Adjuvant Trastuzumab Emtansine Versus Paclitaxel and Trastuzumab in Stage I HER2-Positive Breast Cancer: The ATEMPT Trial.

This ASO perspective reviews the findings of a randomized, phase II clinical trial evaluating adjuvant trastuzumab emtansine (T-DM1) compared with paclitaxel and trastuzumab (TH) in stage I human epidermal growth factor receptor 2-positive breast cancer, as reported recently by the ATEMPT trial investigators. Patients treated with T-DM1 had better disease-free survival but did not have fewer treatment toxicities. The T-DM1-treated group had higher rates of treatment discontinuations, therefore long-term follow-up will be required to evaluate survival differences between T-DM1 and TH.

Phase 1/2 study of topical submicron particle paclitaxel for cutaneous metastases of breast cancer.

PURPOSE: This Phase 1/2 study evaluated safety and efficacy of a topical submicron particle paclitaxel (SPP) in an anhydrous ointment base (SOR007), primarily in breast cancer patients with cutaneous metastases (CM). METHODS: One of three concentrations of SOR007 SPP (0.15%, 1.0%, or 2.0%) was applied twice daily over an area of 50 cm2 under a 3 + 3 phase 1 design for up to 28 days, with the option for expansion to an additional 28 days at the highest dose under a Phase 2a once safety was established. Efficacy was analyzed by lesion measurements and photographs to determine overall response rate (ORR), complete response (CR), and progression free survival by day 28 or 56. RESULTS: Twenty-three subjects were enrolled, 21 with cutaneous metastases of breast cancer (CMOBC). Four subjects received SOR007 0.15% for a median of 28 days (range = 17-29), three at a dose of 1.0% for a median of 28 days (range = 6-29), and sixteen at 2.0% for a median of  55 days (range = 6-60). All doses were well tolerated, and 19 subjects were evaluable for efficacy. At day 28 across all dose levels, 16% (95% CI 3.4 to 39.6%) of subjects achieved an ORR and another 63% (95% CI 34.9-96.8%) had stable disease (SD). The proportion of patients being progression free at 28 days across all treatments was 79% (95 CI 54-94%). CONCLUSION: Application of SOR007 0.15%, 1.0%, and 2.0% to CM was safe and well tolerated with some reduction in lesion pain, and minimal systemic absorption of paclitaxel. Lesion stabilization was observed in most subjects over the study period. A randomized, placebo-controlled trial to confirm these findings is warranted. GOV IDENTIFIER: NCT03101358.

Oncologic safety of axillary lymph node dissection with immediate lymphatic reconstruction.

PURPOSE: Immediate lymphatic reconstruction (ILR) at the time of axillary lymph node dissection (ALND) can reduce the incidence of lymphedema in patients with breast cancer. The oncologic safety of ILR is unknown and has not been reported. The purpose of this study was to evaluate if ILR is associated with increased breast cancer recurrence rates. METHODS: Patients with breast cancer who underwent ALND with ILR from September 2016 to December 2020 were identified from a prospective institutional database. Patient demographics, tumor characteristics, and operative details were recorded. Follow-up included the development of local recurrence as well as distant metastasis. Oncologic outcomes were analyzed. RESULTS: A total of 137 patients underwent ALND with ILR. At cancer presentation, 122 patients (89%) had clinically node positive primary breast cancer, 10 patients (7.3%) had recurrent breast cancer involving the axillary lymph nodes, 3 patients (2.2%) had recurrent breast cancer involving both the breast and axillary nodes, and 2 patients (1.5%) presented with axillary disease/occult breast cancer. For surgical management, 103 patients (75.2%) underwent a mastectomy, 22 patients (16%) underwent lumpectomy and 12 patients (8.8%) had axillary surgery only. The ALND procedure, yielded a median of 15 lymph nodes pathologically identified (range 3-41). At a median follow-up of 32.9 months (range 6-63 months), 17 patients (12.4%) developed a local (n = 1) or distant recurrence (n = 16), however, no axillary recurrences were identified. CONCLUSION: Immediate lymphatic reconstruction in patients with breast cancer undergoing ALND is not associated with short term axillary recurrence and appears oncologically safe.

Circulating Tumor Cell Transcriptomics as Biopsy Surrogates in Metastatic Breast Cancer.

BACKGROUND: Metastatic breast cancer (MBC) and the circulating tumor cells (CTCs) leading to macrometastases are inherently different than primary breast cancer. We evaluated whether whole transcriptome RNA-Seq of CTCs isolated via an epitope-independent approach may serve as a surrogate for biopsies of macrometastases. METHODS: We performed RNA-Seq on fresh metastatic tumor biopsies, CTCs, and peripheral blood (PB) from 19 newly diagnosed MBC patients. CTCs were harvested using the ANGLE Parsortix microfluidics system to isolate cells based on size and deformability, independent of a priori knowledge of cell surface marker expression. RESULTS: Gene expression separated CTCs, metastatic biopsies, and PB into distinct groups despite heterogeneity between patients and sample types. CTCs showed higher expression of immune oncology targets compared with corresponding metastases and PB. Predictive biomarker (n = 64) expression was highly concordant for CTCs and metastases. Repeat observation data post-treatment demonstrated changes in the activation of different biological pathways. Somatic single nucleotide variant analysis showed increasing mutational complexity over time. CONCLUSION: We demonstrate that RNA-Seq of CTCs could serve as a surrogate biomarker for breast cancer macrometastasis and yield clinically relevant insights into disease biology and clinically actionable targets.

Identification of putative actionable alterations in clinically relevant genes in breast cancer.

BACKGROUND: Individualising treatment in breast cancer requires effective predictive biomarkers. While relatively few genomic aberrations are clinically relevant, there is a need for characterising patients across different subtypes to identify actionable alterations. METHODS: We identified genomic alterations in 49 potentially actionable genes for which drugs are available either clinically or via clinical trials. We explored the landscape of mutations and copy number alterations (CNAs) in actionable genes in seven breast cancer subtypes utilising The Cancer Genome Atlas. To dissect the genomic complexity, we analysed the patterns of co-occurrence and mutual exclusivity in actionable genes. RESULTS: We found that >30% of tumours harboured putative actionable events that are targetable by currently available drugs. We identified genes that had multiple targetable alterations, representing candidate targets for combination therapy. Genes predicted to be drivers in primary breast tumours fell into five categories: mTOR pathway, immune checkpoints, oestrogen signalling, tumour suppression and DNA damage repair. Our analysis also revealed that CNAs in 34/49 (69%) and mutations in 13/49 (26%) genes were significantly associated with gene expression, validating copy number events as a dominant oncogenic mechanism in breast cancer. CONCLUSION: These results may enable the acceleration of personalised therapy and improve clinical outcomes in breast cancer.

Genetically Engineered Cell-Derived Nanoparticles for Targeted Breast Cancer Immunotherapy.

Exosomes are nanosized membranous vesicles secreted by a variety of cells. Due to their unique and pharmacologically important properties, cell-derived exosome nanoparticles have drawn significant interest for drug development. By genetically modifying exosomes with two distinct types of surface-displayed monoclonal antibodies, we have developed an exosome platform termed synthetic multivalent antibodies retargeted exosome (SMART-Exo) for controlling cellular immunity. Here, we apply this approach to human epidermal growth factor receptor 2 (HER2)-expressing breast cancer by engineering exosomes through genetic display of both anti-human CD3 and anti-human HER2 antibodies, resulting in SMART-Exos dually targeting T cell CD3 and breast cancer-associated HER2 receptors. By redirecting and activating cytotoxic T cells toward attacking HER2-expressing breast cancer cells, the designed SMART-Exos exhibited highly potent and specific anti-tumor activity both in vitro and in vivo. This work demonstrates preclinical feasibility of utilizing endogenous exosomes for targeted breast cancer immunotherapy and the SMART-Exos as a broadly applicable platform technology for the development of next-generation immuno-nanomedicines.

EP300 knockdown reduces cancer stem cell phenotype, tumor growth and metastasis in triple negative breast cancer.

BACKGROUND: Triple negative breast cancer (TNBC) is an aggressive breast cancer subtype with basal features, lacking the expression of receptors targeted successfully in other breast cancer subtypes. Treatment response to adjuvant and neoadjuvant chemotherapy is often short-lived and metastatic spread occurs at higher rates than other subtypes within the first five years after diagnosis. TNBCs exhibit stem cell features and are enriched for cancer stem cell (CSC) populations. E1A Binding Protein P300 (EP300) is a large protein with multiple cellular functions, including as an effector in stem cell biology. METHODS: We used a genetic knockdown (KD) model of EP300 in TNBC cell lines to investigate the effect on CSC phenotype, tumor growth and metastasis. Side population assay and tumorsphere suspension culture were used in vitro. Xenograft mouse models were used for in vivo studies. We performed in silico analysis of publicly available gene expression data sets to investigate CSC gene expression and molecular pathways as well as survival outcomes associated with EP300 expression in patients with TNBC and basal-like BC. RESULTS: EP300 KD abolished the CSC phenotype by reducing ABCG2 expression, side population cells and tumorsphere formation capacity in vitro as well as tumor formation in a xenograft mouse model in vivo. Metastatic capacity was markedly reduced in EP300 KD cells in vivo, with no detection of circulating tumor cells. TCGA data analysis demonstrated that genes positively correlated with EP300 expression in TNBC and basal-like BC were associated with CSC biology. Survival analysis demonstrated that EP300 expression predicts poor recurrence free survival in TNBC and basal BC. CONCLUSION: We report a novel oncogenic role for EP300 in driving CSC phenotype representing a potential target to address tumor initiation and metastatic spread in TNBC and basal-like BC. EP300 might serve as a prognostic marker and potential therapeutic target in TNBC.

Treatment and Outcomes of Early Stage Breast Cancer in Patients with Hepatic Dysfunction.

BACKGROUND: There exists a dogma of surgical nihilism for patients with cirrhosis and breast cancer causing de-escalation of surgery and impacting survival. We hypothesized that breast cancer surgery would not result in a significant change in the Model for End-Stage Liver Disease-Sodium (MELD-Na) scores before and after surgery. METHODS: We performed a single institutional retrospective review of medical records between January 2013 and July 2019 of patients with concurrent cirrhosis and breast cancer. We used the nonparametric Friedman test to compare differences in MELD-Na scores. RESULTS: Eight patients with both cirrhosis and breast cancer were identified. Median follow-up was 30.5 mo. Half of the patients had Child-Pugh class A cirrhosis and half had Child-Pugh class B cirrhosis. Six (75%) patients underwent lumpectomy and two (25%) underwent mastectomy. There was no statistically significant difference (P = 0.66) in median MELD-Na score before surgery (16) and after surgery (18). Two (25%) patients experienced postoperative complications. Three patients were listed for liver transplantation. Of three listed patients, two (25%) patients underwent successful liver transplantation after breast surgery. One (12.5%) patient died without transplant. Three (37.5%) patients were alive for more than 5 y after breast cancer diagnosis without evidence of cancer recurrence. The eighth patient has remained breast cancer free for more than 6 mo since her surgery. CONCLUSIONS: Surgery for patients with Child-Pugh class A and B cirrhosis and early stage breast cancer did not result in a significant change in MELD-Na score before and after surgery, suggesting that selected patients may benefit from breast cancer surgery with curative intent.

Factors associated with MRI detection of occult lesions in newly diagnosed breast cancers.

BACKGROUND: The use of preoperative magnetic resonance imaging (MRI) for newly diagnosed breast cancer remains controversial. We examined factors associated with detection of occult multicentric, multifocal, and contralateral malignant lesions only seen by MRI. METHODS: We performed a retrospective analysis of consecutive patients undergoing preoperative MRI for breast cancer. Clinicopathologic data were assessed regarding the findings of multifocality, multicentricity, and the presence of contralateral lesions. We analyzed the association of factors with these findings on MRI. RESULTS: Of 857 patients undergoing MRI, 770 patients met inclusion criteria. Mean age was 54.7 years. Biopsy-proven detection rates by MRI for multifocal, multicentric, and contralateral cancers were 6.2% (48 of 770), 1.9% (15 of 770) and 3.1% (24 of 770), respectively. African American race and heterogeneously or extremely dense mammographic density were associated with multifocal cancers on MRI. Larger lesion size and mammographic density were associated with multicentric cancers. Invasive lobular carcinoma (ILC) and progesterone receptor (PR)-positivity were associated with contralateral cancers. CONCLUSIONS: African American race, heterogeneously or extremely dense mammographic density, ILC, and PR-positivity were associated with additional biopsy-proven cancers based on MRI. These factors should be considered when assessing the clinical utility of preoperative breast MRI.

A Pilot Study for the Feasibility of Exome-Sequencing in Circulating Tumor Cells Versus Single Metastatic Biopsies in Breast Cancer.

The comparison of the landscape of somatic alterations in circulating tumor cells (CTCs) versus metastases is challenging. Here, we comprehensively characterized the somatic landscape in bulk (amplified and non-amplified), spike-in breast cancer cells, CTCs, and metastases from breast cancer patients using whole-exome sequencing (WES). We determined the level of genomic concordance for somatic nucleotide variants (SNVs), copy number alterations (CNAs), and structural variants (SVs). The variant allele fractions (VAFs) of somatic variants were remarkably similar between amplified and non-amplified cell line samples as technical replicates. In clinical samples, a significant fraction of somatic variants had low VAFs in CTCs compared to metastases. The most frequently recurrent gene mutations in clinical samples were associated with an elevated C > T mutational signature. We found complex rearrangement patterns including intra- and inter-chromosomal rearrangements, singleton, and recurrent gene fusions, and tandem duplications. We observed high molecular discordance for somatic alterations between paired samples consistent with marked heterogeneity of the somatic landscape. The most prevalent copy number calls were focal deletion events in CTCs and metastases. Our results demonstrate the feasibility of an integrated workflow for the identification of a complete repertoire of somatic alterations and highlight the intrapatient genomic differences that occur between CTCs and metastases.

Adaptive Randomization of Neratinib in Early Breast Cancer.

BACKGROUND: The heterogeneity of breast cancer makes identifying effective therapies challenging. The I-SPY 2 trial, a multicenter, adaptive phase 2 trial of neoadjuvant therapy for high-risk clinical stage II or III breast cancer, evaluated multiple new agents added to standard chemotherapy to assess the effects on rates of pathological complete response (i.e., absence of residual cancer in the breast or lymph nodes at the time of surgery). METHODS: We used adaptive randomization to compare standard neoadjuvant chemotherapy plus the tyrosine kinase inhibitor neratinib with control. Eligible women were categorized according to eight biomarker subtypes on the basis of human epidermal growth factor receptor 2 (HER2) status, hormone-receptor status, and risk according to a 70-gene profile. Neratinib was evaluated against control with regard to 10 biomarker signatures (prospectively defined combinations of subtypes). The primary end point was pathological complete response. Volume changes on serial magnetic resonance imaging were used to assess the likelihood of such a response in each patient. Adaptive assignment to experimental groups within each disease subtype was based on Bayesian probabilities of the superiority of the treatment over control. Enrollment in the experimental group was stopped when the 85% Bayesian predictive probability of success in a confirmatory phase 3 trial of neoadjuvant therapy reached a prespecified threshold for any biomarker signature ("graduation"). Enrollment was stopped for futility if the probability fell to below 10% for every biomarker signature. RESULTS: Neratinib reached the prespecified efficacy threshold with regard to the HER2-positive, hormone-receptor-negative signature. Among patients with HER2-positive, hormone-receptor-negative cancer, the mean estimated rate of pathological complete response was 56% (95% Bayesian probability interval [PI], 37 to 73%) among 115 patients in the neratinib group, as compared with 33% among 78 controls (95% PI, 11 to 54%). The final predictive probability of success in phase 3 testing was 79%. CONCLUSIONS: Neratinib added to standard therapy was highly likely to result in higher rates of pathological complete response than standard chemotherapy with trastuzumab among patients with HER2-positive, hormone-receptor-negative breast cancer. (Funded by QuantumLeap Healthcare Collaborative and others; I-SPY 2 TRIAL ClinicalTrials.gov number, NCT01042379.).

Adaptive Randomization of Veliparib-Carboplatin Treatment in Breast Cancer.

BACKGROUND: The genetic and clinical heterogeneity of breast cancer makes the identification of effective therapies challenging. We designed I-SPY 2, a phase 2, multicenter, adaptively randomized trial to screen multiple experimental regimens in combination with standard neoadjuvant chemotherapy for breast cancer. The goal is to match experimental regimens with responding cancer subtypes. We report results for veliparib, a poly(ADP-ribose) polymerase (PARP) inhibitor, combined with carboplatin. METHODS: In this ongoing trial, women are eligible for participation if they have stage II or III breast cancer with a tumor 2.5 cm or larger in diameter; cancers are categorized into eight biomarker subtypes on the basis of status with regard to human epidermal growth factor receptor 2 (HER2), hormone receptors, and a 70-gene assay. Patients undergo adaptive randomization within each biomarker subtype to receive regimens that have better performance than the standard therapy. Regimens are evaluated within 10 biomarker signatures (i.e., prospectively defined combinations of biomarker subtypes). Veliparib-carboplatin plus standard therapy was considered for HER2-negative tumors and was therefore evaluated in 3 signatures. The primary end point is pathological complete response. Tumor volume changes measured by magnetic resonance imaging during treatment are used to predict whether a patient will have a pathological complete response. Regimens move on from phase 2 if and when they have a high Bayesian predictive probability of success in a subsequent phase 3 neoadjuvant trial within the biomarker signature in which they performed well. RESULTS: With regard to triple-negative breast cancer, veliparib-carboplatin had an 88% predicted probability of success in a phase 3 trial. A total of 72 patients were randomly assigned to receive veliparib-carboplatin, and 44 patients were concurrently assigned to receive control therapy; at the completion of chemotherapy, the estimated rates of pathological complete response in the triple-negative population were 51% (95% Bayesian probability interval [PI], 36 to 66%) in the veliparib-carboplatin group versus 26% (95% PI, 9 to 43%) in the control group. The toxicity of veliparib-carboplatin was greater than that of the control. CONCLUSIONS: The process used in our trial showed that veliparib-carboplatin added to standard therapy resulted in higher rates of pathological complete response than standard therapy alone specifically in triple-negative breast cancer. (Funded by the QuantumLeap Healthcare Collaborative and others; I-SPY 2 TRIAL ClinicalTrials.gov number, NCT01042379.).

Factors Leading to Decreased Rates of Immediate Postmastectomy Reconstruction.

BACKGROUND: This study was performed to determine if there was a difference in immediate breast reconstruction (IBR) rates between our public hospital and private cancer center, which share a common faculty with a consistent management philosophy in multidisciplinary care. We investigated the factors affecting postmastectomy reconstruction and IBR rates. MATERIALS AND METHODS: We retrospectively identified women with clinical stage I-II breast cancer who underwent mastectomy at our public hospital, Los Angeles County Medical Center, and our private cancer center, Keck Hospital of USC/Norris Comprehensive Cancer Center. Univariate and multivariate analyses were performed to study predictors of IBR and any breast reconstruction. RESULTS: Of 293 mastectomy patients, the rate of any breast reconstruction at the private cancer (56.6%) center was higher than that at the public hospital (36.2%). IBR rates for the private cancer center (93.6%) and for patients with private insurance were higher than for the public hospital (40.8%) and likewise for those without insurance (86.7% versus 45.5%). In a multivariate analysis, the odds of IBR at our private cancer center were 22.96 times higher than that at our public hospital. Age >50 y and radiotherapy were independent predictive factors associated with less likelihood of any breast reconstruction. CONCLUSIONS: Patients at the public hospital had a much lower rate of breast reconstruction than the private cancer center patients, even after controlling for stage and the team of treating physicians. Our results showed that older age and radiotherapy affect rates of breast reconstruction, as do hospital system and insurance status.

MRI does not predict pathologic complete response after neoadjuvant chemotherapy for breast cancer.

BACKGROUND: This study assessed whether magnetic resonance imaging (MRI) could accurately predict pathologic complete response (pCR) after neoadjuvant chemotherapy (NAC) for patients receiving standardized treatment, pre- and post-NAC MRI on the same instrumentation using a consistent imaging protocol, interpreted by a single breast fellowship-trained radiologist. METHODS: A single-institution retrospective analysis was performed including clinical, radiographic, and pathologic parameters for all patients with breast cancer treated with NAC from 2015 to 2018. Radiographic complete response (rCR) was defined as absence of suspicious MRI findings in the ipsilateral breast or lymph nodes. pCR was defined as the absence of invasive cancer or ductal carcinoma in-situ in breast or lymph nodes after operation (ypT0N0M0). RESULTS: Data for 102 consecutive patients demonstrated that 44 (43.1%) had rCR and 41 (40.1%) had pCR. pCR occurred in 12 (25.0%) of 48 estrogen receptor positive (ER+) patients, 29 (53.7%) of 54 ER- patients, and 25 (52.1%) of 48 human epidermal growth factor receptor 2 positive patients. The positive predictive value for MRI after NAC was 84.5% and the negative predictive value was 72.7%. The accuracy rate for MRI was 78.6%. Of the 44 patients with rCR, 12 (27.3%) had residual cancer on the pathologic specimen after surgical excision. CONCLUSION: rCR is not accurate enough to serve as a surrogate marker for pCR on MRI after NAC.

RNA-Seq of Circulating Tumor Cells in Stage II-III Breast Cancer.

BACKGROUND: We characterized the whole transcriptome of circulating tumor cells (CTCs) in stage II-III breast cancer to evaluate correlations with primary tumor biology. METHODS: CTCs were isolated from peripheral blood (PB) via immunomagnetic enrichment followed by fluorescence-activated cell sorting (IE/FACS). CTCs, PB, and fresh tumors were profiled using RNA-seq. Formalin-fixed, paraffin-embedded (FFPE) tumors were subjected to RNA-seq and NanoString PAM50 assays with risk of recurrence (ROR) scores. RESULTS: CTCs were detected in 29/33 (88%) patients. We selected 21 cases to attempt RNA-seq (median number of CTCs = 9). Sixteen CTC samples yielded results that passed quality-control metrics, and these samples had a median of 4,311,255 uniquely mapped reads (less than PB or tumors). Intrinsic subtype predicted by comparing estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) versus PAM50 for FFPE tumors was 85% concordant. However, CTC RNA-seq subtype assessed by the PAM50 classification genes was highly discordant, both with the subtype predicted by ER/PR/HER2 and by PAM50 tumors. Two patients died of metastatic disease, both of whom had high ROR scores and high CTC counts. We identified significant genes, canonical pathways, upstream regulators, and molecular interaction networks comparing CTCs by various clinical factors. We also identified a 75-gene signature with highest expression in CTCs and tumors taken together that was prognostic in The Cancer Genome Atlas and Molecular Taxonomy of Breast Cancer International Consortium datasets. CONCLUSION: It is feasible to use RNA-seq of CTCs in non-metastatic patients to discover novel tumor biology characteristics.

Are we overtreating intraductal papillomas?

BACKGROUND: The management of intraductal papillomas (IDPs) diagnosed on core needle biopsy (CNB) remains controversial regarding whether excision is required. We evaluated whether excision of IDPs might be overtreatment based on a consecutive patient population where all IDPs were routinely excised. MATERIALS AND METHODS: We retrospectively reviewed the records of consecutive patients treated with excision of IDPs at our institution from 2009 to 2016. We evaluated the rate of upgrade of IDPs on CNB and factors predicting for malignant upgrade. RESULTS: Of 153 CNB specimens, 136 (88.9%) were IDPs without atypia and 14 (9.2%) showed atypia. The overall upgrade rate on final pathology was 7.3% with 1.3% for invasive cancer, 2.7% for ductal carcinoma in situ, and 3.3% for atypical ductal hyperplasia. Of the 14 patients with atypia on CNB, two of these patients (14.2%) were found to have ductal carcinoma in situ. In the absence of atypia on CNB, upgrade rates were 1.5% for invasive and 1.5% for in situ carcinoma. Personal history of breast cancer and magnetic resonance imaging-guided biopsy predicted for malignant upgrade. CONCLUSIONS: IDPs on CNB have a low chance of harboring an occult malignancy. Given the low probability of upgrade to invasive breast cancer, it is reasonable to consider watchful surveillance in the absence of a prior personal history of breast cancer or atypia on CNB.

The importance of surgical margins in breast cancer.

Achieving negative margins with "no tumor on ink" is an appropriate goal in breast conserving therapy (BCT). Wider margins do not decrease recurrence rates, and re-excision in patients with microscopic positive margins is warranted. Several strategies exist to increase rates of negative margins, including techniques to improve tumor localization, intraoperative assessment of margins and oncoplastic techniques. Negative margins should be the goal of BCT, as this will improve both local control and long-term survival.

Expression profiling of circulating tumor cells in metastatic breast cancer.

Circulating tumor cells (CTCs) are prognostic in all stages of breast cancer. However, since they are extremely rare, little is known about the molecular nature of these cells. We report a novel strategy for the isolation and expression profiling of pure populations of CTCs derived from peripheral blood. We developed a method to isolate CTCs based on immunomagnetic capture followed by fluorescence-activated cell sorting (IE/FACS). After assay validation using the BT474 cell line spiked into blood samples in vitro, RNA from CTCs isolated from the blood of five metastatic breast cancer (MBC) patients was linearly amplified and subjected to gene expression profiling via cDNA microarrays. We isolated a range of 9-993 captured CTCs from five MBC patients' blood and profiled their RNA in comparison to a diverse panel of primary breast tumors (n = 55). Unsupervised hierarchical clustering revealed that CTC profiles clustered with more aggressive subtypes of primary breast tumors and were readily distinguishable from peripheral blood (PB) and normal epithelium. Differential expression analysis revealed CTCs to have downregulated apoptosis, and they were distinguishable from PB by the relative absence of immune-related signals. As expected, CTCs from MBC had significantly higher risk of recurrence scores than primary tumors (p = 0.0073). This study demonstrates that it is feasible to isolate CTCs from PB with high purity through IE/FACS and profile them via gene expression analysis. Our approach may inform the discovery of therapeutic predictors and be useful for real-time identification of emerging resistance mechanisms in MBC patients.