Summary Our knowledge of copy number evolution during the expansion of primary breast tumors is limited 1 , 2 . To investigate this process, we developed a single cell, single-molecule DNA sequencing method and performed copy number analysis of 16,178 single cells from 8 triple-negative breast cancers (TNBCs) and 4 cell lines. Our data shows that breast tumors and cell lines are comprised of a large milieu of subclones (7–22) that are organized into a few (3–5) major superclones. Evolutionary analysis suggests that after clonal TP53 mutations, multiple LOH events and genome doubling, there was a period of transient genomic instability followed by ongoing copy number evolution during the primary tumor expansion. By subcloning single daughter cells in culture, we show that tumor cells re-diversify their genomes and do not retain isogenic properties. These data show that TNBCs continue to evolve chromosome aberrations and maintain a reservoir of subclonal diversity during primary tumor growth.

A B S T R A C T PurposeTo compare the pathologic complete response (pCR) rate and relapse-free survival (RFS) and overall survival (OS) after neoadjuvant systemic chemotherapy (NST) in patients with breast cancer with and without deleterious BRCA1 and BRCA2 mutations. Patients and MethodsA total of 317 women who underwent BRCA genetic testing and were treated with NST for breast cancer between 1997 and 2009 were included in the study. The Kaplan-Meier product-limit method was used to estimate RFS and OS rates. Logistic regression models were fit to determine the associations between BRCA status, pCR, and survival. ResultsFifty-seven (18%) and 23 (7%) patients had BRCA1 and BRCA2 mutations, respectively. Twenty-six (46%) of 57 BRCA1 carriers achieved a pCR, compared with three (13%) of 23 BRCA2 carriers and 53 (22%) of 237 BRCA noncarriers (P Ͻ .001). In the multivariate logistic model, BRCA1 status (odds ratio [OR] ϭ 3.16; 95% CI, 1.55 to 6.42; P ϭ .002), estrogen receptor (ER) negativity (OR ϭ 1.96; 95% CI:1.05 to 3.65; P ϭ .03) and concurrent trastuzumab use (OR ϭ 4.18; 95% CI, 2.04 to 8.57; P Ͻ .001) remained as independent significant predictors for a pCR. At a median follow-up of 3.2 years, 69 patients (22%) experienced a disease recurrence or death. No significant differences were noted in survival outcomes with respect to BRCA status and type of NST received. However, among BRCA1 carriers, patients who achieved a pCR had better 5-year RFS (P ϭ .001) and OS (P ϭ .01) rates than patients who did not. ConclusionBRCA1 status and ER negativity are independently associated with higher pCR rates in patients with breast cancer. Overall prognosis of breast cancer in BRCA carriers is similar to sporadic breast cancers.

Background Increasing numbers of women with breast cancer are electing for contralateral prophylactic mastectomy (CPM) to reduce the risk of developing contralateral breast cancer. The objective of this study was to identify factors that may impact a patient’s decision to undergo CPM. Methods We identified 2504 women with stage 0–III unilateral primary breast cancer who underwent breast surgery at our institution from January 2000 to August 2006 from a prospectively maintained database. We performed logistic regression analyses to determine which factors were associated with undergoing CPM. Results Of 2504 breast cancer patients, 1223 (48.8%) underwent total mastectomy. Of the 1223 patients who underwent mastectomy, 284 (23.2%) underwent immediate or delayed CPM. There were 33 patients (1.3%) who had genetic testing before the surgery; with the use of testing increasing in the latter years of the study (0.1% in 2000–2002 vs. 2.0% in 2003–2006, P<0.0001). Multivariable analysis revealed several factors that were associated with a patient undergoing CPM: age younger than 50 years, white ethnicity, family history of breast cancer, BRCA1/2 mutation testing, invasive lobular histology, clinical stage and use of reconstruction. Conclusions We identified specific patient and tumor characteristics associated with the use of CPM. Although genetic testing is increasing, most women undergoing CPM did not have a known genetic predisposition to breast cancer. Evidence-driven models are needed to better inform women of their absolute risk of contralateral breast cancer as well as their competing risk of recurrence from the primary breast cancer to empower them in their active decision making.

In the absence of histologic criteria that distinguish inflammatory breast cancer (IBC) from non-inflammatory breast cancer (non-IBC), the diagnosis of IBC relies entirely on the existence of clinical criteria as outlined by the Tumor-Node-Metastasis (TNM) classification of breast cancer. The current TNM classification of breast cancer restricts patients presenting with clinical IBC criteria to subcategory T4d. This has the immediate effect of relegating all patients with non-metastatic IBC to stage III regardless of tumor size or nodal spread. For patients presenting with metastatic disease, the TNM classification consigns them to stage IV and does not distinguish patients based on the presence of inflammatory criteria. Recent evidence by our group, as well as others, suggests that patients with IBC criteria have a significantly reduced overall survival among patients who present with distant metastasis at diagnosis (stage IV breast cancer). In light of these results, this manuscript addresses whether the current TNM staging classification accurately represents the distinction between IBC and non-IBC.

Purpose USP-11, a member of the ubiquitin-specific protease family, has emerged as an essential regulator of double-strand break (DSB) repair. Few studies have shown that silencing USP-11 led to hypersensitivity to poly(ADP-ribose) polymerase (PARP) inhibition, ionizing radiation (IR), and DNA-damaging agents. We sought to examine the predictive and prognostic relevance of USP-11 in patients treated with neoadjuvant systemic therapy (NST) for breast cancer. Methods 56 women who were treated with NST for breast cancer between 1999 and 2004 were included in the study. The Kaplan-Meier product-limit method was used to estimate disease-free survival (DFS) and overall survival (OS) rates. Logistic regression models were fit to determine the associations between USP-11 status, pCR and survival. Results Sixteen (29%) patients had high USP-11 expressing tumors, and 40 (71%) patients had low USP-11 expressing tumors. No significant differences were observed in pCR rates with respect to USP-11 status. At a median follow-up of 7.4 years, 33 patients (59%) experienced a disease recurrence or death. Patients with high USP-11 expressing tumors had a higher risk of recurrence (Odds ratio [OR] = 3.87; 95% CI:1.51 to 9.93; P= 0.005) and death (OR = 6.03; 95% CI:2.00 to 18.17; P= 0.001) than those with low USP-11 expressing tumors. Patients who did not achieve a pCR had an increased risk of recurrence (OR = 5.16; 95% CI:1.16 to 23.07; P= 0.03). Conclusions Our data indicates that USP-11 is not a predictor of a pCR after anthracycline-taxane containing NST for breast cancer. Low USP-11 expression was independently correlated with better survival outcomes.