ICAT: a novel algorithm to robustly identify cell states following perturbations in single-cell transcriptomes.

MOTIVATION: The detection of distinct cellular identities is central to the analysis of single-cell RNA sequencing (scRNA-seq) experiments. However, in perturbation experiments, current methods typically fail to correctly match cell states between conditions or erroneously remove population substructure. Here, we present the novel, unsupervised algorithm Identify Cell states Across Treatments (ICAT) that employs self-supervised feature weighting and control-guided clustering to accurately resolve cell states across heterogeneous conditions. RESULTS: Using simulated and real datasets, we show ICAT is superior in identifying and resolving cell states compared with current integration workflows. While requiring no a priori knowledge of extant cell states or discriminatory marker genes, ICAT is robust to low signal strength, high perturbation severity, and disparate cell type proportions. We empirically validate ICAT in a developmental model and find that only ICAT identifies a perturbation-unique cellular response. Taken together, our results demonstrate that ICAT offers a significant improvement in defining cellular responses to perturbation in scRNA-seq data. AVAILABILITY AND IMPLEMENTATION: https://github.com/BradhamLab/icat.

Differences in Re-excision Rates for Breast-Conserving Surgery Using Intraoperative 2D Versus 3D Tomosynthesis Specimen Radiograph.

BACKGROUND: Intraoperative specimen radiographs performed during breast conservation surgery for cancer reduces the need for re-excision for positive margins. We studied 2D versus 3D image-guided cavity margin excision and compared it to final pathology and need for additional surgery. METHODS: We conducted a retrospective review of 657 breast-conserving operations performed for cancer from 2013 to 2018. Procedures were performed by four surgeons at a single tertiary institution with access intraoperatively to 2D and 3D radiographs. Data collected included demographics, intraoperative margin assessment, final pathology, and re-excision rates. RESULTS: A total of 466 patients had 2D and 191 had 3D specimen imaging. The 2D group had a lower mean age and a higher body mass index and proportion of minority patients than the 3D group (P < 0.01). In the 3D group, there was a higher percentage of patients with mammographically denser breasts (P < 0.06); 58% of patients in the 3D group had additional imaging-directed cavity margins excised versus 32% of patients in the 2D group (P < 0.01). In the 2D group, 44 patients (9%) had positive final margins versus 8 patients (4%) in the 3D group (P = 0.02). No difference was found on total volume of excision (P = 0.56). The re-excision rate for the 2D group was 11% versus 5% for the 3D group (P = 0.02; adjusted odds ratio = 0.41, 95% confidence interval 0.19-0.86). CONCLUSIONS: Re-excision rates using both modalities are low. A lower re-excision rate is independently associated with 3D tomosynthesis. This allows surgeons to excise additional margins at the index operation, decreasing reoperations and anxiety/costs for patients.

Mammographic density changes in surgical weight loss-an indication for personalized screening.

BACKGROUND: Obesity and high radiologic breast density independently increase breast cancer risk. We evaluated the effect of surgical weight loss on mammographic density (MD). METHODS: Patients undergoing bariatric surgery and screening mammography (MG) were identified, data regarding demographics, comorbidities, calculated and genetic breast cancer risk was collected. Patients had a MG before and after surgery. Fellowship-trained breast radiologists assigned Breast Imaging Reporting and Data System density categories. RESULTS: Patients underwent sleeve gastrectomy (n = 56) or gastric bypass (n = 7), 78% had hypertension, 48% had diabetes. Four had deleterious BRCA mutations, four were calculated high risk. Mean weight loss = 28.7 kg. Mean initial BMI = 44.3 kg/m2 (range:33-77), final BMI = 33.6 kg/m2 (range:20-62;p < 0.01). Density was unchanged in 53, decreased in 1, increased in 9. Of these 9(14%), 5 changed from almost entirely fatty to scattered MD, and 4 changed from scattered MD to heterogeneously dense. Mean weight loss of the 9 with increased MD was greater than the cohort (37.7vs.28.7 kg;p < 0.01). CONCLUSIONS: Surgical weight loss increased MD in 14%. Increased MD masks malignancies, patients may benefit from additional screening based on calculated risk assessments that include MD.

Bracketed radioactive seed localization vs bracketed wire-localization in breast surgery.

Multiple localizers placed in a bracketed fashion facilitates excision of radiographically extensive breast lesions. In this study, bracketed radioactive seed localization (bRSL) was compared to bracketed wire localization (bWL). We hypothesized that bRSL would achieve adequate margins and decrease re-operation rates with similar or less specimen volumes (SV) than bWL. Retrospective review identified patients who underwent bracketed breast procedures at an academic medical center. Data collected included patient demographics, tumor features, treatment variables, and surgical outcomes. Wilcoxon rank-sum test and chi-square test were used to compare continuous and categorical data, respectively. A multivariable logistic regression model was used to evaluate the association between re-excision and localization technique after adjusting for clinically relevant variables. Patients who underwent bWL were 3.9 times more likely to undergo re-excision compared to patients in bRSL group (OR=3.9, 95% CI: 2.0-7.4). Initial and total SV did not significantly differ between the two groups (P=.4). Patients were significantly more likely to undergo a mastectomy in the bWL group than in the bRSL group (24% vs 7%; P<.01). For patients undergoing excision of radiologically extensive breast lesions, bRSL serves as an alternative to bWL. In this retrospective study, bRSL was associated with a decreased re-excision rate with similar SV and a lower rate of mastectomy when compared to bWL.

Long-Term Survival after Complete Surgical Resection and Adjuvant Immunotherapy for Distant Melanoma Metastases.

BACKGROUND: This phase III study was undertaken to evaluate the efficacy of an allogeneic whole-cell vaccine (Canvaxin™) plus bacillus Calmette-Guerin (BCG) after complete resection of stage IV melanoma. METHODS: After complete resection of ≤5 distant metastases, patients were randomly assigned to BCG+Canvaxin (BCG/Cv) or BCG+placebo (BCG/Pl). The primary endpoint was overall survival (OS); secondary endpoints were disease-free survival (DFS), and immune response measured by skin test (ClinicalTrials.gov identifier: NCT00052156). RESULTS: Beginning in May 1998, 496 patients were randomized. In April 2005, the Data Safety Monitoring Board recommended stopping enrollment due to a low probability of efficacy. At that time, median OS and 5-year OS rate were 38.6 months and 44.9%, respectively, for BCG/Pl versus 31.4 months and 39.6% in the BCG/Cv group (hazard ratio (HR), 1.18; p = 0.250). Follow-up was extended at several trial sites through March 2010. Median OS and 5-year and 10-year survival was 39.1 months, 43.3 and 33.3%, respectively, for BCG/Pl versus 34.9 months, 42.5 and 36.4%, in the BCG/Cv group (HR 1.053; p = 0.696). Median DFS, 5- and 10-year DFS were 7.6 months, 23.8 and 21.7%, respectively, for BCG/Pl versus 8.5 months, 30.0%, and 30.0%, respectively, for the BCG/Cv group (HR 0.882; p = 0.260). Positive DTH skin testing correlated with increased survival. DISCUSSION: In this, the largest study of postsurgical adjuvant therapy for stage IV melanoma reported to date, BCG/Cv did not improve outcomes over BCG/placebo. Favorable long-term survival among study patients suggests that metastasectomy should be considered for selected patients with stage IV melanoma.

Astroglial FMRP-dependent translational down-regulation of mGluR5 underlies glutamate transporter GLT1 dysregulation in the fragile X mouse.

Fragile X syndrome (FXS) is a neurodevelopmental disorder caused by the loss-of-function of fragile X mental retardation protein (FMRP). The loss of FMRP function in neurons abolishes its suppression on mGluR1/5-dependent dendritic protein translation, enhancing mGluR1/5-dependent synaptic plasticity and other disease phenotypes in FXS. In this study, we describe a new activation function of FMRP in regulating protein expression in astroglial cells. We found that astroglial glutamate transporter subtype glutamate transporter 1 (GLT1) and glutamate uptake is significantly reduced in the cortex of fmr1(-/-) mice. Correspondingly, neuronal excitability is also enhanced in acute fmr1(-/-) (but not in fmr1(+/+) control) cortical slices treated with low doses (10 µm) of the GLT1-specific inhibitor dihydrokainate (DHK). Using mismatched astrocyte and neuron co-cultures, we demonstrate that the loss of astroglial (but not neuronal) FMRP particularly reduces neuron-dependent GLT1 expression and glutamate uptake in co-cultures. Interestingly, protein (but not mRNA) expression and the (S)-3,5-dihydroxyphenylglycine-dependent Ca(2+) responses of astroglial mGluR5 receptor are also selectively reduced in fmr1(-/-) astrocytes and brain slices, attenuating neuron-dependent GLT1 expression. Subsequent FMRP immunoprecipitation and QRT-PCR analysis showed that astroglial mGluR5 (but not GLT1) mRNA is associated with FMRP. In summary, our results provide evidence that FMRP positively regulates translational expression of mGluR5 in astroglial cells, and FMRP-dependent down-regulation of mGluR5 underlies GLT1 dysregulation in fmr1(-/-) astrocytes. The dysregulation of GLT1 and reduced glutamate uptake may potentially contribute to enhanced neuronal excitability observed in the mouse model of FXS.

Persistence of Trichomonas vaginalis serostatus in men over time.

PURPOSE: Previous epidemiologic studies have observed positive associations between Trichomonas vaginalis (Tv) serostatus and both prostate cancer (PCa) risk and mortality. However, only a few small older studies have examined Tv antibody persistence over time, all of which were composed mainly of female patients. Therefore, we examined Tv antibody persistence over time, as well as intra-individual variability, among middle- to older-aged men in the Southern Community Cohort Study (SCCS). METHODS: We tested baseline and repeat plasma specimens (collected 1-3 years later) from 248 male participants for Tv antibodies. We used the same enzyme-linked immunosorbent assay as in previous studies of Tv serostatus and PCa. RESULTS: At baseline, 46 (18.5 %) participants were seropositive for Tv infection. Seventy-six percent of these men were still seropositive 1-3 years later. A similar proportion of men "seroconverted" (4.0 %) as "seroreverted" (4.4 %), all of whom had absorbance values near the cutoff point for seropositivity. Overall, substantial agreement was observed between baseline and repeat serostatus (κ = 0.72, 95 % confidence interval 0.60-0.83). CONCLUSION: Tv seropositivity was largely persistent between plasma specimens collected 1-3 years apart from middle- to older-aged men. These high levels of persistence are similar to those observed for other sexually transmitted infections frequently investigated in relation to PCa.

Outcomes of delays in time to treatment in triple negative breast cancer.

BACKGROUND: Compared with other breast cancer subtypes, triple negative breast cancers (TNBC) are associated with higher recurrence rates and worse survival. Because of the aggressive nature of TNBC, outcomes may be more sensitive to delays in time to treatment. This study evaluates whether delays from diagnosis to initial treatment in TNBC impacts survival or locoregional recurrence (LRR). METHODS: Retrospective review of TNBC patients treated between January 2004 and January 2011 at an academic center was performed. Data collected included demographics, pathology, treatment, recurrence, and survival. Interval to treatment was defined as days from pathologic diagnosis to first local or systemic treatment. The t test, Cox regression, and Kaplan-Meier analyses were used to evaluate impact of time to treatment on overall survival and LRR. RESULTS: Median follow-up was 40 months for 301 TNBC patients. Mean interval to treatment was 46 ± 2 days. Higher initial stage yielded worse survival (p < .0001). Interval to treatment did not impact overall survival (p = .24), although there was a trend toward worse survival with delays of >90 days (p = .06). LRR was seen in 20 patients (7 %). Median time to recurrence was 15 months. Time to treatment was 38 ± 6 days for patients with LRR versus 44 ± 2 days without a recurrence (p = .37). Short delay in time to treatment did not impact LRR (p = .54). CONCLUSIONS: In TNBC, a short delay from pathologic diagnosis to initial treatment does not appear to adversely affect survival or LRR. Appropriate time to perform evaluations such as genetic testing, imaging, or additional consultation can be taken to guide optimal treatment options.

Delays in time to treatment and survival impact in breast cancer.

BACKGROUND: Time interval from diagnosis of breast cancer to treatment has been promulgated as one factor that can be used to evaluate cancer care quality. It remains controversial, however, whether a delay to treatment impacts survival. The purpose of this study was to evaluate whether delays from diagnosis to initial treatment in breast cancer impacts survival. MATERIALS AND METHODS: A retrospective review of patients undergoing breast cancer treatment between August 2005 and December 2008 in a comprehensive, multidisciplinary breast oncology program was undertaken. Two hospital systems were included: a county hospital (CH) treating a primarily minority, indigent population and a university hospital (UH) treating a primarily Caucasian, insured population. Interval to treatment, calculated from date of diagnosis to surgery, chemotherapy, or radiation treatment, and overall survival was compared between the two groups. RESULTS: A total of 1337 patients were included; 634 patients were treated in the CH and 703 in the UH. Interval to treatment was longer in the CH compared with the UH (53.4 ± 2.0 vs 33.2 ± 1.2 days; mean ± standard error of the mean [SEM], P < .0001). Patients treated at the CH had overall worse survival (P = .02); however, this difference did not hold true when controlled for stage. Additionally, when time to treatment was analyzed as an individual variable for all patients, there was no impact on survival. CONCLUSIONS: Interval from diagnosis to treatment of breast cancer within the same cancer center was longer at the CH than the UH. There was, however, no effect on overall survival. Time to treatment may not be a meaningful indicator of cancer care quality.

Indications and recommended approach for surgical intervention of metastatic disease to the gallbladder.

Metastatic disease to the gallbladder is unusual. The most common malignancy metastatic to the gallbladder is melanoma, followed by renal cell carcinoma (RCC) and breast cancer. Due to the unusual nature of the disease, there are no trials available for review. Thus, the management for these patients has been based on institutional experience and review of case series. The indications for surgical intervention for melanoma are metastatic disease discrete to the gallbladder and biliary symptoms, which are uncommon for melanoma, but might occur due to cystic duct obstruction culminating in cholecystitis. Laparoscopic cholecystectomy without a lymphadenectomy is emerging as the preferred approach for this metastatic deposit. The vast majority of patients with metastases to the gallbladder from RCC carry a good prognosis and a laparoscopic cholecystectomy should be considered. Patients with metastases to the gallbladder from the breast classically present with biliary symptoms and commonly undergo a laparoscopic cholecystectomy, which invariably demonstrates a deposit in the gallbladder from lobular breast cancer. In the present report, we review the indications for surgical intervention from various malignancies metastatic to the gallbladder and the current consensus for the laparoscopic approach from the diverse metastatic deposits to the gallbladder.

Circulating tumor cells in patients with breast cancer dormancy.

PURPOSE: The purpose of this study was to test the hypothesis that circulating tumor cells (CTCs) are present in patients many years after mastectomy without evidence of disease and that these CTCs are shed from persisting tumor in patients with breast cancer dormancy. EXPERIMENTAL DESIGN: We searched for CTCs in 36 dormancy candidate patients and 26 age-matched controls using stringent criteria for cytomorphology, immunophenotype, and aneusomy. RESULTS: Thirteen of 36 dormancy candidates, 7 to 22 years after mastectomy and without evidence of clinical disease, had CTCs, usually on more than one occasion. Only 1 of 26 controls had a possible CTC (no aneusomy). The statistical difference of these two distributions was significant (exact P = 0.0043). The CTCs in patients whose primary breast cancer was just removed had a half-life measured in 1 to 2.4 hours. CONCLUSIONS: The CTCs that are dying must be replenished every few hours by replicating tumor cells somewhere in the tissues. Hence, there appears to be a balance between tumor replication and cell death for as long as 22 years in dormancy candidates. We conclude that this is one mechanism underlying tumor dormancy.

Impact of weight change during neoadjuvant chemotherapy on pathologic response in triple-negative breast cancer.

Triple-negative breast cancer (TNBC) is an uncommon but aggressive subtype of breast cancer. Obesity has been associated with an increased risk of breast cancer and worse prognosis. Some studies suggest that obese patients are less likely to achieve pathologic complete response (pCR) to neoadjuvant chemotherapy (NCT) and experience worse overall survival. Ki-67 is a proliferation marker that correlates with tumor aggressiveness. The goal of this study was to examine the impact of weight change during NCT for TNBC on pathologic response and Ki-67 reduction. Retrospective review identified 173 TNBC patients treated between 2004 and 2011. Data were collected on patient demographics, pre- and post-NCT body mass index (BMI), Ki-67, and pCR. Data analysis was performed using the two-tailed Student's t-test, analysis of variance (ANOVA), and Fisher's exact test. Sixty-six patients met final study criteria. Forty-three patients lost weight during chemotherapy and 23 gained weight. Patients in the weight gain group were significantly younger (P = 0.0013). There was no significant difference between the two groups in terms of Ki-67 reduction (P = 0.98) or pCR (P = 0.58). When patients were separated into normal weight (BMI<25 kg/m(2) ), overweight (BMI ≥ 25 and <30 kg/m(2) ), and obese (BMI ≥ 30 kg/m(2) ), there was no significant difference in Ki-67 among those groups either before or after NCT. The degree of obesity did not have a significant impact on Ki-67 reduction. Weight change during NCT does not appear to correlate with Ki-67 change or achieving pCR in TNBC. This may reflect the nature of this subtype of breast cancer that is less responsive to the hormonal effects that adipose tissue exerts on cancer cell proliferation.

Surgical complications exert a lasting effect on disease-specific health-related quality of life for patients with colorectal cancer.

BACKGROUND: For individual patients with colorectal cancer, health-related quality of life (HRQL) after treatment is a function of several factors that include preexisting medical conditions, the disease burden, and the treatment that is rendered. The purpose of this study was to identify the factors that were associated with posttreatment HRQL. METHODS: At baseline and again at 12 months after diagnosis, patients completed the colorectal cancer-specific HRQL survey: Functional Assessment of Cancer Therapy (FACT-C). Univariate and multivariate analyses were performed to test the association between patient-, tumor-, and treatment-related variables and 12-month FACT-C total scores. RESULTS: Seventy-one patients completed the FACT-C at diagnosis and subsequently underwent open surgical removal of their primary tumor; 63 patients completed the 12-month survey. In univariate analysis, only chronic obstructive pulmonary disease at diagnosis or the occurrences of perioperative complications were associated with a reduction in 12-month HRQL scores. Considering both the diagnosis of chronic obstructive pulmonary disease and the occurrence of perioperative complications, along with the patient's FACT-C total score at diagnosis, age, tumor location, and stage of disease in a multivariate model, only the perioperative complications (odds ratio, 10.5; 95% CI, 2.1-52) and FACT-C total score at diagnosis (odds ratio, 1.04; 95% CI, 1.005-1.07) were associated significantly with a lower than median HRQL score at 12 months. CONCLUSIONS: For patients who undergo treatment of colorectal cancer, HRQL at 1 year after diagnosis is still influenced significantly and negatively by the occurrence of surgical complications.

Limitations of the Gail model in the specialized breast cancer risk assessment clinic.

The Gail model is a risk assessment tool that is accurate for general breast cancer risk screening. Because of the limited way that this model incorporates family history information, however, there are concerns that it may underestimate risk for many women attending specialized breast cancer risk assessment clinics. We collected comprehensive breast cancer risk factor information for 213 women attending a specialized breast cancer risk assessment clinic using a modified version of the CancerGene software. Breast cancer risk was calculated using the models of Gail and Claus as well as BRCAPRO and the tables of Bodian (for women with lobular neoplasia). Eighty-six percent of the women had a family history of breast cancer. Although 74% of women had risk factor histories that are thought to confound the Gail model (family history of breast cancer in second-degree relatives, family history of breast cancer before the age of 50, family history of bilateral breast cancer, family history of ovarian cancer, or personal history of lobular neoplasia), the inclusion of other models increased the risk level assignment in only 13% of the cases. We conclude that the Gail model is an appropriate risk assessment tool for most women attending specialized clinics, although the inclusion of models better able to account for family history information and personal history of lobular neoplasia is required to accommodate all women.

Validating the performance of the mammary sentinel lymph node team.

BACKGROUND AND OBJECTIVES: The mammary sentinel lymph node (SLN) procedure has the potential to improve the accuracy and lower the morbidity of axillary staging in breast cancer patients, but results are closely linked to experience and can vary widely between institutions. Standardized performance measures need to be established in order to optimize the transition to SLN biopsy only. METHODS: Performance data were prospectively collected for the first 156 mammary SLN procedures performed by three surgeons in our institution. RESULTS: Seventy-five cases were required to achieve an SLN visualization rate of > 80% on preoperative lymphoscintigraphy. The SLN visualization rate was 90% for the last 52 cases. Two surgeons required 25 cases before consistently achieving a > or = 90% SLN identification rate in the operating room and one required 15 cases. The metastasis detection rate increased from 22% for the first 52 cases to 31% for the last 52 cases. The false negative rate for the procedure was 5%. CONCLUSIONS: The following performance criteria and benchmarks are suggested for validating the performance of the SLN team: (1) SLN visualization rate on preoperative lymphoscintigraphy > or = 80%, (2) SLN identification rate in the operating room > or = 90%, (3) False negative rate for the procedure 5%. Thirty procedures per surgeon were sufficient to achieve these benchmarks in our group.