Next-generation transcriptome sequencing of the premenopausal breast epithelium using specimens from a normal human breast tissue bank.

INTRODUCTION: Our efforts to prevent and treat breast cancer are significantly impeded by a lack of knowledge of the biology and developmental genetics of the normal mammary gland. In order to provide the specimens that will facilitate such an understanding, The Susan G. Komen for the Cure Tissue Bank at the IU Simon Cancer Center (KTB) was established. The KTB is, to our knowledge, the only biorepository in the world prospectively established to collect normal, healthy breast tissue from volunteer donors. As a first initiative toward a molecular understanding of the biology and developmental genetics of the normal mammary gland, the effect of the menstrual cycle and hormonal contraceptives on DNA expression in the normal breast epithelium was examined. METHODS: Using normal breast tissue from 20 premenopausal donors to KTB, the changes in the mRNA of the normal breast epithelium as a function of phase of the menstrual cycle and hormonal contraception were assayed using next-generation whole transcriptome sequencing (RNA-Seq). RESULTS: In total, 255 genes representing 1.4% of all genes were deemed to have statistically significant differential expression between the two phases of the menstrual cycle. The overwhelming majority (221; 87%) of the genes have higher expression during the luteal phase. These data provide important insights into the processes occurring during each phase of the menstrual cycle. There was only a single gene significantly differentially expressed when comparing the epithelium of women using hormonal contraception to those in the luteal phase. CONCLUSIONS: We have taken advantage of a unique research resource, the KTB, to complete the first-ever next-generation transcriptome sequencing of the epithelial compartment of 20 normal human breast specimens. This work has produced a comprehensive catalog of the differences in the expression of protein-coding genes as a function of the phase of the menstrual cycle. These data constitute the beginning of a reference data set of the normal mammary gland, which can be consulted for comparison with data developed from malignant specimens, or to mine the effects of the hormonal flux that occurs during the menstrual cycle.

Characterizing the heterogeneity of triple-negative breast cancers using microdissected normal ductal epithelium and RNA-sequencing.

Triple-negative breast cancers (TNBCs) are a heterogeneous set of tumors defined by an absence of actionable therapeutic targets (ER, PR, and HER-2). Microdissected normal ductal epithelium from healthy volunteers represents a novel comparator to reveal insights into TNBC heterogeneity and to inform drug development. Using RNA-sequencing data from our institution and The Cancer Genome Atlas (TCGA) we compared the transcriptomes of 94 TNBCs, 20 microdissected normal breast tissues from healthy volunteers from the Susan G. Komen for the Cure Tissue Bank, and 10 histologically normal tissues adjacent to tumor. Pathway analysis comparing TNBCs to optimized normal controls of microdissected normal epithelium versus classic controls composed of adjacent normal tissue revealed distinct molecular signatures. Differential gene expression of TNBC compared with normal comparators demonstrated important findings for TNBC-specific clinical trials testing targeted agents; lack of over-expression for negative studies and over-expression in studies with drug activity. Next, by comparing each individual TNBC to the set of microdissected normals, we demonstrate that TNBC heterogeneity is attributable to transcriptional chaos, is associated with non-silent DNA mutational load, and explains transcriptional heterogeneity in addition to known molecular subtypes. Finally, chaos analysis identified 146 core genes dysregulated in >90 % of TNBCs revealing an over-expressed central network. In conclusion, use of microdissected normal ductal epithelium from healthy volunteers enables an optimized approach for studying TNBC and uncovers biological heterogeneity mediated by transcriptional chaos.

Central venous port placement: a comparison of axillary versus anterior chest wall placement.

BACKGROUND: To compare morbidity in patients with surgically implanted central venous ports that were placed in the subcutaneous tissues of the mid axillary line at the anterior border of the latissimus muscle (group A) versus the anterior chest wall (group C). METHODS: Between 2003 and 2007, a total of 183 patients with breast cancer were taken to the operating room for central venous port placement for delivery of chemotherapy. Port location was determined by patient and surgeon preference. Patient demographics were collected, and complications were evaluated by electronic medical record review. Complications identified included infection, thrombosis, port problems, and catheter problems. Basic descriptive statistics were generated. Patients with axillary ports were then compared to those with chest wall ports by appropriate t-tests or χ(2) tests. RESULTS: During this period, 137 (75%) of 183 ports were placed in the axillary position. The complication rate was 10% (9% in group A vs. 13% in group C). There were 14 catheter-related complications and 5 port-related complications. There was no statistically significant difference in complications between the two groups (P = 0.45). Patients with axillary ports weighed less (mean 75.8 kg in group A vs. 84.9 kg in group C) and were more likely to have catheters placed in the internal jugular vein (82% in group A vs. 56% in group C). CONCLUSIONS: There is no difference in rate or type of complications between axillary and chest wall port location. Subcutaneous ports can safely be placed in the mid axillary line. Axillary ports spare the patient the negative cosmetic outcomes of chest wall ports.

Decreased Leak Rate and Need for Reintervention with Use of Closed Suction Calibration System: a Bariatric Surgery Quality Improvement Project.

BACKGROUND: Laparoscopic sleeve gastrectomy (SG) continues to grow in popularity as a primary bariatric procedure. The purpose of this study is to determine if leak rates and need for subsequent interventions are changed by the standardized use of a closed suction calibration system (CSCS) at a high-volume urban hospital. METHODS: A retrospective review was conducted between January 1, 2016, and December 31, 2018, on SG patients. All cases performed in 2018 were completed with a closed suction calibration system. Patient demographics, comorbidities, operative variables, and outcomes were collected. Descriptive statistics and chi-squared test were used to compare the two groups. Logistic regression models were adjusted for patient- and procedure-specific factors. RESULTS: Four hundred ninety cases were performed before and 195 after institution of the CSCS. Groups were similar in most characteristics, including median body mass index (BMI) (46.4 vs 45.8 kg/m2, p = 0.79). Those in the closed suction cohort were more likely to have OSA requiring therapy (32.4% vs 46.6%, p < 0.01) and to have their cases performed robotically (55.4% vs 39.6%, p = 0.02). Post introduction of the CSCS, the overall leak rate was 0% (1.4% vs 0%, p = 0.09); overall need for postoperative interventions decreased (9.6% vs 2.6%, p = 0.009). After adjustment, a 69% decrease was observed in need for related additional intervention [aOR 0.31 (0.12-0.81), p = 0.017]. CONCLUSION: The use of a standardized closed suction calibration system resulted in overall decreased leak rates, which was associated with a clinically significant decrease in additional interventions.

Optimizing outcomes in emergency room thoracotomy: a 20-year experience in an urban Level I trauma center.

Emergency room thoracotomy (ERT) has remained a last resort tool of resuscitation in the management of patients with major trauma. The medical records of all patients undergoing ERT for penetrating chest trauma from January 1, 2000 through April 30, 2008 were retrospectively reviewed. The data from this study were added to data collected in two previous studies conducted at our institution for meta-analysis. A total of 102 ERTs were performed. There were 28 Class I patients (27.4%), 58 Class II (56.8%), six Class III (5.8%), and 11 Class IV (10.7%). The number of ERTs performed on Class I patients has decreased from 58.3 per cent in the 1995 group to 35.4 per cent in the 1999 group. There was an overall survival of 7.8 per cent in the current period of review. Overall survival in the 1995 group was 2.5 per cent, 1999 was 2.7 per cent, and 2008 was 7.8 per cent. The majority of the survival benefit occurs in patients who have electrical activity and a blood pressure when examined in the emergency department (Class III and IV). We intend to do future prospective research to further clarify the Class II patients when evaluating the type of rhythm shown on electrocardiogram tracing to move away from the generic pulseless electrical activity category.