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.

Molecular adaptation to neoadjuvant immunotherapy in triple-negative breast cancer.

Therapy-induced molecular adaptation of triple-negative breast cancer is crucial for immunotherapy response and resistance. We analyze tumor biopsies from three different time points in the randomized neoadjuvant GeparNuevo trial (NCT02685059), evaluating the combination of durvalumab with chemotherapy, for longitudinal alterations of gene expression. Durvalumab induces an activation of immune and stromal gene expression as well as a reduction of proliferation-related gene expression.

Hormone Receptor Positive HER2-negative/MammaPrint High-2 Breast Cancers Closely Resemble Triple Negative Breast Cancers.

Purpose: The MammaPrint prognostic assay categorizes breast cancers into high- and low-risk subgroups, and the high-risk group can be further subdivided into high 1 (MP-H1), and very high-risk high-2 (MP/H-2). The aim of this analysis was to assess clinical and molecular differences between the hormone receptor positive/HER2-negative (HR+) MP-H1, -H2, and triple negative (TN) MP-H1 and -H2 cancers.

Experimental Design: Pre-treatment gene expression data from 742 HER2 negative breast cancers enrolled in the I-SPY2 neoadjuvant trial was used.

Trends in breast cancer specific death by clinical stage at diagnoses between 2000-2017.

Background: Approximately 40,000 individuals die from metastatic breast cancer each year. We examined what fractions of annual breast cancer-specific death (BCSD) are due to stage I, II, III, IV disease and if these proportions changed over time.

Methods: We used data from SEER covering 1975 to 2017.

EpidermaQuant: Unsupervised Detection and Quantification of Epidermal Differentiation Markers on H-DAB-Stained Images of Reconstructed Human Epidermis.

The integrity of the reconstructed human epidermis generated in vitro can be assessed using histological analyses combined with immunohistochemical staining of keratinocyte differentiation markers. Technical differences during the preparation and capture of stained images may influence the outcome of computational methods. Due to the specific nature of the analyzed material, no annotated datasets or dedicated methods are publicly available.