CYFIP2 serves as a prognostic biomarker and correlates with tumor immune microenvironment in human cancers

The occurrence and development of malignancies may be affected by many factors, such as genetics, living environment and habits. At present, the efficacy of tumor treatment is still far from satisfactory, probably because the occurrence of tumor is linked to genetic variants [1]. In-depth knowledge of the full range of functions of a gene is meaningful to help us better understand the mechanism of tumorigenesis and promote personalized treatment [2]. With the rapid development of basic research and clinical medicine, people’s understanding of the etiology and pathophysiological processes of diseases has been deepened, and more and more biomarkers involved in tumorigenesis, development and influencing prognosis have been discovered one after another, and play an important role in early diagnosis of tumors, evaluation of therapeutic efficacy and prediction of prognosis [3]. Sensitive and specific biomarkers are especially necessary in clinical precision medicine [4]. Biomarkers can also be used as potential targets for drug design. The discovery of powerful biomarkers and new therapeutic targets is critical to the development of the next generation of precision medicine. During past years, the improvement of high-throughput sequencing based cancer atlas initiatives and omics technologies has brought cancer research into a new era [5]. Computational or bioinformatics approaches have made it more efficient to investigate the ability and function of target molecules as well as their interactions, thereby contributing to a comprehensive understanding of cancer initiation and progression [6].

Lung adenocarcinoma (LUAD) is now the most common histological subtype of primary lung cancer accounting for greater than 40% of cases [7]. Despite achievements in the development of new approaches in the treatment of LUAD, unfortunately, LUAD is still one of the most aggressive and rapidly fatal tumor types with overall survival less than 5 years [8]. Thus, it is important to find stable and reliable biomarkers for LUAD to identify patients with poor prognosis and provide more aggressive treatment [9].

Study identified Cytoplasmic FMR Interacting Protein 2 (CYFIP2) as a p53-inducible gene which was a direct p53 target gene that may be part of a redundant network of genes responsible for p53-dependent apoptosis [10]. During the past decades, accumulating evidence has demonstrated the role of CYFIP2 in different diseases. For obesity and related metabolic disorders, data emphasized the potential of CYFIP2 as a pharmacotherapeutic target for treating obesity and other metabolic disorder [11]. Moreover, CYFIP protein family, including CYFIP1 and CYFIP2, is involved in neural development and maturation as well as in different neural disorders, such as intellectual disabilities, autistic spectrum disorders, and Alzheimer’s disease [12]. Recent studies have shown that CYFIP2 is also closely related to tumor initiation and progression. Fox example, NUAK family kinase 2 (NUAK2) may regulate CYFIP2 expression to promote cervical cancer cell proliferation, migration, invasion and epithelial-to-mesenchymal transition [13]. Circulating CYFIP2 was demonstrated to be significantly upregulated in gastric cancer tissues and cell lines and high expression of circulating CYFIP2 was associated with metastasis and poor prognosis of gastric cancer patients [14]. Studies also indicated that CYFIP2 may take part in the vascular endothelial growth factor receptor signaling pathway and the purine ribonucleoside diphosphate metabolic process [15]. However, the comprehensive function and prognostic landscape of CYFIP2 involved in human cancers are still not fully understood. Thus, understanding its mechanisms may be helpful to enhance diagnosis and treatment and may also promote its potential clinical practice.

Our study, for the first time, focused on the comprehensive landscape of CYFIP2 function based on a multi-omics analysis. We first revealed the expression patterns including its expression in normal tissues, cancer tissues and intracellular localization. Then, we evaluated the clinical utility of CYFIP2 by studying its associations with different clinicopathological characteristics and potential role in the diagnosis and prognosis of different cancers. Moreover, we investigated the potential molecular mechanisms of CYFIP2 in the pathogenesis or clinical prognosis of different cancers, especially in LUAD, by performing co-expression gene analysis, protein–protein iteration network analysis, functional enrichment analysis, genetic alterations and DNA methylation analysis. In addition, we uncovered the landscape of CYFIP2 expression in tumor immunity and microenvironment through the correlation analysis of CYFIP2 expression with immune cell infiltration, immune regulators, and immune-related genes (chemokines, chemokines receptors, and MHC genes). The schematic pipeline for this study is plotted at Fig. 1.

CYFIP2, a p53-inducible gene, has been demonstrated by previous studies to be involved in some tumors. Jiao et al. reported CYFIP2 was a novel p53-mediated pro-apoptotic protein whose expression was decreased in gastric cancer and they showed CYFIP2 knockdown promoted proliferation and colony formation, and inhibited apoptosis in gastric cancer cells [29]. Chang’s study revealed that mutational dynamics and genetic variation, as well as aberrant DNA repair, tumor cell cycle control and apoptotic pathways were associated with CYFIP2 in endometrial cancer in the Taiwanese population [30]. Previous studies also showed that CYFIP2 was downregulated in ccRCC patients with an unfavorable survival outcome and might be a potential promising prognostic biomarker associated with immune infiltration, metabolism, and epithelial–mesenchymal transition process in ccRCC [31]. However, the associations between CYFIP2 and different cancers remain inclusive. Besides, the specific mechanisms of CYFIP2 involved in cancer initiation and progression remain to be unclear. The present study first comprehensively uncovered the landscape of CYFIP2 regarding its expression pattern, clinical relevance, genetic alterations, DNA methylation and immune cell infiltration.

We first explored the expression patterns in different levels including normal tissues, cell lines and tumor tissues. Our study demonstrated that CYFIP2 was aberrantly expressed in different cancers. The difference in CYFIP2 expression levels in different tumor types may reflect distinct underlying functions and mechanisms. In addition, CYFIP2 was identified to have the potential for diagnosis of LUAD. We further found that overexpression of CYFIP2 generally predicted good prognosis for patients with tumors, such as LUAD, thymoma, sarcoma, PDAC, clear cell RCC, and BC. In contrast, its highly expression was correlated with poor prognosis in UCEC and ESCC. In addition, a high level of CYFIP2 expression was shown to be related to a favorable prognosis in LUAD with T1&T2 stage, N0 stage, CR & PR diseases. These results suggest that CYFIP2 may serve as a potential biomarker for diagnosis and predicting the prognosis of tumor patients.

Genetic alterations in the key genes have been demonstrated to be highly involved in the initiation and progression of cancer through regulating important signaling pathways that are indispensable for the fundamental intracellular functions including cell growth, survival, invasion, and metastasis [32]. The genetic alteration profiling of CYFIP2 revealed that its mutation is the most important single factors. The impact of mutant subtypes on prognosis and predictive value in LUAD is becoming increasingly understood [33]. Knowledge of genetic alterations will provide more useful information for the diagnosis, treatment and prognosis of cancer.

DNA methylation is a major form of epigenetic modification and is involved in numerous fundamental biological activities through post-transcriptional regulation of gene expression [34]. Aberrant patterns of DNA methylation can lead to the pathogenesis of many diseases including various cancers [35]. Hypermethylation within the promoter region may contribute to silencing or inactivation of tumor suppressor genes in cancer cells [36]. In addition, recent evidence has indicated that DNA methylation has also important roles in the immune system and influence tumor immunotherapy response as DNA methylation is essential for the proper function of B-cell differentiation and mature cells [37]. The present study showed that DNA methylation of CYFIP2 was downregulated in LUAD, which is consistent with the fact that CYFIP2 had a protective role for LUAD patients.

In complex diseases, a specific gene generally plays a coordinating role through its co-expressed and interacting genes. Our results also indicated that CYFIP2 may have a synergistic effect with its co-expressed genes in the prognosis of LUAD. Moreover, our KEGG analysis revealed that CYFIP2-interacting genes were strongly involved in a series of tumor-related and immune-related signaling pathways. For example, CYFIP2-interacting genes were remarkedly linked with non-small cell lung cancer, which was consistent with our present study that CYFIP2 took part in the initiation and progression of LUAD. CYFIP2-interacting genes were also strongly related to Ras signaling, which is a well-studied pathway that is involved in cell proliferation and growth, cell survival and apoptosis, metabolism, and motility and plays an important role in tumor growth and progression [38]. VEGF signaling pathway and EGFR tyrosine kinase inhibitor resistance are two important pathways for the targeted therapy of LUAD [39, 40]. The PI3K/Akt/mTOR pathway has been one of the most altered molecular pathways implicated in both tumorigenesis and the progression of LUAD [41]. Recent evidence also revealed that the PI3K/AKT/mTOR pathway can play a vital role in regulating PD-L1 expression, the abnormal activation of which can contribute to the increased PD-L1 protein translation [42]. In addition, CYFIP2-interacting genes were significantly associated with some immune-related pathways such as chemokine signaling pathway, B cell receptor signaling pathway, and T cell receptor signaling pathway, which play a vital role of tumor immunity and immunotherapy response [43‐45]. These results confirmed that CYFIP2 played an important role in the tumor development and immune microenvironment.

The immune cells within the TME play important roles in tumorigenesis [46]. It has been known that these tumors associated immune cells may possess tumor-antagonizing or tumor-promoting functions [47]. Tumor-infiltrating immune cells as well as other immune components within the TME can shape an immunosuppressive TME that enables cancer cells to evade surveillance of the immune system [48]. Immune cells are important constituents of the tumor stroma. Studies suggested that the innate immune cells as well as adaptive immune cells contribute to tumor progression when present in the TME [47]. Our study showed the correlation analysis between CYFIP2 expression and immune cell infiltration in pan-cancer. We found that several tumor infiltrating immune cells (Act_B cells, Imm_B cells, macrophage cells, Th1 cells, Tfh cells, CD8 + cells, pDC cells, CD4 + cells and Th17 cells) were correlated with the expression of CYFIP2 in cancers using TISIDB. We further found that positive correlation was indicated between CYFIP2 expression and B cell, CD8 + T cell, CD4 + T cell, macrophage, neutrophil, and dendritic cell in LUAD using TIMER. This finding suggests that there is a potential correlation between CYFIP2 and immune infiltration in LUAD.

Besides that, the CYFIP2 expression presented a significantly correlation with most immune regulators, chemokines, chemokine receptors, and MHC genes. Emerging evidence has supported that immune regulators play a crucial part in establishing an immunosuppressive TME, causing NK cell exhausting and tumor immune escaping [49]. Immune checkpoints blockade can reduce immune escape of tumor cells and limits tumor growth. Thus, targeting immune checkpoints has become one of the most important ways of immunotherapy [50]. Chemokines have been recognized as small, secreted proteins with important roles in directing the migration of immune cells, which is essential for initiating and providing an effective anti-tumor immune response [51]. Each chemokine can activate several different receptors, which also play a predominant part in the coordination of cell trafficking in the immune response processes [52]. MHC genes are clusters of genes encoding molecules that are primarily associated with innate and adaptive immune responses and other molecular and biological processes [53]. These results elucidated the underlying mechanisms of CYFIP2 in tumor immunity and its influence on immune related genes.

Cellular immunotherapy is a hot field in medicine today. From cancer to systemic lupus erythematosus, cellular immunotherapy has shown promise. With clinical progress, cellular immunotherapy is expected to play an even greater role in the clinic. In this study, we suggested that CYFIP2 might be a promising therapeutic strategy for tumor immunotherapy. However, the immunotherapeutic mechanism of CYFIP2 have not been well elucidated. Shabani et al. made the following points that CYFIP2 participated in the vascular endothelial growth factor receptor signaling pathway and the purine ribonucleoside diphosphate metabolic process, respectively [15]. Moreover, Zhao et al. found that CYFIP2 was closely related to T-cell CD8 + , T-cell CD4 + and neutrophils and was highly associated with tumor mutation burden and microsatellite instability in various cancers [54]. In addition, Tong et al. convinced that CYFIP2 was significantly associated with CD4 + cells, CD8 + cells and a series of immune markers via metabolic pathways and epithelial–mesenchymal transition in clear cell renal cell carcinoma [31]. Our study also indicated that CYFIP2 potentially contributed to regulation of tumor-associated and immune-related pathways and regulated immune-related genes. In a word, possible mechanisms through which CYFIP2 might influence tumor immunity are worthy of in-depth study.

There are several limitations in our study. First, most of the present studies were limited to bioinformatics analysis, further study is required to validate these results. Second, the diagnostic and prognostic value of CYFIP2 were evaluated based on TCGA cohorts, which have not been validated by other datasets or clinical data from real-world. In addition, despite the finding indicating that CYFIP2 expression correlated with both immune cell infiltration and patient survival in cancers, we could not prove that CYFIP2 affects patient survival through immune infiltration.

Taken together, our present study indicated that CYFIP2 was aberrantly expressed in various tumors and highly involved in tumor-associated and immune-related pathways. The results also indicated that CYFIP2 could be employed as potential diagnostic and prognostic indicator for numerous tumors. In addition, the abnormal expression of CYFIP2 was linked with immune cells infiltration and may affect tumor immunity by acting on immune regulators and immune-related genes, which may provide a foundation for more precise and personalized immunotherapy in future. However, the mechanisms by which CYFIP2 may affect tumor immunity have not been thoroughly investigated by biological experiments. Thus, further experimental and clinical studies in future are required to promote practical application in immunotherapy and prognosis prediction.