Breast Cancer Spatial Transcriptome Analysis

Spatial transcriptome analysis merges transcriptomics with spatial information, enabling the mapping of gene expression within tissue architecture. In breast cancer, this approach reveals how cell arrangement affects tumor biology and progression. Alfa Cytology offers a complete suite of spatial transcriptome analysis services tailored for breast cancer research, including data generation, analysis, and interpretation.

Introduction of Spatial Transcriptome

As the basic unit of the body, cells cooperate with the microenvironment at a specific spatial location to exert their unique biological functions. Therefore, spatial location information is particularly important for the study and understanding of the mechanisms of cell biology, tumor biology, and other disciplines. Breast cancer (BC) is currently the most commonly diagnosed malignancy, and metastasis remains the leading cause of BC death. However, the dynamics during the evolution of communication are poorly understood. Spatial transcriptomics can combine microscopic imaging and sequencing technology to obtain gene expression data while retaining the spatial position information of samples to the greatest extent. It is a technology that can preserve the spatial position of tissues and simultaneously analyze the transcriptome information of tissue slices. Spatial transcriptome technology was rated as one of the top 7 annual technologies by nature in 2020.

Fig.1 Subsequent steps in breast cancer tumorigenesis, from ductal hyperplasia to metastasis formation. (Özkan H, et al., 2022)

Our Services

Alfa Cytology can provide you with BC spatial transcriptome analysis services. Spatial transcriptome sequencing technology can solve the problem that tissue sequencing makes it difficult to distinguish the gene expression of different cells, and single-cell transcriptome cannot determine the expression of the original location of the cell. Our service process is as follows:

• After the sample is frozen, the Optimal Cutting Temperature (OCT) compound is used for tissue embedding, and position information labeling is required.
• Secondly, according to the research purpose, after BC frozen section preparation, some sections were selected for RNA quality inspection.
• If the RNA quality inspection is qualified, the permeabilization experiment will be carried out-the permeabilization time will be explored, and the experimental conditions of the permeabilization in the follow-up formal experiment will be determined according to the quality and integrity of the RNA release.
• Will continue to complete formal frozen section preparation, formaldehyde fixation, tissue permeabilization, HE staining, microscope photography, and imaging.
• Then attach the tissue section to the capture area on the slide containing the RNA-binding capture probe, and fix and permeabilize it to release the mRNA in the cells and bind to the corresponding capture probe.
• The captured RNA was used as a template for cDNA synthesis and library construction.
• The prepared library was sequenced on the DNBSEQ platform.

Application Fields

Advantages of Our Services

• Rich project experience
• Frontier hotspots and customized analysis services
• Professional team and high-quality service

Alfa Cytology is a leading global CRO company. Our complete, optimized, and easy-to-operate workflows provide you with fast, accurate, and reproducible results to help you achieve your research goals. We provide personalized, innovative, complete sequencing service solutions, if you are interested in learning more about our BC multi-omic analysis services, please feel free to contact us. Our professional and patient staff will get in touch with you as soon as possible.