In this study, we systematically analyzed the association between TP53 status and immune-related phenotypes in patients with LUAD. A TP53-related IRM index was constructed. It was derived from the TCGA cohort and validated in the meta-GEO and Nanjing cohorts. It was found to be remarkably associated with prognosis. The prognostic value of the 6-gene IRM index was independent of multiple known strong prognostic factors. Furthermore, the IRM index allowed us to divide patients with LUAD into 2 subgroups with different immune-related phenotypes. Consequently, we integrated the IRM with multiple clinical factors into a nomogram with robust OS prediction.
Through multi-functional enrichment analysis of DEGs, we observed obvious enrichment in the humoral immune response. The consistent pathway enrichment analysis results were further verified in selected IRDEGs. Furthermore, 6 IRM-related genes were found to participate in multiple immunosuppression-related pathways. Afterward, we divided the patients with LUAD into 2 subgroups with different prognosis and immune-related phenotypes. In all 3 cohorts, high-index patients showed worse survival than low-index patients. Meanwhile, the IRM index was positively correlated with the expression of several important immune checkpoints. In previous research, NSCLC progression was positively associated with the increased expression of T cell exhaustion markers, such as PD-1, TIM3, and CTLA416, which is consistent with the results of our research.
CRHR2 belongs to the G-protein coupled receptor superfamily, regulating corticotropin-releasing hormone to perform biological functions17, which widely expressed in the gastrointestinal tract, lung and skeletal muscle18. CRHR2 stimulates intracellular cAMP pathway, including activation of nuclear factor-kB and expression of TNF-β in T cells19,20. BPIFB1 and BPIFB2 belong to the bactericidal/permeability-increasing-fold-containing family21. BPIFB1 and BPIFB2 protein are most highly expressed in the trachea and lung22 and bind to the Gram-negative bacteria and exert antibacterial function23,24. Moreover, it has been reported that BPIFB1 is abnormally expressed in tumors, which suggests that it plays a role in tumor development25. INHA encodes a member of the TGF-β superfamily of proteins (RefSeq, Aug 2016), which perform the functions of activated cytokine and hormone26,27. SSTR5 is a predominant component of somatostatin receptor subtypes, which regulates inhibitory effects on endocrine and exocrine secretions28. SSTR5 has a significant regulating-inflammatory effect via regulating somatostatin, which demonstrated in different animal models29,30. SCGB3A1 belong to secretoglobin gene superfamily, which are cytokine-like small molecular weight secreted proteins and predominantly expressed in lung airway epithelial cells31. Secretoglobins are thought to be involved in immunomodulatory32. Moreover, SCGB3A1 has been reported as a tumor suppressor in various human tumors including breast, prostate, lung, and pancreatic carcinomas33,34.
In chronic diseases, T cells malfunction due to T cell exhaustion, which increases the expression of inhibitory receptors incorporating PD-1, LAG3, TIM3, CTLA4, and TIGIT35–39, resulting in fewer cytokines and loss of antitumor capabilities. The limited efficacy of immunotherapy may be due to the production of dysfunctional T cells in the TME40. Therefore, regulators that reverse the state of T cell dysfunction are the focus of current research. For example, tertiary lymphoid structure immune activity dysfunction is reversed and antitumor capabilities are enhanced after treatment with anti-PD-1/PD-L1 and anti-CTLA-4 immune checkpoint inhibitors in humans and mice41–44. The PD-L1/PD-1 axis is an important regulatory pathway of T cell exhaustion in tumors. DD1α expression induced by p53, which is encoded by TP53, has been shown to upregulate PD-1 and PD-L1, as cancer cells respond to genotoxic stress and DNA damage, which then promotes the gradual priming of immune surveillance45. This finding clarified the relationship between p53 and immune checkpoint inhibitors, which may indicate the intrinsic molecular mechanism of the relationship between the IRM index and the expression of immune checkpoints. PD-L1 has abundant expression in cancer cells and the tumor extracellular matrix, and blocking the PD-L1/PD-1 axis can enhance the antitumor capabilities of T cells46. In our study, the IRM index was positively correlated with the expression of immune checkpoints, which shows that as the IRM index grows, T cells are exhausted, and their antitumor abilities decrease. This explains the poor prognosis of high-index patients with LUAD. It can be speculated that immunotherapies that block the pathways that suppress tumor immune responses for patients with LUAD in the high-index group may increase the presentation of cancer-associated antigens, resulting in the recovery of the immune response of CD8 + T cells47, which may then result in better immunotherapy effects.
In the immune infiltration analysis between the high- and low-index patients, the high-index patients with LUAD had remarkably higher proportions of neutrophils and resting memory CD4 + T cells and lower proportions of memory B cells and Tregs. Memory resting CD4 + T cells can be further differentiated into multiple cell subpopulations and confer different functions, including blocking CD8 + T cell activation and NK cell killing and suppressing the immune response to autoantigens and exogenous antigens48. In human NSCLC, neutrophils play a key role in tumor immunity49. In mice, neutrophils infiltrating tumors can either promote carcinogenesis by supporting tumor-related inflammation, angiogenesis, and metastasis and inhibiting T cell activation or restrict tumor growth through the expression of antitumor and cytotoxic mediators50. Nevertheless, because the tumor is in an irreversible continuous chronic inflammatory state, suppressive neutrophils are constantly mobilized and become the dominant subpopulation of neutrophils51, which may suppress the immune response and promote malignant progression. In our study, the high-index patients with LUAD had significantly higher proportions of neutrophils and resting memory CD4 + T cells, restricting the function of CD8 + T cells and NK cells in the tumor development process, resulting in malignant tumor progression and worse OS. It is reasonable to speculate that the high-index patients with LUAD may have improved CD8 + T cell function and receive better efficacy by using an immune checkpoint inhibitor that blocks the PD-1/PD-L1 axis.
Tregs are an inhibitory subpopulation of CD4 + T cells. Cancer-associated fibroblasts in the extracellular matrix express COX-2, which promotes PGE2 secretion to induce immunosuppressive FOXP3 + Tregs52, which then accumulate in primary tumor tissues and the peripheral blood to promote immune evasion46. Progressing tumors can inhibit CD8 + T cells through several approaches, including Tregs, which can directly suppress the antitumor functions of CD8 + T cells53. The immunosuppressive state of the high-index patients with LUAD may not through the suppression of CD8 + T cells immune response by Tregs. Tumor-infiltrating B cells are a key component of the TME. B cells and CD4 + T cells together form tertiary lymphoid structures, which are related to better outcomes54. This is consistent with the results of our study, as low-index patients had better prognoses. A variety of cytokines, including tumor necrosis factor (TNF), interleukin (IL)-2, IL-6, and interferon gamma (IFNγ), which are secreted by B cells, could assist B cells to recruit other immune effector cells and activate immune responses, including T cells. Memory B cells may play a role in inhibiting antigen presentation, thereby driving the expansion of memory and naive T cell responses. Memory B cells and plasma cells show similar characteristics of facilitating an acquired immune response, which also contributes to an effective T cell response after immune checkpoint inhibitor therapy55. The high-index patients with LUAD had lower proportions of memory B cells, indicating that the suppression of T cell antitumor functions in such patients may be due to the decline of memory B cell antigen presentation functions, which is related to worse OS.
Our research supplies a novel angle regarding LUAD immune microenvironment groupings and immunotherapy responses. However, since our study is a retrospective study, it has limitations and needs to be further validated by prospective studies. Furthermore, mechanistic studies of the IRM index-related genes and immune-infiltrating cells need to be implemented to explain their clinical application. In subsequent research, we will focus on single-cell transcriptome studies of immune-infiltrating cells in patients with LUAD with different IRM indexes.
In conclusion, the IRM index is a robust clinical biomarker that can assign patients with LUAD to subgroups with significantly different prognoses and immune-related phenotypes, which may explain the molecular mechanism of different prognoses from the perspective of immunology.