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Saturday, December 4 • 10:30am - 10:40am
OP 39 - Quantification and visualization of the tumor microenvironment heterogeneity from spatial transcriptomic experiments

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OP-39
Quantification and visualization of the tumor microenvironment heterogeneity from spatial transcriptomic experiments

Presenting Author: Oscar Ospina, Moffitt Cancer Center

Co-Author(s):
Alex Soupir, Moffitt Cancer Center
Christopher Wilson, Moffitt Cancer Center
Anders Berglund, Moffitt Cancer Center
Inna Smalley, Moffitt Cancer Center
Kenneth Tsai, Moffitt Cancer Center

Abstract: Spatially-resolved transcriptomics (ST) allows for a better assessment of tissue structure and function. In the context of cancer research, ST promises to deepen our understanding of the tumor microenvironment and lead to improved cancer prognosis and therapies. We present spatialGE, an R package for the visualization and quantification of gene expression heterogeneity from ST experiments. Our software has adapted geostatistical methods for the 1) generation of high-resolution gene expression surfaces via spatial interpolation and 2) the quantification of spatial heterogeneity measures that can be compared against clinical information (e.g., patient survival). In addition, spatialGE includes 3) cell deconvolution methods at the spot level; 4) a fast spatially-informed clustering approach (STClust); and 5) a new data structure that allows storage and analysis of multiple ST samples simultaneously. To demonstrate the utility of spatialGE, we used a publicly available ST data set from stage III melanoma lymph node biopsies [Thrane et al (2018); Cancer Research]. Spatial variation in gene expression was observed in a number of genes, including key cancer and immune-related genes such as PMEL and IGLL5. After applying deconvolution methods (e.g., xCell, ESTIMATE), B cells showed high spatial variation across the sampled locations. Moreover, tissue sections showing the highest non-uniform spatial distributions of B cell (as quantified by Moran’s I and Geary’s C) were extracted from a patient with the highest survival time. These results provide support to the hypothesis that spatial heterogeneity in the tumor microenvironment is a potential predictor of patient outcomes.


Presenters
avatar for Oscar Ospina

Oscar Ospina

Moffitt Cancer Center


Saturday December 4, 2021 10:30am - 10:40am MST
Ballroom Salon 1