Evaluation of immune infiltrating of thyroid cancer based on the intrinsic correlation between pair-wise immune genes

Abstract

IntroductionUnlike most mutation-driven cancers, thyroid cancer is thought to be highly dependent on changes in human hormone levels. It has become research hotspot using the change of gene expression level as a detection and diagnostic marker. The internal relationship between two genes and disease development is used to avoid the instability caused by single gene fluctuation.AimIt is possible to achieve early diagnosis in thyroid cancer during tumorigenesis and recurrence using IGPS (immune gene pairs). MethodsWe extracted thyroid cancer data from The Cancer Genome Atlas (TCGA), using CIBERSORT algorithm to infiltrate out 22 immune cells types. We screened out IGPS that differ significantly between different groups, then used LinearSVC model to learn and screen features, combined with deep learning neural network model to predict benign and malignant cancer as well as patients at different groups. Key findingsThere are significant differences of immune cell ratio in tumor stages and relapse samples. We screen out 42 and 64 IGPS for in normal-tumor and non-relapsed groups respectively, for example ASCC3-MAP3K7 and ATF2-SOCS5, have significant correlation in IGPS expression. Then we use the IGPS to train the tumor diagnostic classifier, obtain average AUC are both 0.99 after ten times cross-validation. SignificanceThe IGPS gives us new insight to explore immune cell infiltration of thyroid cancer, deep learning model can be further used in early diagnosis of thyroid cancer and estimation of the risk of recurrence.