Heterogeneity within molecular subtypes of breast cancer DOI
Kevin M. Turner, Syn Kok Yeo, Tammy M. Holm

et al.

AJP Cell Physiology, Journal Year: 2021, Volume and Issue: 321(2), P. C343 - C354

Published: June 30, 2021

Breast cancer is the quintessential example of how molecular characterization tumor biology guides therapeutic decisions. From discovery estrogen receptor to current clinical profiles evolving single-cell analytics, and compartmentalization breast into divergent subtypes clear. However, competing with this model recognition intratumoral heterogeneity, which acknowledges possibility that multiple different exist within a single tumor. Intratumoral heterogeneity driven by both intrinsic effects cells themselves as well extrinsic from surrounding microenvironment. There emerging evidence these are not static; rather, plasticity between possible. Interconversion seemingly drives progression, metastases, treatment resistance. Therapeutic strategies must, therefore, contend changing phenotypes in an individual patient's Identifying targetable drivers may improve durability disease progression.

Language: Английский

Novel tumor-associated macrophage populations and subpopulations by single cell RNA sequencing DOI Creative Commons
Juanjuan Wang,

Ningning Zhu,

Lei Su

et al.

Frontiers in Immunology, Journal Year: 2024, Volume and Issue: 14

Published: Jan. 29, 2024

Tumor-associated macrophages (TAMs) are present in almost all solid tumor tissues. 16They play critical roles immune regulation, angiogenesis, stem cell activation, invasion and metastasis, resistance to therapy. However, it is unclear how TAMs perform these functions. With the application of single-cell RNA sequencing (scRNA-seq), has become possible identify TAM subpopulations associated with distinct In this review, we discuss four novel tumors based on core gene signatures by scRNA-seq, including FCN1 + , SPP1 C1Q CCL18 TAMs. Functional enrichment expression scRNA-seq data from different tissues found that may induce inflammation; potentially involved cancer whereas participate regulation suppression; And cells terminal immunosuppressive not only have a stronger function but also enhance metastasis. can be further divided into populations Meanwhile, will emerging evidence highlighting separating macrophage there exist potential disconnects between types identified their actual function.

Language: Английский

Citations

23
A comprehensive single-cell breast tumor atlas defines epithelial and immune heterogeneity and interactions predicting anti-PD-1 therapy response DOI Creative Commons

Lily Xu,

Kaitlyn Saunders,

Shao-Po Huang

et al.

Cell Reports Medicine, Journal Year: 2024, Volume and Issue: 5(5), P. 101511 - 101511

Published: April 12, 2024

We present an integrated single-cell RNA sequencing atlas of the primary breast tumor microenvironment (TME) containing 236,363 cells from 119 biopsy samples across eight datasets. In this study, we leverage resource for multiple analyses immune and cancer epithelial cell heterogeneity. define natural killer (NK) heterogeneity through six subsets in TME. Because NK correlates with heterogeneity, characterize at level single-gene expression, molecular subtype, 10 categories reflecting intratumoral transcriptional develop InteractPrint, which considers how influences cancer-immune interactions. use T InteractPrint to predict response checkpoint inhibition (ICI) two clinical trials testing neoadjuvant anti-PD-1 therapy. was predictive both versus PD-L1 (AUC = 0.82, 0.83 vs. 0.50, 0.72). This enables additional high-resolution investigations

Language: Английский

Citations

16
edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets DOI Creative Commons
Yunshun Chen, Lizhong Chen, Aaron T. L. Lun

et al.

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(2)

Published: Jan. 11, 2025

Abstract edgeR is an R/Bioconductor software package for differential analyses of sequencing data in the form read counts genes or genomic features. Over past 15 years, has been a popular choice statistical analysis from technologies such as RNA-seq ChIP-seq. pioneered use negative binomial distribution to model count with replicates and generalized linear models analyze complex experimental designs. implements empirical Bayes moderation methods allow reliable inference when number small. This article announces version 4, which includes new developments across range application areas. Infrastructure improvements include support fractional counts, implementation fitting C treatment quasi-likelihood pipeline that improves accuracy small counts. The revised functionality methylation analysis, transcript expression, exon usage, testing relative fold-change threshold pathway analysis. reviews framework computational edgeR, briefly summarizing all existing features functionalities but special attention those have not described previously.

Language: Английский

Citations

10
Neutrophils physically interact with tumor cells to form a signaling niche promoting breast cancer aggressiveness DOI

Sandra Camargo,

Ori Moskowitz,

Amir Giladi

et al.

Nature Cancer, Journal Year: 2025, Volume and Issue: unknown

Published: March 7, 2025

Language: Английский

Citations

2
Heterogeneity within molecular subtypes of breast cancer DOI
Kevin M. Turner, Syn Kok Yeo, Tammy M. Holm

et al.

AJP Cell Physiology, Journal Year: 2021, Volume and Issue: 321(2), P. C343 - C354

Published: June 30, 2021

Breast cancer is the quintessential example of how molecular characterization tumor biology guides therapeutic decisions. From discovery estrogen receptor to current clinical profiles evolving single-cell analytics, and compartmentalization breast into divergent subtypes clear. However, competing with this model recognition intratumoral heterogeneity, which acknowledges possibility that multiple different exist within a single tumor. Intratumoral heterogeneity driven by both intrinsic effects cells themselves as well extrinsic from surrounding microenvironment. There emerging evidence these are not static; rather, plasticity between possible. Interconversion seemingly drives progression, metastases, treatment resistance. Therapeutic strategies must, therefore, contend changing phenotypes in an individual patient's Identifying targetable drivers may improve durability disease progression.

Language: Английский

Citations

99