A comprehensive overview of metaplastic breast cancer: clinical features and molecular aberrations

TP Reddy, RR Rosato, X Li, S Moulder… - Breast Cancer …, 2020 - Springer
Metaplastic breast cancer (MpBC) is an exceedingly rare breast cancer variant that is
therapeutically challenging and aggressive. MpBC is defined by the histological presence of …

[PDF][PDF] ComBat-seq: batch effect adjustment for RNA-seq count data

Y Zhang, G Parmigiani… - NAR genomics and …, 2020 - academic.oup.com
The benefit of integrating batches of genomic data to increase statistical power is often
hindered by batch effects, or unwanted variation in data caused by differences in technical …

Molecular features of metaplastic breast carcinoma: an infrequent subtype of triple negative breast carcinoma

S González-Martínez, B Pérez-Mies, I Carretero-Barrio… - Cancers, 2020 - mdpi.com
Metaplastic breast carcinoma (MBC) is a heterogeneous group of infrequent invasive
carcinomas that display differentiation of the neoplastic epithelium towards squamous cells …

Starfysh integrates spatial transcriptomic and histologic data to reveal heterogeneous tumor–immune hubs

S He, Y Jin, A Nazaret, L Shi, X Chen… - Nature …, 2024 - nature.com
Spatially resolved gene expression profiling provides insight into tissue organization and
cell–cell crosstalk; however, sequencing-based spatial transcriptomics (ST) lacks single-cell …

Molecular characterization and prospective evaluation of pathologic response and outcomes with neoadjuvant therapy in metaplastic triple-negative breast cancer

C Yam, N Abuhadra, R Sun, BE Adrada, QQ Ding… - Clinical Cancer …, 2022 - AACR
Abstract Purpose: Metaplastic breast cancer (MpBC) is a rare subtype of breast cancer that
is commonly triple-negative and poorly responsive to neoadjuvant therapy in retrospective …

pyComBat, a Python tool for batch effects correction in high-throughput molecular data using empirical Bayes methods

A Behdenna, M Colange, J Haziza, A Gema, G Appé… - BMC …, 2023 - Springer
Background Variability in datasets is not only the product of biological processes: they are
also the product of technical biases. ComBat and ComBat-Seq are among the most widely …

SPARC in cancer‐associated fibroblasts is an independent poor prognostic factor in non‐metastatic triple‐negative breast cancer and exhibits pro‐tumor activity

LB Alcaraz, A Mallavialle, C Mollevi… - … Journal of Cancer, 2023 - Wiley Online Library
Triple‐negative breast cancer (TNBC) is the most aggressive breast cancer subtype and
lacks specific targeted therapeutic agents. The current mechanistic evidence from cell …

Epithelial mesenchymal transition and immune response in metaplastic breast carcinoma

S González-Martínez, B Pérez-Mies, D Pizarro… - International Journal of …, 2021 - mdpi.com
Metaplastic breast carcinoma (MBC) is a heterogeneous group of infrequent triple negative
(TN) invasive carcinomas with poor prognosis. MBCs have a different clinical behavior from …

[HTML][HTML] A 9-kDa matricellular SPARC fragment released by cathepsin D exhibits pro-tumor activity in the triple-negative breast cancer microenvironment

LB Alcaraz, A Mallavialle, T David, D Derocq… - Theranostics, 2021 - ncbi.nlm.nih.gov
Rationale: Alternative therapeutic strategies based on tumor-specific molecular targets are
urgently needed for triple-negative breast cancer (TNBC). The protease cathepsin D (cath …

A multi-objective optimization approach for the identification of cancer biomarkers from RNA-seq data

V Coleto-Alcudia, MA Vega-Rodríguez - Expert Systems with Applications, 2022 - Elsevier
Identification of biomarkers is essential for the diagnosis and prognosis of certain diseases,
like cancer. Gene selection purpose is finding the minimum number of genes that can …