A comprehensive understanding of tumor heterogeneity, tumor microenvironment and the mechanisms of drug resistance is fundamental to advancing breast cancer research. While single-cell RNA sequencing has resolved the issue of "temporal dynamic expression" of genes at the single-cell level, the lack of spatial information still prevents us from gaining a comprehensive understanding of breast cancer. The introduction and application of spatial transcriptomics addresses this limitation. As the annual technical method of 2020, spatial transcriptomics preserves the spatial location of tissues and resolves RNA-seq data to help localize and differentiate the active expression of functional genes within a specific tissue region, enabling the study of spatial location attributes of gene locations and cellular tissue environments. In the context of breast cancer, spatial transcriptomics can assist in the identification of novel breast cancer subtypes and spatially discriminative features that show promise for individualized precise treatment. This article summarized the key technical approaches, recent advances in spatial transcriptomics and its applications in breast cancer, and discusses the limitations of current spatial transcriptomics methods and the prospects for future development, with a view to advancing the application of this technology in clinical practice.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11693744PMC
http://dx.doi.org/10.3389/fimmu.2024.1499301DOI Listing

Publication Analysis

Top Keywords

spatial transcriptomics
24
breast cancer
24
spatial
9
tumor heterogeneity
8
comprehensive understanding
8
spatial location
8
breast
6
cancer
6
transcriptomics
5
transcriptomics breast
4

Similar Publications

Background And Aims: Oncogenic KRAS mutations are present in approximately 90% of pancreatic ductal adenocarcinoma (PDAC). However, Kras mutation alone is insufficient to transform precancerous cells into metastatic PDAC. This study investigates how KRAS-mutated epithelial cells acquire the capacity to escape senescence or even immune clearance, thereby progressing to advanced PDAC.

View Article and Find Full Text PDF

Predicting long-term recurrence of disease in breast cancer (BC) patients remains a significant challenge for patients with early stage disease who are at low to intermediate risk of relapse as determined using current clinical tools. Prognostic assays which utilize bulk transcriptomics ignore the spatial context of the cellular material and are, therefore, of limited value in the development of mechanistic models. In this study, Fourier-transform infrared (FTIR) chemical images of BC tissue were used to train deep learning models to predict future disease recurrence.

View Article and Find Full Text PDF

Multiplexed transcriptomic analyzes of the plant embryonic hourglass.

Nat Commun

January 2025

School of Integrative Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, USA.

Zoologists have adduced morphological convergence among embryonic stages of closely related taxa, which has been called the phylotypic stage of embryogenesis. Transcriptomic analyzes reveal an hourglass pattern of gene expression during plant and animal embryogenesis, characterized by the accumulation of evolutionarily older and conserved transcripts during mid-embryogenesis, whereas younger less-conserved transcripts predominate at earlier and later embryonic stages. In contrast, comparisons of embryonic gene expression among different animal phyla describe an inverse hourglass pattern, where expression is correlated during early and late stages but not during mid-embryo development.

View Article and Find Full Text PDF

A constitutive interferon-high immunophenotype defines response to immunotherapy in colorectal cancer.

Cancer Cell

January 2025

Cancer Systems Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Centre for Cancer Evolution, Bart's Cancer Institute, Queen Mary University London, London EC1M 6AU, UK. Electronic address:

Fewer than 50% of metastatic deficient mismatch repair (dMMR) colorectal cancer (CRC) patients respond to immune checkpoint inhibition (ICI). Identifying and expanding this patient population remains a pressing clinical need. Here, we report that an interferon-high immunophenotype locally enriched in cytotoxic lymphocytes and antigen-presenting macrophages is required for response.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!