Comprehensive Analysis of Prognostic Value of MEX3A and Its Relationship with Immune Infiltrates in Ovarian Cancer

Bioinformatics analyses and experimental validation of the role of phagocytosis in low-grade glioma

BACKGROUND

Phagocytosis is of vital importance in tumor immune response. The alteration of phagocytosis in low-grade glioma (LGG) has not been investigated.

METHODS

The mRNA, copy number variation, single nucleotide variation, and methylation levels of phagocytosis-related genes were summarized in pan-cancer. Non-negative matrix factorization clustering was utilized to identify two LGG subtypes. LASSO regression analysis was performed to construct a phagocytosis-related prognostic signature (PRPS). Immune characteristics, immunotherapy response, and targeted-drug sensitivity were further explored. The phagocytosis activity in glioma was evaluated using scRNA-seq data. Multiplex immunohistochemical (m-IHC) technology was performed to identify the tumor-infiltrating immune cells in LGG.

RESULTS

The phagocytosis-related genes altered obviously in pan-cancer compared with corresponding normal tissues. Two LGG subtypes were obtained and the subtype with poor prognosis was combined with lower tumor purity, more active immune-related pathways, increasing infiltration of CD4+ T cells, CD8+ T cells, and natural killer (NK) cells, decreasing infiltration of macrophages, mast cells, and neutrophils, distinct pathway activity and cell death status, greater response to immunotherapy, and higher sensitivity to cyclophosphamide, erlotinib, gefitinib, lapatinib, and sorafenib. In addition, a PRPS involving 10 genes (i.e., SLC11A1, CAMK1D, PLA2G5, STAP1, ALOX15, PLCG2, SFTPD, AZU1, RAB27A, and LAMTOR2) was constructed to estimate the risk level of each LGG sample and high risk LGG patients had poor prognosis, upregulated infiltration of neutrophil, macrophage, Treg, and myeloid dendritic cell, down regulated infiltration of monocyte and NK cell, and increasing expression of large number of immune checkpoint genes. The phagocytosis activity is notably active in monocyte/macrophage. The m-IHC results confirmed increased infiltration of macrophages and neutrophils in LGG samples with high SLC11A1 expression.

CONCLUSION

The molecular characteristics of phagocytosis were revealed and the PRPS laid the foundation for personalized therapy in LGG.

Nonsense-Mediated mRNA Decay as a Mediator of Tumorigenesis

Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved and well-characterized biological mechanism that ensures the fidelity and regulation of gene expression. Initially, NMD was described as a cellular surveillance or quality control process to promote selective recognition and rapid degradation of erroneous transcripts harboring a premature translation-termination codon (PTC). As estimated, one-third of mutated and disease-causing mRNAs were reported to be targeted and degraded by NMD, suggesting the significance of this intricate mechanism in maintaining cellular integrity. It was later revealed that NMD also elicits down-regulation of many endogenous mRNAs without mutations (~10% of the human transcriptome). Therefore, NMD modulates gene expression to evade the generation of aberrant truncated proteins with detrimental functions, compromised activities, or dominant-negative effects, as well as by controlling the abundance of endogenous mRNAs. By regulating gene expression, NMD promotes diverse biological functions during development and differentiation, and facilitates cellular responses to adaptation, physiological changes, stresses, environmental insults, etc. Mutations or alterations (such as abnormal expression, degradation, post-translational modification, etc.) that impair the function or expression of proteins associated with the NMD pathway can be deleterious to cells and may cause pathological consequences, as implicated in developmental and intellectual disabilities, genetic defects, and cancer. Growing evidence in past decades has highlighted NMD as a critical driver of tumorigenesis. Advances in sequencing technologies provided the opportunity to identify many NMD substrate mRNAs in tumor samples compared to matched normal tissues. Interestingly, many of these changes are tumor-specific and are often fine-tuned in a tumor-specific manner, suggesting the complex regulation of NMD in cancer. Tumor cells differentially exploit NMD for survival benefits. Some tumors promote NMD to degrade a subset of mRNAs, such as those encoding tumor suppressors, stress response proteins, signaling proteins, RNA binding proteins, splicing factors, and immunogenic neoantigens. In contrast, some tumors suppress NMD to facilitate the expression of oncoproteins or other proteins beneficial for tumor growth and progression. In this review, we discuss how NMD is regulated as a critical mediator of oncogenesis to promote the development and progression of tumor cells. Understanding how NMD affects tumorigenesis differentially will pave the way for the development of more effective and less toxic, targeted therapeutic opportunities in the era of personalized medicine.

MEX3A Mediates p53 Degradation to Suppress Ferroptosis and Facilitate Ovarian Cancer Tumorigenesis

Epithelial ovarian cancer is a highly heterogeneous and malignant female cancer with an overall low survival rate. Mutations in p53 are prevalent in the major ovarian cancer histotype, high-grade serous ovarian carcinoma (HGSOC), while p53 mutations are much less frequent in other ovarian cancer subtypes, particularly in ovarian clear cell carcinoma (OCCC). Advanced stage OCCC with wild-type (WT) p53 has a worse prognosis and increased drug resistance, metastasis, and recurrence than HGSOC. The mechanisms responsible for driving the aggressiveness of WT p53-expressing ovarian cancer remain poorly understood. Here, we found that upregulation of MEX3A, a dual-function protein containing a RING finger domain and an RNA-binding domain, was critical for tumorigenesis in WT p53-expressing ovarian cancer. MEX3A overexpression enhanced the growth and clonogenicity of OCCC cell lines. In contrast, depletion of MEX3A in OCCC cells, as well as ovarian teratocarcinoma cells, reduced cell survival and proliferative ability. MEX3A depletion also inhibited tumor growth and prolonged survival in orthotopic xenograft models. MEX3A depletion did not alter p53 mRNA level but did increase p53 protein stability. MEX3A-mediated p53 protein degradation was crucial to suppress ferroptosis and enhance tumorigenesis. Consistently, p53 knockdown reversed the effects of MEX3A depletion. Together, our observations identified MEX3A as an important oncogenic factor promoting tumorigenesis in ovarian cancer cells expressing WT p53.

SIGNIFICANCE

Degradation of p53 mediated by MEX3A drives ovarian cancer growth by circumventing p53 tumor suppressive functions, suggesting targeting MEX3A as a potential strategy for treating of ovarian cancer expressing WT p53.

RNA-Binding Protein MEX3A Interacting with DVL3 Stabilizes Wnt/β-Catenin Signaling in Endometrial Carcinoma

Disease recurrence and metastasis lead to poor prognosis in patients with advanced endometrial carcinoma (EC). RNA-binding proteins (RBPs) are closely associated with tumor initiation and metastasis, but the function and molecular mechanisms of RBPs in EC are unclear. RBPs were screened and identified using the TCGA, GEO, and RBPTD databases. The effect of MEX3A on EC was verified by in vitro and in vivo experiments. Gene set enrichment analysis (GSEA), immunofluorescence (IF), and co-immunoprecipitation (Co-IP) were used to identify potential molecular mechanisms of action. We identified 148 differentially expressed RBPs in EC. MEX3A was upregulated and related to poor prognosis in patients with EC. In vitro and vivo experiments demonstrated that MEX3A promoted the growth, migration, and invasion capacities of EC cells. Mechanistically, DVL3, a positive regulator of the Wnt/β-catenin pathway, also increased the proliferation and metastasis of EC cells. MEX3A enhanced EMT and played a pro-carcinogenic role by interacting with DVL3 to stabilize β-catenin and upregulated the expression of its downstream target genes. MEX3A is upregulated in EC and promotes tumor progression by activating EMT and regulating the Wnt/β-catenin pathway via DVL3. MEX3A may therefore be a novel therapeutic target for EC.

Ovarian cancer subtypes based on the regulatory genes of RNA modifications: Novel prediction model of prognosis

BACKGROUND

Ovarian cancer (OC) is a female reproductive system tumor. RNA modifications play key roles in gene expression regulation. The growing evidence demonstrates that RNA methylation is critical for various biological functions, and that its dysregulation is related to the progression of cancer in human.

METHOD

OC samples were classified into different subtypes (Clusters 1 and 2) based on various RNA-modification regulatory genes (RRGs) in the process of RNA modifications (m1A, m6A, m6Am, m5C, m7G, ac4C, m3C, and Ψ) by nonnegative matrix factorization method (NMF). Based on differently expressed RRGs (DERRGs) between clusters, a pathologically specific RNA-modification regulatory gene signature was constructed with Lasso regression. Kaplan-Meier analysis and receiver operating characteristic (ROC) curves were used to evaluate the prognostic ability of the identified model. The correlations of clinicopathological features, immune subtypes, immune scores, immune cells, and tumor mutation burden (TMB) were also estimated between different NMF clusters and riskscore groups.

RESULTS

In this study, 59 RRGs in the process of RNA modifications (m1A, m6A, m6Am, m5C, m7G, ac4C, m3C, and Ψ) were obtained from TCGA database. These RRGs were interactional, and sample clusters based on these regulators were significantly correlated with survival rate, clinical characteristics (involving survival status and pathologic stage), drug sensibility, and immune microenvironment. Furthermore, Lasso regression based on these 21 DERRGs between clusters 1 and 2 constructed a four-DERRG signature (ALYREF, ZC3H13, WTAP, and METTL1). Based on this signature, 307 OC patients were classified into high- and low-risk groups based on median value of riskscores from lasso regression. This identified signature was significantly associated with overall survival, radiation therapy, age, clinical stage, cancer status, and immune cells (involving CD4+ memory resting T cells, plasma cells, and Macrophages M1) of ovarian cancer patients. Further, GSEA revealed that multiple biological behaviors were significantly enriched in different groups.

CONCLUSIONS

OC patients were classified into two subtypes per these RRGs. This study identified four-DERRG signature (ALYREF, ZC3H13, WTAP, and METTL1) in OC, which was an independent prognostic model for patient stratification, prognostic evaluation, and prediction of response to immunotherapy in ovarian cancer by classifying OC patients into high- and low-risk groups.