Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

mySORT: A Web Framework by using Deconvolution Approach to Estimating Immune Cell Composition from Complex Tissues

Version 1 : Received: 12 November 2020 / Approved: 13 November 2020 / Online: 13 November 2020 (14:18:40 CET)

How to cite: Chen, S.; Yu, B.; Kuo, W.; Lin, Y.; Su, S.; Lu, I.; Lin, C. mySORT: A Web Framework by using Deconvolution Approach to Estimating Immune Cell Composition from Complex Tissues. Preprints 2020, 2020110385 (doi: 10.20944/preprints202011.0385.v1). Chen, S.; Yu, B.; Kuo, W.; Lin, Y.; Su, S.; Lu, I.; Lin, C. mySORT: A Web Framework by using Deconvolution Approach to Estimating Immune Cell Composition from Complex Tissues. Preprints 2020, 2020110385 (doi: 10.20944/preprints202011.0385.v1).

Abstract

Cancer immunotherapy reaches a remarkable achievement in various cancer types and brings new possibilities to improve cancer patients’ long-term survival. However, outcomes vary from case to case, and the present protocol benefits a small fraction of patients. One notable factor is the tumor microenvironment, especially the immune cell components, that may reflect the immune response's status quo on site. Thus, understanding the content of infiltrating immune cells in tumors is not only for research interesting but also a crucial subject toward precision medicine. We implement an algorithm for resolving relative proportions of twenty-one immune cell subclasses from a human tissue profiled transcriptome by microarray technology to reach the goal above. By selecting gene features and then adopting ?-Support Vector Regression, we can construct a deconvolution model and resolve the immune cell context. The excellent consistency between the estimated values and the correct immune-cell composition further demonstrates this approach provides a more natural alternative to revealing samples' immune cell content and reliable results like recent single-cell technologies. Based on this algorithm, the web-based deconvolution tool implemented named mySORT provides a user-friendly interface for estimating the immune cell content by uploading gene expression profiling. We also present comprehensive visualization 2D/3D plots in mySORT so that users can easily make a comparison between different samples. Finally, we synthesized pseudo-bulk expression data from single-cell transcriptomic datasets of 17 melanoma and 16 head and neck cancer patients. The deconvolution results of microarray-based data in the previous study and synthetic pseudo-bulk data all proved the excellent performance of mySORT. We believe that mySORT can help researchers in all fields easily understand complex immune microenvironment. The website of mySORT is freely accessible on https://symbiosis.iis.sinica.edu.tw/mySORT/.

Subject Areas

Cancer; Immunotherapy; Deconvolution; Alpha diversity; Beta diversity; Precision medicine; Microenvironment; Single-cell RNA sequencing

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