The m6A methylation regulator-based signature for predicting the prognosis of prostate cancer

Stabilization of RRBP1 mRNA via an m6A-dependent manner in prostate cancer constitutes a therapeutic vulnerability amenable to small-peptide inhibition of METTL3

Mounting evidence has implicated the RNA m6A methylation catalyzed by METTL3 in a wide range of physiological and pathological processes, including tumorigenesis. The detailed m6A landscape and molecular mechanism of METTL3 in prostate cancer (PCa) remains ill-defined. We find that METTL3 is overexpressed in PCa and correlates with worse patient survival. Functional studies establish METTL3 as an oncoprotein dependent on its m6A enzymatic activity in both AR+ and AR- PCa cells. To dissect the regulatory network of m6A pathway in PCa, we map the m6A landscape in clinical tumor samples using m6A-seq and identify genome-wide METTL3-binding transcripts via RIP-seq. Mechanistically, we discover RRBP1 as a direct METTL3 target in which METTL3 stabilizes RRBP1 mRNA in an m6A-dependent manner. RRBP1 positively correlates with METTL3 expression in PCa cohorts and exerts an oncogenic role in aggressive PCa cells. Leveraging the 3D structural protein-protein interaction between METTL3 and METTL14, we successfully develop two potential METTL3 peptide inhibitors (RM3 and RSM3) that effectively suppress cancer cell proliferation in vitro and tumor growth in vivo. Collectively, our study reveals a novel METTL3/m6A/RRBP1 axis in enhancing aggressive traits of PCa, which can be therapeutically targeted by small-peptide METTL3 antagonists.

RNA N6-methyladenosine modifications in urological cancers: from mechanism to application

The N6-methyladenosine (m6A) modification is the most common modification of messenger RNAs in eukaryotes and has crucial roles in multiple cancers, including in urological malignancies such as renal cell carcinoma, bladder cancer and prostate cancer. The m6A RNA modification is controlled by three types of regulators, including methyltransferases (writers), demethylases (erasers) and RNA-binding proteins (readers), which are responsible for gene regulation at the post-transcriptional level. This Review summarizes the current evidence indicating that aberrant or dysregulated m6A modification is associated with urological cancer development, progression and prognosis. The complex and context-dependent effects of dysregulated m6A modifications in urological cancers are described, along with the potential for aberrantly expressed m6A regulators to provide valuable diagnostic and prognostic biomarkers as well as new therapeutic targets.

RNA m6a Methylation Regulator Expression in Castration-Resistant Prostate Cancer Progression and Its Genetic Associations

N6-methyladenosine (m6A) methylation, a prevalent epitranscriptomic modification, plays a crucial role in regulating mRNA expression, stability, and translation in mammals. M6A regulators have gained attention for their potential implications in tumorigenesis and clinical applications, such as cancer diagnosis and therapeutics. The existing literature predominantly addresses m6A regulators in the context of primary prostate cancer (PCa). However, a notable gap in the knowledge emerges regarding the dynamic expression patterns of these regulators as PCa progresses towards the castration-resistant stage (CRPC). Employing sequential window acquisition of all theoretical mass spectra (SWATH-MS) and RNAseq analysis, we comprehensively profiled the expression of 27 m6A regulators in hormone/androgen-dependent and -independent PCa cell lines, revealing distinct clustering between tumor and adjacent normal prostate tissues. High-grade PCa tumors demonstrated the upregulation of METTL3, RBM15B, and HNRNAPA2B1 and the downregulation of ZC3H13, NUDT21, and FTO. Notably, we identified six m6A regulators associated with PCa survival. Additionally, association analysis of the PCa-associated risk loci in the cancer genome atlas program (TCGA) data unveiled genetic variations near the WTAP, HNRNPA2B1, and FTO genes as significant expression quantitative trait loci. In summary, our study unraveled abnormalities in m6A regulator expression in PCa progression, elucidating their association with PCa risk loci. Considering the heterogeneity within the PCa phenotypes and treatment responses, our findings suggest that prognostic stratification based on m6A regulator expression could enhance PCa diagnosis and prognosis.

Systematic review and integrated analysis of prognostic gene signatures for prostate cancer patients

Prostate cancer (PC) is one of the most common cancers in men and becoming the second leading cause of cancer fatalities. At present, the lack of effective strategies for prognosis of PC patients is still a problem to be solved. Therefore, it is significant to identify potential gene signatures for PC patients' prognosis. Here, we summarized 71 different prognostic gene signatures for PC and concluded 3 strategies for signature construction after extensive investigation. In addition, 14 genes frequently appeared in 71 different gene signatures, which enriched in mitotic and cell cycle. This review provides extensive understanding and integrated analysis of current prognostic signatures of PC, which may help researchers to construct gene signatures of PC and guide future clinical treatment.

RNA m6A modification in prostate cancer: A new weapon for its diagnosis and therapy

Prostate cancer (PCa) is the most common malignant tumor and the second leading cause of cancer-related mortality in men worldwide. Despite significant advances in PCa therapy, the underlying molecular mechanisms have yet to be fully elucidated. Recently, epigenetic modification has emerged as a key player in tumor progression, and RNA-based N6-methyladenosine (m6A) epigenetic modification was found to be crucial. This review summarizes comprehensive state-of-art mechanisms underlying m6A modification, its implication in the pathogenesis, and advancement of PCa in protein-coding and non-coding RNA contexts, its relevance to PCa immunotherapy, and the ongoing clinical trials for PCa treatment. This review presents potential m6A-based targets and paves a new avenue for diagnosing and treating PCa, providing new guidelines for future related research through a systematic review of previous results.

Functions and mechanisms of N6‑methyladenosine in prostate cancer (Review)

Prostate cancer (PCa) has long been a major public health problem affecting men worldwide. Even with treatment, it can develop into castration-resistant PCa. With the continuous advancement in epigenetics, researchers have explored N6-methyladenosine (m⁶A) in search of a more effective and lasting treatment for PCa. m⁶A is widely distributed in mammalian cells and influences various aspects of mRNA metabolism. Recently, it has been associated with the development or suppression of various types of cancer, including PCa. This review summarizes the recent findings on m⁶A regulation and its functions and mechanisms in cells, focusing on the various functional proteins operating within m⁶A in PCa cells. Moreover, the potential clinical value of exploiting m⁶A modification as an early diagnostic marker in PCa diagnosis and therapeutics was discussed. m⁶A may also be used as an indicator to evaluate treatment outcome and prognosis.

m6A Methylation Regulators Are Predictive Biomarkers for Tumour Metastasis in Prostate Cancer

Simple Summary

Recurrence and metastatic progression always lead to dismal outcomes in prostate cancer (PCa). There is no reliable biomarker for the prediction of recurrence and metastasis other than the Prostate Cancer Antigen (PCA). N6-methyladenosine (m⁶A) is the most common post-transcriptional mRNA modification and is regulated by m⁶A regulators dynamically. Since m⁶A modification is associated with cancer development and outgrowth, we performed a consensus clustering on PCa with regard to the gene expression of all m⁶A regulators. We identified three subtypes of Pca with distinct m⁶A expression patterns and enriched biological pathways. We also established an m⁶A score for metastasis prediction based on our clustering, which is potentially a predictive biomarker for Pca metastasis.

Abstract

Prostate cancer (PCa) is one of the most common cancers in men. Usually, most PCas at initial diagnosis are localized and hormone-dependent, and grow slowly. Patients with localized PCas have a nearly 100% 5-year survival rate; however, the 5-year survival rate of metastatic or progressive PCa is still dismal. N6-methyladenosine (m⁶A) is the most common post-transcriptional mRNA modification and is dynamically regulated by m⁶A regulators. A few studies have shown that the abnormal expression of m⁶A regulators is significantly associated with cancer progression and immune cell infiltration, but the roles of these regulators in PCa remain unclear. Here, we examined the expression profiles and methylation levels of 21 m⁶A regulators across the Cancer Genome Atlas (TCGA), 495 PCas by consensus clustering, and correlated the expression of m⁶A regulators with PCa progression and immune cell infiltration. Consensus clustering was applied for subtyping Pca samples into clusters based on the expression profiles of m⁶A regulators. Each subtype’s signature genes were obtained by a pairwise differential expression analysis. Featured pathways of m⁶A subtypes were predicted by Gene Ontology. The m⁶A score was developed to predict m⁶A activation. The association of the m⁶A score with patients’ survival, metastasis and immune cell infiltration was also investigated. We identified three distinct clusters in PCa based on the expression profiles of 21 m⁶A regulators by consensus clustering. The differential expression and pathway analyses on the three clusters uncovered the m⁶A regulators involved in metabolic processes and immune responses in PCa. Moreover, we developed an m⁶A score to evaluate the m⁶A regulator activation for PCa. The m⁶A score is significantly associated with Gleason scores and metastasis in PCa. The predictive capacity of the m⁶A score on PCa metastasis was also validated in another independent cohort with an area under the curve of 89.5%. Hence, our study revealed the critical role of m⁶A regulators in PCa progression and the m⁶A score is a promising predictive biomarker for PCa metastasis.

Molecular Characterization and Clinical Relevance of N6-Methyladenosine Regulators in Metastatic Prostate Cancer

Prostate cancer is a leading malignancy in the male population globally. N6-methylation of adenosine (m6A) is the most prevalent mRNA modification and plays an essential role in various biological processes in vivo. However, the potential roles of m6A in metastatic prostate cancer are largely unknown. In this study, we evaluated and identified two m6A modification patterns based on 21 m6A regulators in four public metastatic prostate cancer datasets. Different modification patterns correlated with distinct molecular characteristics. According to m6A-associated genes, we constructed a prognostic model, called m6Ascore, to predict the outcomes of patients with metastatic prostate cancer. We found that high m6A score level was related to dismal prognosis and characterized by higher cell cycle, DNA repair and mismatch repair pathway score. In vitro experiments confirmed that upregulation of METTL14, an m6A writer, enhanced the invasion, metastasis, and sensitivity of prostate cancer cells to poly (ADP-ribose) polymerase inhibitor. Conversely, down-regulation of potential target genes of m6A had the opposite effect. Finally, we validated that a higher m6A score was associated with a worse prognosis and a higher Gleason score in The Cancer Genome Atlas Program (TCGA) cohort. This work illustrated the nonnegligible role of m6A modification in multiple biological processes of metastatic prostate cancer. Evaluating the m6A risk scores of individual tumours will guide more effective judgement of prognosis as well as treatments for metastatic prostate cancer in clinical practice.

Construction of a Comprehensive Diagnostic Scoring Model for Prostate Cancer Based on a Novel Six-Gene Panel

Accumulating evidence indicates that the N6-methyladenosine (m6A) modification plays a critical role in human cancers. Given the current understanding of m6A modification, this process is believed to be dynamically regulated by m6A regulators. Although the discovery of m6A regulators has greatly enhanced our understanding of the mechanism underlying m6A modification in cancers, the function and role of m6A in the context of prostate cancer (PCa) remain unclear. Here, we aimed to establish a comprehensive diagnostic scoring model that can act as a complement to prostate-specific antigen (PSA) screening. To achieve this, we first drew the landscape of m6A regulators and constructed a LASSO-Cox model using three risk genes (METTL14, HNRNP2AB1, and YTHDF2). Particularly, METTL14 expression was found to be significantly related to overall survival, tumor T stage, relapse rate, and tumor microenvironment of PCa patients, showing that it has important prognostic value. Furthermore, for the sake of improving the predictive ability, we presented a comprehensive diagnostic scoring model based on a novel 6-gene panel by combining with genes found in our previous study, and its application potential was further validated by the whole TCGA and ICGC cohorts. Our study provides additional clues and insights regarding the treatment and diagnosis of PCa patients.

Comprehensive Landscape of HOXA2, HOXA9, and HOXA10 as Potential Biomarkers for Predicting Progression and Prognosis in Prostate Cancer

Prostate cancer (PCa) is recognized as a common malignancy in male patients. The homeobox A cluster (HOXA) family members have been confirmed to be implicated in the development of several types of tumors. However, the expression pattern and prognostic values of HOXA genes in PCa have not been investigated. In this study, we analyzed TCGA datasets and identified six HOXA family members which showed a dysregulated expression in PCa specimens compared with nontumor specimens. We also explored the potential mechanisms involved in the dysregulation of HOXA family members in PCa, and the results of Pearson's correlation revealed that most HOXA members were negatively related to the methylation degree. Moreover, we explored the prognostic values of HOXA family members and identified six survival-related HOXA members. Importantly, HOXA2, HOXA9, and HOXA10 were identified as critical PCa-related genes which were abnormally expressed in PCa and associated with clinical outcomes of PCa patients. Then, we explored the association between the above three genes and immune cell infiltration. We observed that the levels of HOXA2, HOXA9, and HOXA10 were associated with the levels of immune infiltration of several kinds of immune cells. Overall, our findings identified the potential values of the HOXA family for outcome prediction in PCa, which might facilitate personalized counselling and treatment in PCa.

Methyltransferase-like 3 induces the development of cervical cancer by enhancing insulin-like growth factor 2 mRNA-binding proteins 3-mediated apoptotic chromatin condensation inducer 1 mRNA stability

N6-methyladenosine (m6A) plays a critical role in the tumorigenesis of cervical cancer (CC). Here, we aimed to investigate the potential role of methyltransferase-like 3 (METTL3) in CC. Gene expression was determined via real-time quantitative polymerase chain reaction. Cellular functions were detected using colony formation, 5-ethynyl-2'-deoxyuridine (EdU), and Transwell assays. The interactions among METTL3, insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3), and apoptotic chromatin condensation inducer 1 (ACIN1) were confirmed using the MeRIP and RIP assays. An in vivo assay was performed to verify the role of METTL3 in CC development. METTL3 is overexpressed in CC, and therefore, its knockdown inhibits the proliferation and migration of CC cells. Silencing METTL3 inhibits tumor growth in vivo. Moreover, a positive association was observed between METTL3 and ACIN1. METTL3 interacts with IGF2BP3 to promote the mRNA stability of ACIN1, the overexpression of which induces the aggressiveness of CC cells. METTL3 promotes ACIN1 mRNA stability to accelerate CC progression, implying that METTL3 is a promising biomarker in CC.

Construction of a risk prediction model using m6A RNA methylation regulators in prostate cancer: comprehensive bioinformatic analysis and histological validation

Background

Epigenetic reprogramming reportedly has a crucial role in prostate cancer (PCa) progression. RNA modification is a hot topic in epigenetics, and N6-methyladenosine (m6A) accounts for approximately 60% of RNA chemical modifications. The aim of this study was to evaluate the m6A modification patterns in PCa patients and construct a risk prediction model using m6A RNA regulators.

Materials and methods

Analyses were based on the levels of 25 m6A regulators in The Cancer Genome Atlas (TCGA). Differentially expressed gene (DEG) and survival analyses were performed according to TCGA-PRAD clinicopathologic and follow-up information. To detect the influences of m6A regulators and their DEGs, consensus clustering analysis was performed, and tumor mutational burden (TMB) estimation and tumor microenvironment (TME) cell infiltration were assessed. mRNA levels of representative genes were verified using clinical PCa data.

Results

Diverse expression patterns of m6A regulators between tumor and normal (TN) tissues were detected regarding Gleason score (GS), pathological T stage (pT), TP53 mutation, and survival comparisons, with HNRNPA2B1 and IGFBP3 being intersecting genes. HNRNPA2B1 was upregulated in advanced stages (GS > 7, pT3, HR > 1, and TP53 mutation), as verified using clinical PCa tissue. Three distinct m6A modification patterns were identified through consensus clustering analysis, but no significant difference was found among these groups in recurrence-free survival (RFS) analysis. Six DEGs of m6A clusters (m6Aclusters) were screened through univariate Cox regression analysis. MMAB and PAIAP2 were intersecting genes for the five clinical factors. MMAB, which was upregulated in PCa compared with TN, was verified using clinical PCa samples. Three distinct subgroups were established according to the 6 DEGs. Cluster A involved the most advanced stages and had the poorest RFS. The m6A score (m6Ascore) was calculated based on the 6 genes, and the low m6Ascore group showed poor RFS with a negative association with infiltration for 16 of 23 immune-related cells.

Conclusion

We screened DEGs of m6Aclusters and identified 6 genes (BAIAP2, TEX264, MMAB, JAGN1, TIMM8AP1, and IMP3), with which we constructed a highly predictive model with prognostic value by dividing TCGA-PRAD into three distinct subgroups and performing m6Ascore analysis. This study helps to elucidate the integral effects of m6A modification patterns on PCa progression.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12935-021-02438-1.

RNA m6A Methylation Regulators Multi-Omics Analysis in Prostate Cancer

RNA N6-methyladenosine (m6A) methylation is known to be the most popular RNA modification in animals. Many research reports have elaborated on the effects of m6A regulators in medical practice, such as diagnosis, prognosis, and treatment. M6A modification has evident impacts on many aspects of RNA metabolism, just like RNA splicing, processing, translation, and stability. M6A also has a magnificent role in numerous types of cancers. We analyzed the prostate cancer datasets, from The Cancer Genome Atlas (TCGA) database, for every recognized m6A regulator in their gene expression, DNA methylation status and copy number variations (CNVs). We also systematically analyzed the relationship between different m6A regulators and the prognosis of prostate cancer. The results illustrated considerable differences in the expression of various m6A regulators between the prostate and normal cancer samples. At the same time, there were evident differences in the expression of various m6A regulators in prostate cancers with different Gleason scores. Subsequently, we determined CBLL1, FTO, YTHDC1, HNRNPA2B1 as crucial m6A regulators of prostate cancer. Premised on the expression of CBLL1, we also identified potential therapeutic agents for prostate cancer, and knockdown of FTO prominently inhibited prostate cells migration and invasion in vitro experiment.

Recent advances in functional annotation and prediction of the epitranscriptome

RNA modifications, in particular N⁶-methyladenosine (m⁶A), participate in every stages of RNA metabolism and play diverse roles in essential biological processes and disease pathogenesis. Thanks to the advances in sequencing technology, tens of thousands of RNA modification sites can be identified in a typical high-throughput experiment; however, it remains a major challenge to decipher the functional relevance of these sites, such as, affecting alternative splicing, regulation circuit in essential biological processes or association to diseases. As the focus of RNA epigenetics gradually shifts from site discovery to functional studies, we review here recent progress in functional annotation and prediction of RNA modification sites from a bioinformatics perspective. The review covers naïve annotation with associated biological events, e.g., single nucleotide polymorphism (SNP), RNA binding protein (RBP) and alternative splicing, prediction of key sites and their regulatory functions, inference of disease association, and mining the diagnosis and prognosis value of RNA modification regulators. We further discussed the limitations of existing approaches and some future perspectives.

Identification of an Immune-Related Gene Signature to Improve Prognosis Prediction in Colorectal Cancer Patients

BACKGROUND

Despite recent advance in immune therapy, great heterogeneity exists in the outcomes of colorectal cancer (CRC) patients. In this study, we aimed to analyze the immune-related gene (IRG) expression profiles from three independent public databases and develop an effective signature to forecast patient's prognosis.

METHODS

IRGs were collected from the ImmPort database. The CRC dataset from The Cancer Genome Atlas (TCGA) database was used to identify a prognostic gene signature, which was verified in another two CRC datasets from the Gene Expression Omnibus (GEO). Gene function enrichment analysis was conducted. A prognostic nomogram was built incorporating the IRG signature with clinical risk factors.

RESULTS

The three datasets had 487, 579, and 224 patients, respectively. A prognostic six-gene-signature (CCL22, LIMK1, MAPKAPK3, FLOT1, GPRC5B, and IL20RB) was developed through feature selection that showed good differentiation between the low- and high-risk groups in the training set (p < 0.001), which was later confirmed in the two validation groups (log-rank p < 0.05). The signature outperformed tumor TNM staging for survival prediction. GO and KEGG functional annotation analysis suggested that the signature was significantly enriched in metabolic processes and regulation of immunity (p < 0.05). When combined with clinical risk factors, the model showed robust prediction capability.

CONCLUSION

The immune-related six-gene signature is a reliable prognostic indicator for CRC patients and could provide insight for personalized cancer management.

RNA m6A Modification in Cancers: Molecular Mechanisms and Potential Clinical Applications

N6-Methyladenosine (m6A) RNA modification brings a new dawn for RNA modification researches in recent years. This posttranscriptional RNA modification is dynamic and reversible, and is regulated by methylases ("writers"), demethylases ("erasers"), and proteins that preferentially recognize m6A modifications ("readers"). The change of RNA m6A modification regulates RNA metabolism in eucaryon, including translation, splicing, exporting, decay, and processing. Thereby the dysregulation of m6A may lead to tumorigenesis and progression. Given the tumorigenic role of abnormal m6A expression, m6A regulators may function as potential clinical therapeutic targets for cancers. In this review, we emphasize on the underlying mechanisms of m6A modifications in tumorigenesis and further introduce the potential m6A regulators-associated therapeutic targets for tumor therapy.