Bioinformatics Seminar
Time: 11AM
Venue: Davis Auditorium and Online
31 October 2023
Exploring breast cancer microenvironment using single cell and spatial transcriptomics
Jinming ChengWEHI Bioinformatics
Breast cancer is the most common cancer and the leading cause of cancer death in women worldwide. Almost all breast cancers arise from the terminal duct lobular units of the mammary duct system. The surrounding stromal and immune microenvironment of mammary duct plays important roles in breast cancer genesis and development. Fibroblast is the major stromal cell type around mammary duct epithelium and has functions like extracellular matrix formation, tissue repair and immune regulation. In this study, we took advantage of single cell RNA-sequencing to investigate development of normal fibroblast of mouse mammary gland at five different stages (Puberty, Adult, Pregnancy, Lactation and Involution), drug treated fibroblast and cancer associated fibroblast. In addition, imaging-based spatial transcriptomics allows us to investigate cancer cells and surrounding microenvironment cells at single cell resolution preserving the spatial information. One key step is to correctly annotate the cell types of imaging-based spatial data with only hundreds of genes. We compare one manual annotation method and five reference-based annotation methods on imaging-based Xenium data of human HER2+ cancer, ER+ cancer and normal breast to discuss the advantages and disadvantages of all six methods in terms of their computational performances.