data collection, biospecimen acquisition, and genomic data generation to date. Examples of clinicogenomic analyses are shown in Table 2. De-identified linked genomic, clinical, and pt-reported data is shared regularly via public and semi-public databases (mbcproject.org, cBioPortal, dbGaP, NCI Genomic Data Commons). To date, this data has been cited in over 20 published journal articles. Study updates are shared with participants regularly. The MBCproject continues to enroll new patients, generate additional data, and perform integrated clinical and genomic analyses with the goal of building a dataset that is representative of patients with MBC. We have partnered with over 30 non-profit breast cancer advocacy groups. We also have several community engagement efforts underway to more directly reach patients in underrepresented communities, including partnerships with faith-based organizations and colleges/universities, as well as targeted engagement with the African American community. In addition, in partnership with Latinx patients, advocates, and researchers, the project has been translated into Spanish and is expected to launch in late 2020. Partnering directly with pts rapidly enables thousands of pts to remotely share tumors, blood, saliva, and medical records to accelerate research. The resulting publicly shared clinically annotated database is a resource that allows researchers to identify patients with specific phenotypes, who have often been challenging to identify with traditional approaches. Clinical data collection, biospecimen acquisition, and genomic data generation:NumberConsent signed (US &amp; CA)3245 ptsSurvey #1 submitted(demographics, diagnosis details, receptor status, clinical experiences)3245 ptsSurvey #2 submitted(pathology details, sites of metastasis, treatments with start and stop dates)1638 ptsMedical record received1352 ptsSaliva sample received2004 ptsBlood sample received1121 ptsTumor samples received585 tumor samples from 424 ptsDigital image of tumor slide H&amp;E generated585 tumor samplesWES from germline complete458 germline samplesWES from tumor (primary and metastatic) samples complete343 tumor samplesRNA-seq from tumor (primary and metastatic) samples complete228 tumor samplesULP-WGS from cfDNA (taken in metastatic setting) complete993 blood samplesWES from circulating tumor DNA (taken in metastatic setting) complete143 blood samples CohortConsented (US &amp; CA)Tumor WES completeTumor RNA-seq completePts diagnosed &amp;lt; 40 yrs of age107312071De novo MBC112712183Late recurrence (&amp;gt;5 years after dx)8307752Long term survivors (MBC &amp;gt; 10yrs)158115Resistance to CDK4/6 inhibitors70914839NED at time of f/u survey4238939Triple Negative Breast Cancer3107531Patients with 2 or more tumor biopsies / cfDNA samples collected by the MBCproject2876138 Citation Format: Nikhil Wagle, Corrie Painter, Elana Anastasio, Michael Dunphy, Mary McGillicuddy, Esha Jain, Brett Tomson, Tania G. Hernandez, Beena Thomas, Dewey Kim, Alyssa L. Damon, Shahrayz Shah, Rafael Ramos, Colleen Nguyen, Lee O'Neil, Sarah Winnicki, Sara Balch, Rachel Stoddard, Taylor Cusher, Parker Chastain, Jorge Gomez Tejeda Zanudo, Jorge Buendia-Buendia, Ofir Cohen, Netsanet Tsegai, Lauren Sterlin, Ulcha F. Ulysse, Imani Boykin, Kate Sine, Oyin Alao, Jacqueline Lucia, Eric S. Lander, Todd R. Golub. The metastatic breast cancer project: Generating the clinical and genomic landscape of metastatic breast cancer through patient-partnered research [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr OT-18-01.

Genomic landscape of metastatic breast cancer identifies preferentially dysregulated pathways and targets.

Nearly all breast cancer deaths result from metastatic disease. Despite this, the genomic events that drive metastatic recurrence are poorly understood. We performed whole-exome and shallow whole-genome sequencing to identify genes and pathways preferentially mutated or copy-number altered in metastases compared with the paired primary tumors from which they arose. Seven genes were preferentially mutated in metastases - MYLK, PEAK1, SLC2A4RG, EVC2, XIRP2, PALB2, and ESR1 - 5 of which are not significantly mutated in any type of human primary cancer. Four regions were preferentially copy-number altered: loss of STK11 and CDKN2A/B, as well as gain of PTK6 and the membrane-bound progesterone receptor, PAQR8. PAQR8 gain was mutually exclusive with mutations in the nuclear estrogen and progesterone receptors, suggesting a role in treatment resistance. Several pathways were preferentially mutated or altered in metastases, including mTOR, CDK/RB, cAMP/PKA, WNT, HKMT, and focal adhesion. Immunohistochemical analyses revealed that metastases preferentially inactivate pRB, upregulate the mTORC1 and WNT signaling pathways, and exhibit nuclear localization of activated PKA. Our findings identify multiple therapeutic targets in metastatic recurrence that are not significantly mutated in primary cancers, implicate membrane progesterone signaling and nuclear PKA in metastatic recurrence, and provide genomic bases for the efficacy of mTORC1, CDK4/6, and PARP inhibitors in metastatic breast cancer.

The genomic landscape of metastatic breast cancer: Insights from 11,000 tumors.

BackgroundMetastatic breast cancer is the leading cause of cancer death in women, but the genomics of metastasis in breast cancer are poorly studied.MethodsWe explored a set of 11,616 breast tumors, including 5,034 metastases, which had undergone targeted sequencing during standard clinical care.ResultsBesides the known hotspot mutations in ESR1, we observed a metastatic enrichment of previously unreported, lower-prevalence mutations in the ligand-binding domain, implying that these mutations may also be functional. Furthermore, individual ESR1 hotspots are significantly enriched in specific metastatic tissues and histologies, suggesting functional differences between these mutations. Other alterations enriched across all metastases include loss of function of the CDK4 regulator CDKN1B, and mutations in the transcription factor CTCF. Mutations enriched at specific metastatic sites generally reflect biology of the target tissue and may be adaptations to growth in the local environment. These include PTEN and ASXL1 alterations in brain metastases and NOTCH1 alterations in skin. We observed an enrichment of KRAS, KEAP1, STK11 and EGFR mutations in lung metastases. However, the patterns of other mutations in these tumors indicate that these are misdiagnosed lung primaries rather than breast metastases.ConclusionsAn order-of-magnitude increase in samples relative to previous studies allowed us to detect novel genomic characteristics of metastatic cancer and to expand and clarify previous findings.

Abstract PD8-01: The metastatic breast cancer project: Generating the clinical and genomic landscape of metastatic breast cancer through patient-partnered research

Abstract Background: The Metastatic Breast Cancer Project (MBCproject) is a research study that directly engages patients (pts) through social media and advocacy groups, and empowers them to share their samples, clinical information, and experiences. The goal is to create a publicly available dataset of linked genomic, clinical, and pt-reported data to enable research. Methods: In collaboration with pts, advocates, and advocacy groups, a website (MBCproject.org) was developed that allows pts with metastatic breast cancer (MBC) anywhere in the U.S. or Canada to register. Registered pts are sent an online consent form that asks for permission to obtain and analyze their medical records and samples. Once enrolled, pts are sent a saliva kit and a blood kit and asked to mail back a saliva sample, which is used to extract germline DNA, and/or a blood sample, which is used to extract germline DNA and cell free DNA (cfDNA). We contact participants’ medical providers and obtain medical records and a portion of their stored tumor biopsies. Whole exome sequencing (WES) is performed on tumor DNA, germline DNA, and cfDNA; transcriptome sequencing (RNA-seq) is performed on tumor RNA. Medical records and pt-reported data are abstracted to create a detailed clinical record for each pt. All de-identified data are shared regularly via public databases (cbioportal.org, mbcproject.org, dbGaP, NCI Genomic Data Commons) without restrictions. Study updates are shared with participants regularly. Results: From 10/20/15-7/8/19, 5357 women and men with MBC registered. 3290 pts receiving care at over 1700 different institutions consented to share medical records and tumor/saliva/blood samples, and to have genomic analysis performed. Details of clinical data collection, biospecimen acquisition, and genomic data generation to date are outlined in the Table. WES from 463 tumors obtained from 326 pts have been generated (with matched germline WES), including 61 pts with 2 timepoints, 19 pts w 3 timepoints, and 11 pts w 4+ timepoints. 278 tumor exomes were from the breast/regional lymph nodes, 63 from distant metastatic sites and 122 from cfDNA. 110 tumor exomes were from samples obtained before the diagnosis of MBC, 258 from after the diagnosis of MBC, and 95 to be determined (TBD). 161 tumor exomes were obtained prior to any therapy, 204 following some therapy, and 98 TBD. Clinically annotated genomic data are used to study specific pt cohorts (including rare subsets and outliers) and to identify mechanisms of response and resistance to therapies. Examples of the clinical and genomic analyses that will be presented include: - Pts diagnosed &amp;lt;40 yrs of age (1108 pts enrolled; 120 with tumor WES) - de novo MBC (1122 pts enrolled; 121 with tumor WES) - Late recurrence, &amp;gt;5 yrs after diagnosis (830 pts enrolled; 77 with tumor WES) - Long-term survivors, &amp;gt;10 yrs with MBC (159 pts enrolled; 11 with tumor WES) - Resistance to CDK4/6 inhibitors (709 pts enrolled; 148 with tumor WES) Conclusions: Partnering directly with pts enables rapid identification of thousands of pts willing to share tumors, blood, saliva, and medical records to accelerate research. This approach allows for identification of patients with specific phenotypes, who have been challenging to identify with traditional approaches. Remote acquisition of medical records and saliva/blood/tumor samples is feasible. This clinically annotated dataset is a shared resource for the research community. Table 1Clinical data collection, biospecimen acquisition, and genomic data generation:NumberConsent signed3290 ptsSurvey #1 submitted3290 pts(demographics, diagnosis details, receptor status, clinical experiences)Survey #2 submitted1435 pts(pathology details, sites of metastasis, treatments with start and stop dates)Medical record received1307 ptsSaliva sample received1976 ptsBlood sample received1121 ptsTumor samples received482 tumor samples from 346 ptsDigital image of tumor slide H&amp;E generated482 tumor samplesWES from germline complete310 germline samplesWES from tumor sample complete341 tumor samplesRNA-seq from tumor sample complete229 tumor samplesULP-WGS from cfDNA complete947 blood samplesWES from circulating tumor DNA complete122 blood samples Citation Format: Nikhil Wagle, Corrie Painter, Elana Anastasio, Michael Dunphy, Mary McGillicuddy, Esha Jain, Tania G Hernandez, Sara Balch, Beena Thomas, Dewey Kim, Alyssa L. Damon, Shahrayz Shah, Brett N. Tomson, Rachel Stoddard, Colleen Nguyen, Jorge Buendia-Buendia, Ofir Cohen, Jorge Gomez Tejeda Zanudo, Netsanet Tsegai, Lauren Sterlin, Ulcha Fergie Ulysse, Kathryn Sine, Oyin Alao, Jacqueline Lucia, Eric S. Lander, Todd R. Golub. The metastatic breast cancer project: Generating the clinical and genomic landscape of metastatic breast cancer through patient-partnered research [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr PD8-01.

Abstract P3-01-05: Liquid biopsy methods and machine learning modeling to understand organ tropism and metastatization behavior of metastatic breast cancer

Abstract Background: Liquid biopsy provides a growing amount of real-time data about prognosis and the genomic landscape of metastatic breast cancer (MBC) and its comprehensive analysis is an emerging clinical need. Machine Learning (ML) data-driven models are able to “learn” information about a system and to adaptively improve their performance by directly observing its data. This enables the discovery of hidden patterns in complex heterogeneous and high dimensional data. The aim of this study was to explore the combination of clinical characteristics, circulating tumor DNA-detected aberrations (ctDNA) and CTC enumeration in estimating target organs more susceptible to MBC involvement using a ML modeling approach. Methods: The study retrospectively analyzed 88 MBC patients (pts) treated and characterized for CTCs and circulating tumor DNA (ctDNA) at Northwestern University (Chicago, IL) independently from treatment line. Blood samples were collected at baseline, concomitantly with imaging. CTCs were isolated through the CellSearch™ kit (Menarini Silicon Biosystems, PA), while ctDNA was analyzed using the Guardant360™ NGS-based assay (Guardant Health, CA). All features were normalized and included in a random forest algorithm implemented in Python (Scikit learn, BSD license), node splitting criterion for the decision tree classifiers was varied using Gini index and entropy. Hyperparameters of the random forest were then optimized including number of trees and the minimum leaf size by implementing hyperparameter grid search using 10-fold cross validation. Results: The median number of lines at baseline collection was 1 (interquartile range: 1-3), while the median number of metastatic sites was 3 (inter quartile range: 1-3) with the most observed sites being bone (37%), lymph nodes (29%), lung (27%) and liver (25%). The cohort consisted of 43% hormone receptor positive (HRpos), 32% TNBC, and 25% HER2-positive MBC. In the overall population, continuous CTC number (n_CTC), inflammatory breast cancer diagnosis (IBC), and aberrations in ESR1, KITand CDK4were the main features linked to liver metastases (AUC: 0.842), n_CTC, ESR1, PIK3CA, CCNE1and CDK6were the features linked to bone involvement (AUC: 0.770), while PIK3CA, METand MYC, were linked to lung organotropism (AUC: 0.701). Factors linked to the metastatization net combination pattern were then explored within each MBC subtype. Intriguingly, AR, n_CTC, TP53and ESR1were the main drivers in HRpos MBC (Mean per class error0.46), while EGFR, KITand NOTCH1were the main features in TNBC (Mean per class error 0.605). Consistently, n_CTC, ERBB2, PIK3CAwere the driving features among HER2 positive MBC pts (Mean per class error 0.87). Conclusions: This novel analysis demonstrates that liquid biopsy integrating both CTCs enumeration and genomic characterization by ctDNA could prove useful in a detailed description of the metastatic process, allowing a more tailored monitoring and therapeutic approach. Intriguingly, features linked to Epithelial to Mesenchymal transition were found to be a potential driver of the metastatization behavior, underlining the need to further elucidate the clinical impact of this process. Citation Format: Lorenzo Gerratana, Andrew A Davis, Maurizio Polano, Qiang Zhang, Ami N Shah, Chenyu Lin, Debora Basile, Giuseppe Toffoli, Firas Wehbe, Fabio Puglisi, Amir Behdad, Leonidas C Platanias, William J Gradishar, Massimo Cristofanilli. Liquid biopsy methods and machine learning modeling to understand organ tropism and metastatization behavior of metastatic breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-01-05.

The genomic landscape of metastatic breast cancer highlights changes in mutation and signature frequencies.

The whole-genome sequencing of prospectively collected tissue biopsies from 442 patients with metastatic breast cancer reveals that, compared to primary breast cancer, tumor mutational burden doubles, the relative contributions of mutational signatures shift and the mutation frequency of six known driver genes increases in metastatic breast cancer. Significant associations with pretreatment are also observed. The contribution of mutational signature 17 is significantly enriched in patients pretreated with fluorouracil, taxanes, platinum and/or eribulin, whereas the de novo mutational signature I identified in this study is significantly associated with pretreatment containing platinum-based chemotherapy. Clinically relevant subgroups of tumors are identified, exhibiting either homologous recombination deficiency (13%), high tumor mutational burden (11%) or specific alterations (24%) linked to sensitivity to FDA-approved drugs. This study provides insights into the biology of metastatic breast cancer and identifies clinically useful genomic features for the future improvement of patient management.

Hybrid capture-based genomic profiling of circulating tumor DNA from patients with metastatic breast cancer.

e12569 Background: Breast cancer is the most common malignancy among women worldwide. It is particularly important to provide precise therapies based on genomic alterations, especially for metastatic breast cancers (MBC), which exhibit a high tumor heterogeneity and dynamic changes during the course of disease progression. However, genomic sampling upon metastatic tissue biopsy frequently encountered difficulties due to its inherent invasive approach such as insufficient samples and clinical risks. Our study aims to assess the genomic alternation landscape of metastatic breast cancer detected by blood-based circulating tumor DNA (ctDNA) and evaluate the assay performance. Methods: We performed hybrid capture-based next-generation sequencing (NGS) of 150 genes on ctDNA from 203 female patients with MBC. The mean sequencing depth was more than 3000×. The results were compared with our internal tissue genomic database (297 female patients with MBC) tested by NGS and TCGA database (N=982) tested by whole exome sequencing. Genomic alterations including single nucleotide variation (SNV), insertions/deletions, copy number variations, gene rearrangement and fusions were assessed. Results: Genomic data from 203 female patients with metastatic breast cancer were analyzed via ctDNA [median age 53 years (range, 46–61 years)]. Evidence of ctDNA as estimated by the maximum somatic allele frequency (MSAF) was detected in 95.6% of the patients (median=7.1 alterations/patient), and 97.0% of the patients had at least one characterized altered gene. The most frequently mutated genes identified for SNV occurred in TP53 (47.8%), PIK3CA (36.0%), and ESR1 (16.3%) upon ctDNA analysis and TP53 (73.2%), PIK3CA (38.4%), and ESR1 (4.0%) from our internal tissue database. However, in TCGA cohort, where most patients were presented with early stage diseases, the most mutated gene in terms of SNV was PIK3CA (32.5%), followed by TP53 (30.7%) and TTN (16.0%). The status of ERBB2 amplifications had a high concordance among ctDNA (14.8%), tissue (14.9%), and TCGA database (13.5%). The MSAF level was significantly higher for the fusion-present cases (P=0.048) or amplification cases (p&lt;0.0001) than non-fusion or non-amplification cases. Conclusions: Our study has suggested that ctDNA profiling is a feasible approach for the molecular analysis in metastatic breast cancer and may better capture the mutational landscape of MBC for further clinical implications.

Whole transcriptome sequencing in metastatic cancer: A review of expression outliers in 113 metastatic breast cancer patients.

3080 Background: The genomic profiling of breast cancers has led to a greater understanding of the mutational landscape of metastatic breast cancer (MBC) with potential therapeutic implications. Despite these advances, there is a paucity of data regarding the additive value and relevance of gene expression across histological and molecular subtypes, which represents the majority of informative and actionable findings identified in the BC Cancer personalized oncogenomics program (POG). Methods: Informative findings with potential clinical application from whole genome sequencing (WGS) and whole transcriptome sequencing (WTS) in MBC patients between 2012-2018 were reviewed. Variants observed in pathway genes of potential clinical relevance, as defined by a curated list of genes, were examined across histological subtypes. High and low expression outliers relative to TCGA breast cases, defined as expression greater than 98th percentile and FC &gt; 2 compared to Illumina breast dataset and lower than 25th percentile and FC &lt; -2 compared to Illumina breast dataset, respectively, were then analyzed to establish how many outliers were observed in pathways of potential clinical relevance. Results: A total of 113 cases were included. WGS revealed that TP53 was the most frequent single nucleotide variant (SNV) in triple negative breast cancer (23/30, 77%), whereas PIK3CA (37/78, 47%), PTEN (11/78, 14%) and ESR1 (19/78, 24%) were most frequent in ER positive cases and CDKN2A (2/18, 11%) in HER2 positive cases. Across all subtypes, the mTOR and cell cycle pathways were found to have the highest frequency of SNVs, with the identification of 86 and 71 variants, respectively. Expression data for 113 RNA-sequenced patients revealed a high frequency of expression outliers in the mTOR pathway (26 high expression and 424 low expression outlier genes) and cell cycle pathways (35 high expression and 331 low expression outlier genes), but also in the WNT pathway (96 high expression and 490 lower expression outlier genes) and NOTCH pathway (84 high expression and 564 low expression outlier genes). Conclusions: Frequently identified SNVs across histological subtypes were correlated with expression outliers in pathways of clinical relevance in breast cancer. Additional informative findings, in pathways of potential clinical relevance not historically targeted in breast cancer, were identified with WTS. The clinical utility of these findings warrants further study.

Genomic characterization of metastatic breast cancers.

Metastasis is the main cause of death for patients with breast cancer. Many studies have characterized the genomic landscape of breast cancer during its early stages. However, there is evidence that genomic alterations are acquired during the evolution of cancers from their early to late stages, and that the genomic landscape of early cancers is not representative of that of lethal cancers1-7. Here we investigated the landscape of somatic alterations in 617 metastatic breast cancers. Nine driver genes (TP53, ESR1, GATA3, KMT2C, NCOR1, AKT1, NF1, RIC8A and RB1) were more frequently mutated in metastatic breast cancers that expressed hormone receptors (oestrogen and/or progesterone receptors; HR+) but did not have high levels of HER2 (HER2-; n=381), when compared to early breast cancers from The Cancer Genome Atlas. In addition, 18 amplicons were more frequently observed in HR+/HER2- metastatic breast cancers. These cancers showed an increase in mutational signatures S2, S3, S10, S13 and S17. Among the gene alterations that were enriched in HR+/HER2- metastatic breast cancers, mutations in TP53, RB1 and NF1, together with S10, S13 and S17, were associated with poor outcome. Metastatic triple-negative breast cancers showed an increase in the frequency of somatic biallelic loss-of-function mutations in genes related to homologous recombination DNA repair, compared to early triple-negative breast cancers (7% versus 2%). Finally, metastatic breast cancers showed an increase in mutational burden and clonal diversity compared to early breast cancers. Thus, the genomic landscape of metastatic breast cancer is enriched in clinically relevant genomic alterations and is more complex than that of early breast cancer. The identification of genomic alterations associated with poor outcome will allow earlier and better selection of patients who require the use of treatments that are still in clinical trials. The genetic complexity observed in advanced breast cancer suggests that such treatments should be introduced as early as possible in the disease course.