RNA-Guided RNA Modifications: Biogenesis, Functions, and Applications

Analysis of human brain RNA-seq data reveals combined effects of 4 types of RNA modifications and 18 types of programmed cell death on Alzheimer's disease

BACKGROUND

RNA modification plays a critical role in Alzheimer's disease (AD) by modulating the expression and function of AD-related genes, thereby affecting AD occurrence and progression. Programmed cell death is closely related to neuronal death and associated with neuronal loss and cognitive function changes in AD. However, the mechanism of their joint action on AD remains unknown and requires further exploration.

METHODS

We used the MSBB RNA-seq dataset to analyze the correlation between RNA modification, programmed cell death, and AD. We used combined studies of RNA modification and programmed cell death to distinguish subgroups of patients, and the results highlight the strong correlation between RNA modification-related programmed cell death and AD. A weighted gene co-expression network was constructed, and the pivotal roles of programmed cell death genes in key modules were identified. Finally, by combining unsupervised consensus clustering, gene co-expression networks, and machine learning algorithms, an RNA modification-related programmed cell death network was constructed, and the pivotal roles of programmed cell death genes in key modules were identified. An RNA modification-related programmed cell death risk score was calculated to predict the occurrence of AD.

RESULTS

RPCD-related genes classified patients into subgroups with distinct clinical characteristics. Nineteen key genes were identified and an RPCD risk score was constructed based on the key genes. This score can be used for the diagnosis of AD and the assessment of disease progression in patients. The diagnostic efficacy of the RPCD risk score and the key genes was validated in the ROSMAP, GEO, and ADNI datasets.

CONCLUSION

This study uncovered that RNA modification-related PCD is of significance for AD progression and early prediction, providing insights from a new perspective for the study of disease mechanisms in AD.

The potential impact of RNA splicing abnormalities on immune regulation in endometrial cancer

RNA splicing controls the post-transcriptional level of gene expression, allowing for the synthesis of many transcripts with various configurations and roles. Variations in RNA splicing regulatory factors, including splicing factors, signaling pathways, epigenetic modifications, and environmental factors, are typically the origin of tumor-associated splicing anomalies. Furthermore, thorough literature assessments on the intricate connection between tumor-related splicing dysregulation and tumor immunity are currently lacking. Therefore, we also thoroughly discuss putative targets associated with RNA splicing in endometrial cancer (EC) and the possible impacts of aberrant RNA splicing on the immune control of tumor cells and tumor microenvironment (TME), which contributes to enhancing the utilization of immunotherapy in the management of EC and offers an alternative viewpoint for the exploration of cancer therapies and plausible prognostic indicators.

Progress in Tandem Mass Spectrometry Data Analysis for Nucleic Acids

Mass spectrometry (MS) has become a critical tool in the characterization of covalently modified nucleic acids. Well-developed bottom-up approaches, where nucleic acids are digested with an endonuclease and the resulting oligonucleotides are separated before MS and MS/MS analysis, provide substantial insight into modified nucleotides in biological and synthetic nucleic. Top-down MS presents an alternative approach where the entire nucleic acid molecule is introduced to the mass spectrometer intact and then fragmented by MS/MS. Current top-down MS workflows have incorporated automated, on-line HPLC workflows to enable rapid desalting of nucleic acid samples for facile mass analysis without complication from adduction. Furthermore, optimization of MS/MS parameters utilizing collision, electron, or photon-based activation methods have enabled effective bond cleavage throughout the phosphodiester backbone while limiting secondary fragmentation, allowing characterization of progressively larger (~100 nt) nucleic acids and localization of covalent modifications. Development of software applications to perform automated identification of fragment ions has accelerated the broader adoption of mass spectrometry for analysis of nucleic acids. This review focuses on progress in tandem mass spectrometry for characterization of nucleic acids with particular emphasis on the software tools that have proven critical for advancing the field.

Deep learning modeling of RNA ac4C deposition reveals the importance of plant alternative splicing

The N4-acetylcytidine (ac4C) modification has recently been characterized as a noncanonical RNA marker in plants. While the precise installation of ac4C sites in individual plant transcripts continues to present challenges, the biological roles of ac4C in specific plant species are gradually being deciphered. Herein, we utilized a deep learning technique called iac4C (intelligent ac4C) to predict ac4C sites in mRNA. ac4C deposition was effectively forecasted by the iac4C model (AUROC = 0.948), revealing a reliable distribution pattern primarily situated in the transcribing area as opposed to regions that are not translated. The iac4C deep learning approach using a combination of BiGRU and self-attention mechanisms both validates previous studies showing a positive correlation between ac4C and RNA splicing in plant species and reveals new examples of other splicing events associated with ac4C. Our advanced deep learning algorithm for analyzing ac4C enables swift identification of important biological phenomena that would otherwise be challenging to uncover through traditional experimental approaches. These findings provide insight into the essential regulatory function of site-specific ac4C deposition in alternative splicing processes. The source code and datasets for iac4C are available at https://github.com/xlwei507/iac4C .

RNA ac4C modification in cancer: Unraveling multifaceted roles and promising therapeutic horizons

RNA modifications play a crucial role in cancer development, profoundly influencing various stages of the RNA lifecycle. These stages encompass nuclear processing, nuclear export, splicing, and translation in the cytoplasm. Among RNA modifications, RNA ac4C modification, also known as N4-acetylcytidine, stands out for its unique role in acetylation processes. Specific proteins regulate RNA ac4C modification, maintaining the dynamic and reversible nature of these changes. This review explores the molecular mechanisms and biological functions of RNA ac4C modification. It examines the intricate ways in which RNA ac4C modification influences the pathogenesis and progression of cancer. Additionally, the review provides an integrated overview of the current methodologies for detecting RNA ac4C modification. Exploring the potential applications of manipulating this modification suggests avenues for novel therapeutic strategies, potentially leading to more effective cancer treatments in the future.

Writers, readers, and erasers RNA modifications and drug resistance in cancer

Drug resistance in cancer cells significantly diminishes treatment efficacy, leading to recurrence and metastasis. A critical factor contributing to this resistance is the epigenetic alteration of gene expression via RNA modifications, such as N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), 7-methylguanosine (m7G), pseudouridine (Ψ), and adenosine-to-inosine (A-to-I) editing. These modifications are pivotal in regulating RNA splicing, translation, transport, degradation, and stability. Governed by "writers," "readers," and "erasers," RNA modifications impact numerous biological processes and cancer progression, including cell proliferation, stemness, autophagy, invasion, and apoptosis. Aberrant RNA modifications can lead to drug resistance and adverse outcomes in various cancers. Thus, targeting RNA modification regulators offers a promising strategy for overcoming drug resistance and enhancing treatment efficacy. This review consolidates recent research on the role of prevalent RNA modifications in cancer drug resistance, with a focus on m6A, m1A, m5C, m7G, Ψ, and A-to-I editing. Additionally, it examines the regulatory mechanisms of RNA modifications linked to drug resistance in cancer and underscores the existing limitations in this field.

Clinical significance of RNA methylation in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a primary liver malignancy with high mortality rates and poor prognosis. Recent advances in high-throughput sequencing and bioinformatic technologies have greatly enhanced the understanding of the genetic and epigenetic changes in liver cancer. Among these changes, RNA methylation, the most prevalent internal RNA modification, has emerged as a significant contributor of the development and progression of HCC. Growing evidence has reported significantly abnormal levels of RNA methylation and dysregulation of RNA-methylation-related enzymes in HCC tissues and cell lines. These alterations in RNA methylation play a crucial role in the regulation of various genes and signaling pathways involved in HCC, thereby promoting tumor progression. Understanding the pathogenesis of RNA methylation in HCC would help in developing prognostic biomarkers and targeted therapies for HCC. Targeting RNA-methylation-related molecules has shown promising potential in the management of HCC, in terms of developing novel prognostic biomarkers and therapies for HCC. Exploring the clinical application of targeted RNA methylation may provide new insights and approaches for the management of HCC. Further research in this field is warranted to fully understand the functional roles and underlying mechanisms of RNA methylation in HCC. In this review, we described the multifaceted functional roles and potential mechanisms of RNA methylation in HCC. Moreover, the prospects of clinical application of targeted RNA methylation for HCC management are discussed, which may provide the basis for subsequent in-depth research on RNA methylation in HCC.