DATE: September 17, 2019
TIME: 9:00am PDT
Spatial Transcriptomics (ST) technology reveals gene expression from up to one thousand spots across a tissue section. In this webinar, Dr. Hanna Eriksson and Kim Thrane from Karolinska Institute will present the workflow of ST and show how they adapted the protocol for lymph node metastasis of cutaneous malignant melanoma (CMM). By exploring the spatial gene expression data from four lymph node metastasis, they confirmed the anticipated inter- and intratumoral heterogeneity as well as identify a shared gene expression profile in lymphoid tissue. ST is believed to be a valuable tool for a better understanding of tumor progression and responses to treatment. Kim will discuss: Spatial Transcriptomics - Bridging histology and RNA-seq The Spatial Transcriptomics (ST) technology provides transcriptome-wide RNA-seq data from hundreds of 100µm-sized spots within a tissue section. In this presentation I will go through the principles of the method, describe the tissue optimization procedure and show examples on data visualization. I will also talk about how Spatial Transcriptomics has been further developed by 10x genomics to become Visium, with increased sensitivity and higher spatial resolution. Hanna will discuss: Exploring genetic heterogeneity in Stage III Cutaneous Malignant Melanoma The prognosis in melanoma differ markedly within stage groups and melanoma is one of the most immunogenic and genetically heterogenous of all cancers. The ST technology based on melanoma lymph node biopsies has successfully generated sequencing data of transcriptomes from over 2,200 tissue domains. By using a strategy for deconvolution along with traditional approaches for dimensionality reduction of transcriptome-wide data, the transcriptional landscape within the tissue was visualized and gene expression profiles linked to histological entities were identified. Our unsupervised data demonstrated a more complex spatial intratumoral composition. By applying the ST technology to generate gene expression profiles, a new landscape of the melanoma metastases becomes evident. This should inspire further analyses to understand the multiple components of tumor progression and therapy outcome in a spatial context.
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