Parallel Analyses by Mass Spectrometry (MS) and Reverse Phase Protein Array (RPPA) Reveal Complementary Proteomic Profiles in Triple-Negative Breast Cancer (TNBC) Patient Tissues and Cell Cultures.

High-plex proteomic technologies have made substantial contributions to mechanism studies and biomarker discovery in complex diseases, particularly cancer. Despite technological advancements, inherent limitations in individual proteomic approaches persist, impeding the achievement of comprehensive quantitative insights into the proteome. In this study, we employed two widely used proteomic technologies, mass spectrometry (MS) and reverse phase protein array (RPPA) to analyze identical samples, aiming to systematically assess the outcomes and performance of the different technologies.

cascAGS: Comparative Analysis of SNP Calling Methods for Human Genome Data in the Absence of Gold Standard.

The development of third-generation sequencing has accelerated the boom of single nucleotide polymorphism (SNP) calling methods, but evaluating accuracy remains challenging owing to the absence of the SNP gold standard. The definitions for without-gold-standard and performance metrics and their estimation are urgently needed. Additionally, the possible correlations between different SNP loci should also be further explored.

Bridging Discoveries and Treatments: The New Landscape of Breast Cancer Research.

Welcome to our Special Issue, "Advances in Breast Cancer Research and Treatment" of , where we have embarked on a comprehensive exploration of groundbreaking studies that advance our understanding and management of breast cancer [...

MSGM: An Advanced Deep Multi-Size Guiding Matching Network for Whole Slide Histopathology Images Addressing Staining Variation and Low Visibility Challenges.

Matching whole slide histopathology images to provide comprehensive information on homologous tissues is beneficial for cancer diagnosis. However, the challenge arises with the Giga-pixel whole slide images (WSIs) when aiming for high-accuracy matching. Learning-based methods are difficult to generalize well with large-size WSIs, necessitating the integration of traditional matching methods to enhance accuracy as the size increases.

An orientation-free ring feature descriptor with stain-variability normalization for pathology image matching.

Comprehensively analyzing the corresponding regions in the images of serial slices stained using different methods is a common but important operation in pathological diagnosis. To help increase the efficiency of the analysis, various image registration methods are proposed to match the corresponding regions in different images, but their performance is highly influenced by the rotations, deformations, and variations of staining between the serial pathology images. In this work, we propose an orientation-free ring feature descriptor with stain-variability normalization for pathology image matching.

Biomarker Alteration after Neoadjuvant Endocrine Therapy or Chemotherapy in Estrogen Receptor-Positive Breast Cancer.

In estrogen receptor (ER)-positive breast cancer, changes in biomarker expression after neoadjuvant therapy indicate the therapeutic response and are prognostic. However, there is limited information about the biomarker alteration caused by neoadjuvant endocrine therapy in ER-positive and human epidermal growth factor receptor 2 (HER2)-negative breast cancer. We recruited ER-positive/HER2-negative breast cancer patients who received neoadjuvant chemotherapy (NCT), neoadjuvant endocrine therapy (NET), or sequential neoadjuvant endocrine-chemotherapy (NECT) at Peking University Cancer Hospital from 2015 to 2021.

Adverse Events of PD-1 or PD-L1 Inhibitors in Triple-Negative Breast Cancer: A Systematic Review and Meta-Analysis.

(1) Background: This study aimed to develop a comprehensive understanding of the treatment-related adverse events when using PD-1 or PD-L1 inhibitors in triple-negative breast cancer (TNBC). (2) Methods: We conducted a meta-analysis of Phase II/III randomized clinical trials. Studies were searched for using PubMed, Embase, and Cochrane Library from 1 March 1980 till 30 June 2022.

Survival in Breast Cancer Patients with Bone Metastasis: A Multicenter Real-World Study on the Prognostic Impact of Intensive Postoperative Bone Scan after Initial Diagnosis of Breast Cancer (CSBrS-023).

The prognostic value of intensive postoperative bone scan (BS) screening, which is performed in asymptomatic patients with breast cancer (BC) after surgery, remained unclear. Patients diagnosed with BC with bone metastasis (BM) from five medical centers in China during the years 2005−2013 were retrospectively collected. Propensity score matching (PSM) was performed to balance the baseline characteristics.

Germline Variants in 32 Cancer-Related Genes among 700 Chinese Breast Cancer Patients by Next-Generation Sequencing: A Clinic-Based, Observational Study.

Breast cancer (BC) is associated with hereditary components, and some deleterious germline variants have been regarded as effective therapeutic targets. We conducted a clinic-based, observational study to better understand the distribution of deleterious germline variants and assess any clinicopathological predictors related to the variants among Chinese BC patients using a 32 cancer-related genes next-generation sequencing panel. Between November 2020 and February 2022, a total of 700 BC patients were recruited, and 13.

Two-Dose Vaccination Significantly Prolongs the Duration from Symptom Onset to Death: A Retrospective Study Based on 173,894 SARS-CoV-2 Cases in Khyber Pakhtunkhwa, Pakistan.

This research was carried out to quantify the duration from symptom onset to recovery/death (SOR/SOD) during the first four waves and the Alpha/Delta period of the epidemic in Khyber Pakhtunkhwa, Pakistan, and identify the associated factors. A total of 173,894 COVID-19 cases were admitted between 16 March 2020 and 30 November 2021, including 458 intensive care unit (ICU) cases. The results showed that the case fatality rate (CFR) increased with age, and females had a higher CFR.

Expression of DNA Helicase Genes Was Correlated with Homologous Recombination Deficiency in Breast Cancer.

Homologous recombination deficiency which is currently measured by the homologous recombination deficiency (HRD) score including score of telomeric allelic imbalance (TAI), large-scale transition (LST), and loss of heterozygosity (LOH) is highly related with sensitivity to platinum-containing drug and PARP inhibitors. DNA helicases are essential components for the homologous recombination repair process in which DNA helicases unwind double-strand DNA utilizing ATP hydrolysis. In our study, the correlation between the expression of DNA helicase genes and HRD score in breast cancer was analyzed.

BM-Net: CNN-Based MobileNet-V3 and Bilinear Structure for Breast Cancer Detection in Whole Slide Images.

Breast cancer is one of the most common types of cancer and is the leading cause of cancer-related death. Diagnosis of breast cancer is based on the evaluation of pathology slides. In the era of digital pathology, these slides can be converted into digital whole slide images (WSIs) for further analysis.

Detection of Structural Variations and Fusion Genes in Breast Cancer Samples Using Third-Generation Sequencing.

Structural variations (SVs) are common genetic alterations in the human genome that could cause different phenotypes and diseases, including cancer. However, the detection of structural variations using the second-generation sequencing was limited by its short read length, which restrained our understanding of structural variations. In this study, we developed a 28-gene panel for long-read sequencing and employed it to Oxford Nanopore Technologies and Pacific Biosciences platforms.

The natural history of breast cancer: a chronological analysis of breast cancer progression using data from the SEER database.

Background: Numerous mathematical models and retrospective analyses have been conducted to explore the natural progression of breast cancer, but there is no precise timeline as to how long it takes breast cancer to progress from stages 0 to IV. Studying the natural history of breast cancer requires the follow-up of a large cohort of patients who received no treatment following diagnosis for a long period, but this has become unpractical in the modern era. In this study, we quantified the natural progression of breast cancer using the Surveillance, Epidemiology, and End Results (SEER) database which was collected the clinical-pathological characteristics and survival data of untreated breast cancer patients.

Intraparenchymal breast leiomyoma and atypical leiomyoma.

Background: Breast leiomyoma is a rare benign mesenchymal tumor, accounting for less than 1% of all breast neoplasms. Cases of breast atypical leiomyoma is even more rarely reported and its diagnostic criteria together with its clinical courses is not cleared defined.

Case Presentation: We described two patients with breast leiomyomas.

Triple-Negative Apocrine Breast Carcinoma Has Better Prognosis despite Poor Response to Neoadjuvant Chemotherapy.

Apocrine carcinoma is a rare subtype of invasive ductal breast cancer that shows apocrine differentiation and largely triple-negative immunohistology. Triple-negative breast cancers are known to have more aggressive clinical courses. However, unlike most other subtypes, it is reported that triple-negative apocrine carcinoma (TNAC) has a better prognosis.

Gene expression trend changes in breast cancer populations over two decades: insights from The Cancer Genome Atlas database.

Background: Breast cancer has remained the most common malignancy in women over the past two decades. As lifestyle and living environments have changed, alterations to the disease spectrum have inevitably occurred in this time. As molecular profiling has become a routine diagnostic and objective indicator of breast cancer etiology, we analyzed changes in gene expression in breast cancer populations over two decades using The Cancer Genome Atlas database.

Modeling effective tumor burden of primary lesion and metastatic lymph node in breast cancer patients from the SEER database.

Background: Characterizing the role of the primary tumor and axillary lymph nodes (ALNs) in metastasis progression can provide a rational basis for effective local control and systemic treatments.

Methods: We employed data from the Surveillance, Epidemiology, and End Results (SEER) database to perform survival analysis and modeling to estimate breast cancer (BC) progression in both untreated and treated patients. Effective tumor burden was defined as the number of cancer cells that can lead to distant metastasis.

Identification and Functional Characterization of a Novel Nonsense Variant in in a Southern Chinese Family With High Myopia.

has been associated with X-linked, female-limited, high myopia. However, using exome sequencing (ES), we identified the first high myopia case with hemizygous -related mutation in a male patient in a Southern Chinese family. This novel truncated mutation (: c.

A Machine Learning Approach to Differentiate Two Specific Breast Cancer Subtypes Using Androgen Receptor Pathway Genes.

Triple-negative breast cancer is a heterogeneous disease with different molecular and histological subtypes. The Androgen receptor is expressed in a portion of triple-negative breast cancer cases and the activation of the androgen receptor pathway is thought to be a molecular subtyping signature as well as a therapeutic target for triple-negative breast cancer. Thus, identification of the androgen receptor pathway status is important for both molecular characterization andclinical management.

Classification of PR-positive and PR-negative subtypes in ER-positive and HER2-negative breast cancers based on pathway scores.

Purpose: PR loss in ER+/HER2- breast cancer indicates worse prognosis and insensitivity to anti-estrogen therapy, while the mechanisms of PR loss in ER+/HER2- breast cancer remain unrevealed.

Methods: In this study, ER+/PR+/HER2- and ER+/PR-/HER2- breast cancer cases from TCGA were used. 1387 pathways were analyzed and used as variables for classifying the two groups with LASSO regression.