Immunosignature Screening for Multiple Cancer Subtypes Based on Expression Rule

Frontiers in Bioengineering and Biotechnology

YunHua Zhang¹  XiaoYong Pan³  Tao Zeng⁵  Yu-Dong Cai⁶  Yu-Hang Zhang⁷  Tao Huang⁷  Lei Chen⁸ 

[1] Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, Hefei, China;College of Information Engineering, Shanghai Maritime University, Shanghai, China;IDLab, Department for Electronics and Information Systems, Ghent University, Ghent, Belgium;Key Laboratory of System Control and Information Processing, Ministry of Education of China, Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Shanghai, China;Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China;School of Life Sciences, Shanghai University, Shanghai, China;Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China;Shanghai Key Laboratory of Pure Mathematics and Mathematical Practice (PMMP), East China Normal University, Shanghai, China;

关键词: cancer subtype;    expression rule;    immunosignature;    multi-class classification;    feature selection;   

DOI  :  10.3389/fbioe.2019.00370

来源: DOAJ

【 摘 要 】

Liquid biopsy (i.e., fluid biopsy) involves a series of clinical examination approaches. Monitoring of cancer immunological status by the “immunosignature” of patients presents a novel method for tumor-associated liquid biopsy. The major work content and the core technological difficulties for the monitoring of cancer immunosignature are the recognition of cancer-related immune-activating antigens by high-throughput screening approaches. Currently, one key task of immunosignature-based liquid biopsy is the qualitative and quantitative identification of typical tumor-specific antigens. In this study, we reused two sets of peptide microarray data that detected the expression level of potential antigenic peptides derived from tumor tissues to avoid the detection differences induced by chip platforms. Several machine learning algorithms were applied on these two sets. First, the Monte Carlo Feature Selection (MCFS) method was used to analyze features in two sets. A feature list was obtained according to the MCFS results on each set. Second, incremental feature selection method incorporating one classification algorithm (support vector machine or random forest) followed to extract optimal features and construct optimal classifiers. On the other hand, the repeated incremental pruning to produce error reduction, a rule learning algorithm, was applied on key features yielded by the MCFS method to extract quantitative rules for accurate cancer immune monitoring and pathologic diagnosis. Finally, obtained key features and quantitative rules were extensively analyzed.

【 授权许可】

Unknown