Comparative analysis of Ficoll-Hypaque and CytoLyt techniques for blood removal in breast cancer malignant effusions: effects on RNA quality and sequencing outcomes.

Introduction: To optimize RNA sequencing (RNA-seq) outcomes, we investigated preanalytical variables in malignant effusions containing metastatic breast cancer. We compared 2 processing methods-Ficoll-Hypaque density gradient enrichment and CytoLyt hemolysis-focusing on their effects on RNA quality, transcript abundance, and variant detection from cytospin slides, relative to fresh-frozen samples. Additionally, we compared read-based and Unique Molecular Identifier (UMI)-based library preparation methods.

Evaluation of zero counts to better understand the discrepancies between bulk and single-cell RNA-Seq platforms.

Recent advances in sample preparation and sequencing technology have made it possible to profile the transcriptomes of individual cells using single-cell RNA sequencing (scRNA-Seq). Compared to bulk RNA-Seq data, single-cell data often contain a higher percentage of zero reads, mainly due to lower sequencing depth per cell, which affects mostly measurements of low-expression genes. However, discrepancies between platforms are observed regardless of expression level.

Surgical External Iliac Artery Access for Transcatheter Aortic Valve Replacement Is a Safe, Suitable Alternative to Common Femoral Artery Access.

Background Many patients undergoing transcatheter aortic valve replacement (TAVR) have peripheral artery disease necessitating surgical access. This study reviews the preoperative risk factors, procedural characteristics, and outcomes in patients undergoing surgical common femoral artery (CFA) and external iliac artery (EIA) access through a retro-inguinal groin incision for TAVR. Methods A single-center TAVR database was retrospectively analyzed for patients undergoing surgical cutdown (January 1, 2016 - December 31, 2020).

Technological Advances to Address the Challenging Abdominal Aortic Aneurysm Neck.

There have been significant technologic advances in endovascular aortic therapies since the introduction of conventional infrarenal endovascular aortic aneurysm repair (EVAR). These advances have sought to address the weaknesses of conventional EVAR- particularly the difficult or "hostile" infrarenal aortic aneurysm neck. We review anatomical features that create a hostile neck and the most recent advancements to overcome these limitations.

AKT/mTOR signaling modulates resistance to endocrine therapy and CDK4/6 inhibition in metastatic breast cancers.

Endocrine therapy (ET) in combination with CDK4/6 inhibition is routinely used as first-line treatment for HR+/HER2- metastatic breast cancer (MBC) patients. However, 30-40% of patients quickly develop disease progression. In this open-label multicenter clinical trial, we utilized a hypothesis-driven protein/phosphoprotein-based approach to identify predictive markers of response to ET plus CDK4/6 inhibition in pre-treatment tissue biopsies.

Assessment of stained direct cytology smears of breast cancer for whole transcriptome and targeted messenger RNA sequencing.

Background: Rather than surgical resection, cytologic specimens are often used as first-line clinical diagnostic procedures due to higher safety, speed, and cost-effectiveness. Archival diagnostic cytology slides containing cancer can be equivalent to tissue biopsies for DNA mutation testing, but the accuracy of transcriptomic profiling by RNA sequencing (RNA-seq) is less understood.

Methods: This study compares the results from whole transcriptome RNA-seq and a targeted RNA-seq assay of stained cytology smears (CS) versus matched tumor tissue samples preserved fresh-frozen (FF) and processed as formalin-fixed paraffin-embedded (FFPE) sections.

Comprehensive Analysis of Metabolic Isozyme Targets in Cancer.

Unlabelled: Metabolic reprogramming is a hallmark of malignant transformation, and loss of isozyme diversity (LID) contributes to this process. Isozymes are distinct proteins that catalyze the same enzymatic reaction but can have different kinetic characteristics, subcellular localization, and tissue specificity. Cancer-dominant isozymes that catalyze rate-limiting reactions in critical metabolic processes represent potential therapeutic targets.

Intravascular Lithotripsy in the Treatment of Lower Extremity Peripheral Arterial Disease.

Endovascular intervention has become first-line treatment for the majority of atherosclerotic lesions associated with peripheral artery disease. Traditionally, treatment modalities have included various types of balloon angioplasty and stenting. However, recent technological advancements have introduced the concept of endovascular lithotripsy as a novel alternative to angioplasty and stenting.

Data augmentation based on waterfall plots to increase value of response data generated by small single arm Phase II trials.

Waterfall plots have been increasingly used to visualize tumor response measurements in Phase II clinical trials. Despite the growing popularity of waterfall plots, quantitative summaries and distribution features of the data indicating antitumor activities are typically not reported. Statistical summaries from the raw and augmented data may provide valuable information for understanding such features.

Intra- and Interlaboratory Reproducibility of the Sensitivity to Endocrine Therapy Assay for Stage II/III Breast Cancer.

Background: The sensitivity to endocrine therapy assay (SET2,3) predicts treatment outcomes in Stage II-III breast cancer. SET2,3 measures transcription related to estrogen and progesterone receptors (SETER/PR index) and the molecular subtype (RNA4: ESR1, PGR, ERBB2, AURKA) from formalin-fixed paraffin-embedded (FFPE) tissue sections.

Methods: We designed a nested study across 3 pathology laboratories, each testing 60 breast cancers twice in controlled batches.

Diffuse Alveolar Hemorrhage after Receiving Oral Levonorgerstrel for Emergency Contraception: A Case Report.

Introduction: Drug-induced diffuse alveolar hemorrhage (DAH) has been associated with the administration of various medications, among which levonorgestrel (LN) has not been reported until now.

Case Presentation: This case study describes a 42-year-old woman who presented with hemoptysis, hypoxemia, and radiological depiction of ground glass opacities, 3 days after she had received emergency contraceptive medication containing levonorgestrel. Emergent bronchoscopy was performed, and BAL was diagnostic of diffuse alveolar hemorrhage (DAH).

Treatment scheduling effects on the evolution of drug resistance in heterogeneous cancer cell populations.

The effect of scheduling of targeted therapy combinations on drug resistance is underexplored in triple-negative breast cancer (TNBC). TNBC constitutes heterogeneous cancer cell populations the composition of which can change dynamically during treatment resulting in the selection of resistant clones with a fitness advantage. We evaluated crizotinib (ALK/MET inhibitor) and navitoclax (ABT-263; Bcl-2/Bcl-xL inhibitor) combinations in a large design consisting of 696 two-cycle sequential and concomitant treatment regimens with varying treatment dose, duration, and drug holiday length over a 26-day period in MDA-MB-231 TNBC cells and found that patterns of resistance depend on the schedule and sequence in which the drugs are given.

Whole-genome sequencing of phenotypically distinct inflammatory breast cancers reveals similar genomic alterations to non-inflammatory breast cancers.

Background: Inflammatory breast cancer (IBC) has a highly invasive and metastatic phenotype. However, little is known about its genetic drivers. To address this, we report the largest cohort of whole-genome sequencing (WGS) of IBC cases.

Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells.

Cancer cells employ various defense mechanisms against drug-induced cell death. Investigating multi-omics landscapes of cancer cells before and after treatment can reveal resistance mechanisms and inform new therapeutic strategies. We assessed the effects of navitoclax, a BCL2 family inhibitor, on the transcriptome, methylome, chromatin structure, and copy number variations of MDA-MB-231 triple-negative breast cancer (TNBC) cells.

Increasing accrual of minority patients in breast cancer clinical trials.

Background: Black and Hispanic patients participate in clinical trials at lower rates than white patients nationally; lack of diversity in clinical trials prevents appropriate safety and efficacy testing of new treatments in these populations.

Methods: The Oncology Welcomes New Haven into Trials (OWN IT) initiative at the Yale Cancer Center used a multi-tiered approach to improve breast cancer minority clinical trial accrual through community focus groups, ongoing community outreach, institutional executive council representation, grand rounds presentation, and didactic lectures with healthcare providers. Eligibility criteria of breast cancer trials at Smilow Cancer Center were reviewed using clinicaltrials.

Treatment efficacy for pharyngeal Neisseria gonorrhoeae: a systematic review and meta-analysis of randomized controlled trials.

Background: Rising gonorrhoea rates require highly effective treatments to reduce transmission and prevent development of antimicrobial resistance. Currently the most effective treatments for pharyngeal gonorrhoea remain unclear. This review aimed to estimate treatment efficacy for pharyngeal gonorrhoea.

Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden.

Cancers harbor many somatic mutations and germline variants, we hypothesized that the combined effect of germline variants that alter the structure, expression, or function of protein-coding regions of cancer-biology related genes (gHFI) determines which and how many somatic mutations (sM) must occur for malignant transformation. We show that gHFI and sM affect overlapping genes and the average number of gHFI in cancer hallmark genes is higher in patients who develop cancer at a younger age (r = -0.77, P = 0.

Analysis of Pre- and Posttreatment Tissues from the SWOG S0800 Trial Reveals an Effect of Neoadjuvant Chemotherapy on the Breast Cancer Genome.

Purpose: We performed whole-exome sequencing (WES) of pre- and posttreatment cancer tissues to assess the somatic mutation landscape of tumors before and after neoadjuvant taxane and anthracycline chemotherapy with or without bevacizumab.

Experimental Design: Twenty-nine pretreatment biopsies from the SWOG S0800 trial were subjected to WES to identify mutational patterns associated with response to neoadjuvant chemotherapy. Nine matching samples with residual cancer after therapy were also analyzed to assess changes in mutational patterns in response to therapy.

The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues.

Background: Utilization of RNA sequencing methods to measure gene expression from archival formalin-fixed paraffin-embedded (FFPE) tumor samples in translational research and clinical trials requires reliable interpretation of the impact of pre-analytical variables on the data obtained, particularly the methods used to preserve samples and to purify RNA.

Methods: Matched tissue samples from 12 breast cancers were fresh frozen (FF) and preserved in RNAlater or fixed in formalin and processed as FFPE tissue. Total RNA was extracted and purified from FF samples using the Qiagen RNeasy kit, and in duplicate from FFPE tissue sections using three different kits (Norgen, Qiagen and Roche).

Identification and Validation of a Novel Biologics Target in Triple Negative Breast Cancer.

The goal of this study was to identify a novel target for antibody-drug conjugate (ADC) development in triple negative breast cancer (TNBC), which has limited treatment options, using gene expression datasets and in vitro siRNA/CRISPR and in vivo functional assays. We analyzed 4467 breast cancers and identified GABRP as top expressed gene in TNBC with low expression in most normal tissues. GABRP protein was localized to cell membrane with broad range of receptors/cell (815-53,714) and expressed by nearly half of breast cancers tissues.

SET: a robust 18-gene predictor for sensitivity to endocrine therapy for metastatic breast cancer.

There is a clinical need to predict sensitivity of metastatic hormone receptor-positive and HER2-negative (HR+/HER2-) breast cancer to endocrine therapy, and targeted RNA sequencing (RNAseq) offers diagnostic potential to measure both transcriptional activity and functional mutation. We developed the SET index to measure gene expression microarray probe sets that were correlated with hormone receptors ( and ) and robust to preanalytical and analytical influences. We tested SET index in biopsies of metastastic HR+/HER2- breast cancer against the treatment outcomes in 140 patients.

The impact of communication style on patient satisfaction.

Background: Communication between patients and health providers influences patient satisfaction, but it is unknown whether similarity in communication styles results in higher patient satisfaction.

Methods: This study was conducted in the Smilow Cancer Hospital Breast Center. During routine follow-up visits, patients completed a Communication Styles Assessment (CSA), health survey (SF-12), Princess Margaret Hospital Satisfaction with Doctor Questionnaire, and brief demographic form.