Multi-omics Data Analyses Construct TME and Identify the Immune-Related Prognosis Signatures in Human LUAD

Abstract

Lung cancer has been the focus of attention for many researchers in recent years for the leading contribution to cancer-related death worldwide, in which lung adenocarcinoma (LUAD) is the most common histological type. However, the potential mechanism behind LUAD initiation and progression remains unclear. Aiming to dissect the tumor microenvironment of LUAD and to discover more informative prognosis signatures, we investigated the immune-related differences in three types of genetic or epigenetic characteristics (expression status, somatic mutation, and DNA methylation) and considered the potential roles that these alterations have in the immune response and both the immune-related metabolic and neural systems by analyzing the multi-omics data from The Cancer Genome Atlas (TCGA) portal. Additionally, a four-step strategy based on lasso regression and Cox regression was used to construct the prognostic prediction model. For the prognostic predictions on the independent test set, the performance of the trained models (average concordance index [C-index] = 0.839) is satisfied, with average 1-year, 3-year, and 5-year areas under the curve (AUCs) equal to 0.796, 0.786, and 0.777. Finally, the overall model was constructed based on all samples, which comprised 27 variables and achieved a high degree of accuracy on the 1-year (AUC = 0.861), 3-year (AUC = 0.850), and 5-year (AUC = 0.916) survival predictions.

Association of clock-like mutational signature with immune checkpoint inhibitor outcome in patients with melanoma and NSCLC

“…Immune phenotypes in determining the prognosis of various types of cancers were increasingly recognized 23 , 24 , 25 , 26 and highlighted baseline levels of tumor-infiltrating lymphocytes (e.g., CD8 + , CD3 + T cells, etc.) markedly correlated with the likelihood of immune response and survival outcome.…”

CD74 Correlated With Malignancies and Immune Microenvironment in Gliomas

“…Immune microenvironment was implicated to play an important role in cancer progression ( Quail and Joyce, 2017 ; Zhang et al, 2020a ; Zhang et al, 2020b ; Wang et al, 2020 ). CD74 was the receptor of MIF and the CD74-MIF signaling pathway regulated the activity of macrophages and other immune cells ( Borghese and Clanchy, 2011 ; Figueiredo et al, 2018 ).…”

Multi-Omics Data Analyses Construct a Six Immune-Related Genes Prognostic Model for Cervical Cancer in Tumor Microenvironment

“…Numerous previous research studies concentrated mainly on the RNA-seq profiles, which are characterized by some disadvantages in comprehensively clarifying the potential mechanisms involved ( Sun et al, 2019 ; Liu et al, 2020 ; Ma J. et al, 2020 ; Zhao et al, 2020 ; Yang et al, 2021 ). Many researchers have recently concentrated on investigating prognostic factors by integrative multi-omics data analysis, which yielded more powerful results and provided a more comprehensive view of the TME ( Gu et al, 2020 ; Ma H. et al, 2020 ; Yan et al, 2020 ; Zhang Y. et al, 2020 ; Xu et al, 2021 ). Nevertheless, few multi-omics studies have investigated the TME of CC.…”