The Key Role of RNA Modification in Breast Cancer

Integrative machine learning model of RNA modifications predict prognosis and treatment response in patients with breast cancer

BACKGROUND

Breast cancer, a highly heterogeneous and complex disease, remains the leading cause of cancer-related death among women worldwide. Despite advances in treatment modalities, effective prognostic models and therapeutic strategies are still urgently needed.

METHODS

We retrospectively analyzed 15 independent breast cancer cohorts to explore the role of RNA modifications in the prognosis of patients with breast cancer. By integrating nine types of RNA modifications, we developed a comprehensive machine learning-based RNA modification signature (CMRS). Furthermore, single-cell RNA sequencing data were analyzed to understand the biological mechanisms underlying CMRS. In addition, immune infiltration levels were evaluated via six different algorithms, and immune checkpoint inhibitor responsiveness was predicted. Moreover, the response of high-CMIS patients to chemotherapy was predicted via multiple datasets. Finally, immunohistochemistry was performed on tissue samples from breast cancer patients to validate protein expression levels.

RESULTS

Our analysis revealed five key RNA modification-related genes (ENO1, ARAF, WT1, GADD45A, and BIRC3) associated with breast cancer prognosis. The CMRS model demonstrated high predictive accuracy across multiple cohorts and was significantly correlated with patient survival outcomes. Multiomics analysis revealed that high CMRS was associated with increased tumor mutational burden and distinct mutational signatures, particularly in pathways related to TP53, MYC, and cell proliferation. Single-cell analysis highlighted the involvement of epithelial cells and MYC signaling in high CMRS activity. Cell‒cell communication analysis revealed reduced interaction strength in hig CMRS patients, indicating poor prognosis. Furthermore, low CMRS patients presented increased immune cell infiltration and improved responsiveness to immune checkpoint inhibitors, whereas high CMRS patients were identified as potential candidates for treatment with panobinostat and vincristine.

CONCLUSION

Our study elucidates the significant role of RNA modifications in breast cancer prognosis and treatment. The CMRS model serves as a sensitive biomarker for predicting patient survival and treatment responsiveness, offering a new avenue for personalized therapy in patients with breast cancer.

The Mechanisms, Research Status, and Future Prospects of m6A Modification in Breast Cancer

N6-methyladenosine (m6A) modification is a significant methylation alteration frequently observed in eukaryotic RNAs, garnering considerable attention in the field of breast cancer research in recent years. The m6A modification profoundly influences the onset, progression, and prognosis of breast cancer by regulating RNA stability, translation efficiency, and degradation processes. Numerous studies have demonstrated that m6A regulatory factors, including METTL3, METTL14, and ALKBH5, play pivotal roles in breast cancer cells, affecting cell proliferation, metastasis, and drug resistance. Furthermore, the interactions between m6A modification and non-coding RNAs, as well as its role in the tumor microenvironment, have increasingly attracted researchers' interest. Although numerous studies have elucidated the dual roles of m6A in breast cancer, its specific molecular mechanisms remain to be thoroughly investigated. Future research should explore various aspects, including the role of m6A in different subtypes of breast cancer, its involvement in chemotherapy resistance, and its interactions with the tumor microenvironment. This exploration will contribute to advancements in the diagnosis and treatment of breast cancer. The present article aims to systematically summarize the research progress on m6A modification in breast cancer, offering novel insights and strategies for future related research and clinical applications.

Epitranscriptomic orchestrations: Unveiling the regulatory paradigm of m6A, A-to-I editing, and m5C in breast cancer via long noncoding RNAs and microRNAs

Breast cancer (BC) poses a persistent global health challenge, particularly in countries with elevated human development indices linked to factors such as increased life expectancy, education, and wealth. Despite therapeutic progress, challenges persist, and the role of epitranscriptomic RNA modifications in BC remains inadequately understood. The epitranscriptome, comprising diverse posttranscriptional modifications on RNA molecules, holds the potential to intricately modulate RNA function and regulation, implicating dysregulation in various diseases, including BC. Noncoding RNAs (ncRNAs), acting as posttranscriptional regulators, influence physiological and pathological processes, including cancer. RNA modifications in long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) add an extra layer to gene expression control. This review delves into recent insights into epitranscriptomic RNA modifications, such as N-6-methyladenosine (m6A), adenine-to-inosine (A-to-I) editing, and 5-methylcytosine (m5C), specifically in the context of lncRNA and miRNAs in BC, highlighting their potential implications in BC development and progression. Understanding this intricate regulatory landscape is vital for deciphering the molecular mechanisms underlying BC and identifying potential therapeutic targets.

Research progress of N1-methyladenosine RNA modification in cancer

N1-methyladenosine (m1A) is a post-transcriptionally modified RNA molecule that plays a pivotal role in the regulation of various biological functions and activities. Especially in cancer cell invasion, proliferation and cell cycle regulation. Over recent years, there has been a burgeoning interest in investigating the m1A modification of RNA. Most studies have focused on the regulation of m1A in cancer enrichment areas and different regions. This review provides a comprehensive overview of the methodologies employed for the detection of m1A modification. Furthermore, this review delves into the key players in m1A modification, known as the "writers," "erasers," and "readers." m1A modification is modified by the m1A methyltransferases, or writers, such as TRMT6, TRMT61A, TRMT61B, TRMT10C, NML, and, removed by the demethylases, or erasers, including FTO and ALKBH1, ALKBH3. It is recognized by m1A-binding proteins YTHDF1, TYHDF2, TYHDF3, and TYHDC1, also known as "readers". Additionally, we explore the intricate relationship between m1A modification and its regulators and their implications for the development and progression of specific types of cancer, we discuss how m1A modification can potentially facilitate the discovery of novel approaches for cancer diagnosis, treatment, and prognosis. Our summary of m1A methylated adenosine modification detection methods and regulatory mechanisms in various cancers provides useful insights for cancer diagnosis, treatment, and prognosis. Video Abstract.

m6A readers, writers, erasers, and the m6A epitranscriptome in breast cancer

Epitranscriptomic modification of RNA regulates human development, health, and disease. The true diversity of the transcriptome in breast cancer including chemical modification of transcribed RNA (epitranscriptomics) is not well understood due to limitations of technology and bioinformatic analysis. N-6-methyladenosine (m6A) is the most abundant epitranscriptomic modification of mRNA and regulates splicing, stability, translation, and intracellular localization of transcripts depending on m6A association with reader RNA-binding proteins. m6A methylation is catalyzed by the METTL3 complex and removed by specific m6A demethylase ALKBH5, with the role of FTO as an 'eraser' uncertain. In this review, we provide an overview of epitranscriptomics related to mRNA and focus on m6A in mRNA and its detection. We summarize current knowledge on altered levels of writers, readers, and erasers of m6A and their roles in breast cancer and their association with prognosis. We summarize studies identifying m6A peaks and sites in genes in breast cancer cells.