Uncovering Surgical Dynamics and Trends in Early Breast Cancer Stage at Diagnosis: Key Insights From a Two-Decade Argentine Database Analysis.

Purpose: Breast cancer remains a major public health challenge worldwide, and understanding the trends and changes in breast cancer diagnosis and treatment over time is crucial for improving patient outcomes and guiding public health strategies. The Argentine Society of Mastology has maintained a comprehensive Breast Cancer Registry that provides valuable data for analyzing these trends.

Materials And Methods: This retrospective analysis of the Breast Cancer Registry database evaluated changes in stages at the time of surgery, patterns of surgical care, and factors associated with higher stage diagnoses in patients with breast cancer in Argentina from January 2000 to December 2019.

Comparative single-cell transcriptomic analysis reveals putative differentiation drivers and potential origin of vertebrate retina.

Despite known single-cell expression profiles in vertebrate retinas, understanding of their developmental and evolutionary expression patterns among homologous cell classes remains limited. We examined and compared approximately 240 000 retinal cells from four species and found significant similarities among homologous cell classes, indicating inherent regulatory patterns. To understand these shared patterns, we constructed gene regulatory networks for each developmental stage for three of these species.

TF-EPI: an interpretable enhancer-promoter interaction detection method based on Transformer.

The detection of enhancer-promoter interactions (EPIs) is crucial for understanding gene expression regulation, disease mechanisms, and more. In this study, we developed TF-EPI, a deep learning model based on Transformer designed to detect these interactions solely from DNA sequences. The performance of TF-EPI surpassed that of other state-of-the-art methods on multiple benchmark datasets.

Single-cell transcriptomic analysis of B cells reveals new insights into atypical memory B cells in COVID-19.

Here, we performed single-cell RNA sequencing of S1 and receptor binding domain protein-specific B cells from convalescent COVID-19 patients with different clinical manifestations. This study aimed to evaluate the role and developmental pathway of atypical memory B cells (MBCs) in response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The results revealed a proinflammatory signature across B cell subsets associated with disease severity, as evidenced by the upregulation of genes such as GADD45B, MAP3K8, and NFKBIA in critical and severe individuals.

Integrative analysis of cancer multimodality data identifying COPS5 as a novel biomarker of diffuse large B-cell lymphoma.

Preventing, diagnosing, and treating diseases requires accurate clinical biomarkers, which remains challenging. Recently, advanced computational approaches have accelerated the discovery of promising biomarkers from high-dimensional multimodal data. Although machine-learning methods have greatly contributed to the research fields, handling data sparseness, which is not unusual in research settings, is still an issue as it leads to limited interpretability and performance in the presence of missing information.

HyGAnno: hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data.

Reliable cell type annotations are crucial for investigating cellular heterogeneity in single-cell omics data. Although various computational approaches have been proposed for single-cell RNA sequencing (scRNA-seq) annotation, high-quality cell labels are still lacking in single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) data, because of extreme sparsity and inconsistent chromatin accessibility between datasets. Here, we present a novel automated cell annotation method that transfers cell type information from a well-labeled scRNA-seq reference to an unlabeled scATAC-seq target, via a parallel graph neural network, in a semi-supervised manner.

The role of modern parameters and their relationship with recurrence risk as assessed by Oncotype DX: real-world evidence.

Genomic analysis through various platforms is an essential tool for determining prognosis and treatment in a significant subgroup of early-stage breast cancer patients with hormone receptor-positive and human epidermal growth factor receptor 2 (HER2)-negative status. Additionally, combined clinical and pathological characteristics can accurately predict the recurrence score (RS), as demonstrated by the University of Tennessee risk nomogram. In this study, we aimed to identify classical clinical-pathological factors associated with high RS in a local population, including modern parameters such as current abemaciclib treatment recommendations, HER2-low status, different Ki-67 cutoff values, and samples obtained from secondary primary tumours.

Multi-omics computational analysis unveils the involvement of AP-1 and CTCF in hysteresis of chromatin states during macrophage polarization.

Macrophages display extreme plasticity, and the mechanisms and applications of polarization and de-/repolarization of macrophages have been extensively investigated. However, the regulation of macrophage hysteresis after de-/repolarization remains unclear. In this study, by using a large-scale computational analysis of macrophage multi-omics data, we report a list of hysteresis genes that maintain their expression patterns after polarization and de-/repolarization.

Epigenetic characterization of housekeeping core promoters and their importance in tumor suppression.

In this research, we elucidate the presence of around 11,000 housekeeping cis-regulatory elements (HK-CREs) and describe their main characteristics. Besides the trivial promoters of housekeeping genes, most HK-CREs reside in promoter regions and are involved in a broader role beyond housekeeping gene regulation. HK-CREs are conserved regions rich in unmethylated CpG sites.

Intercellular crosstalk in adult dental pulp is mediated by heparin-binding growth factors Pleiotrophin and Midkine.

Background: In-depth knowledge of the cellular and molecular composition of dental pulp (DP) and the crosstalk between DP cells that drive tissue homeostasis are not well understood. To address these questions, we performed a comparative analysis of publicly available single-cell transcriptomes of healthy adult human DP to 5 other reference tissues: peripheral blood mononuclear cells, bone marrow, adipose tissue, lung, and skin.

Results: Our analysis revealed that DP resident cells have a unique gene expression profile when compared to the reference tissues, and that DP fibroblasts are the main cell type contributing to this expression profile.

Unbiased integration of single cell transcriptome replicates.

Single cell transcriptomic approaches are becoming mainstream, with replicate experiments commonly performed with the same single cell technology. Methods that enable integration of these datasets by removing batch effects while preserving biological information are required for unbiased data interpretation. Here, we introduce Canek for this purpose.

Cyclin-Dependent Kinase 4/6 Inhibitor Outcomes in Patients With Advanced Breast Cancer Carrying Germline Pathogenic Variants in DNA Repair-Related Genes.

Purpose: In recent years, unprecedented benefits have been observed with the development of cyclin-dependent kinase (CDK) 4 and 6 inhibitors for the treatment of hormone receptor-positive/human epidermal growth factor receptor 2-negative metastatic breast cancer. However, there is scarce evidence of their value in specific populations, such as patients carrying germline pathogenic variants in DNA repair-related genes.

Patients And Methods: We retrospectively studied the efficacy of CDK 4/6 inhibitors plus endocrine therapy in patients with hormone receptor-positive/human epidermal growth factor receptor 2-negative advanced breast cancer.

Breast Cancer in Young Women Presents With More Aggressive Pathologic Characteristics: Retrospective Analysis From an Argentine National Database.

Purpose: Multiple studies have reported that breast cancer in young patients is associated with aggressive characteristics, and it is suggested that prognosis is worse independently of pathologic variables.

Patients And Methods: We performed a retrospective analysis of the Breast Cancer Registry of the Argentinian Society of Mastology, including public and private centers. Patients ≤ 40 years of age at diagnosis were classified as "young," and patients ≤ 35 years of age at diagnosis were classified as "very young.