Establishment of m7G-related gene pair signature to predict overall survival in colorectal cancer

Applications of gene pair methods in clinical research: advancing precision medicine

The rapid evolution of high-throughput sequencing technologies has revolutionized biomedical research, producing vast amounts of gene expression data that hold immense potential for biological discovery and clinical applications. Effectively mining these large-scale, high-dimensional data is crucial for facilitating disease detection, subtype differentiation, and understanding the molecular mechanisms underlying disease progression. However, the conventional paradigm of single-gene profiling, measuring absolute expression levels of individual genes, faces critical limitations in clinical implementation. These include vulnerability to batch effects and platform-dependent normalization requirements. In contrast, emerging approaches analyzing relative expression relationships between gene pairs demonstrate unique advantages. By focusing on binary comparisons of two genes' expression magnitudes, these methods inherently normalize experimental variations while capturing biologically stable interaction patterns. In this review, we systematically evaluate gene pair-based analytical frameworks. We classify eleven computational approaches into two fundamental categories: expression value-based methods quantifying differential expression patterns, and rank-based methods exploiting transcriptional ordering relationships. To bridge methodological development with practical implementation, we establish a reproducible analytical pipeline incorporating feature selection, classifier construction, and model evaluation modules using real-world benchmark datasets from pulmonary tuberculosis studies. These findings position gene pair analysis as a transformative paradigm for mining high-dimensional omics data, with direct implications for precision biomarker discovery and mechanistic studies of disease progression.

Comprehensive analysis of RNA methylation-related genes to identify molecular cluster for predicting prognosis and immune profiles in bladder cancer

m6A, m5C and m7G are common types of RNA methylation modifications that are widely involved in key mechanisms regulating malignancy. However, the role of RNA methylation-related genes in the immune microenvironment of bladder cancer (BLCA) remains elusive. In this study, we established RNA methylation molecular subtypes by analyzing the TCGA and GEO datasets. Risk model and nomogram were constructed by LASSO and multivariate Cox regression analysis and validated by external datasets. Genetic variations, functional enrichment analysis and immune cell infiltration were analyzed. The expression levels of hub genes were detected by real-time polymerase chain reaction (qRT-PCR) and immunohistochemistry (IHC). The effect of FN1 on cellular function was determined using experimental assays. Finally, we identified a 7-gene signature associated with BLCA prognosis. GSE19423 validated the predictive value of the risk model. The IMvigor210 data showed the model had promising predictive efficacy for BLCA immunotherapy. Significant differences in biological function, immune cell infiltration and drug sensitivity were observed between high- and low-risk groups. Furthermore, FN1 was upregulated in BLCA, as determined by qRT-PCR and IHC. Depletion of FN1 using siRNA impaired cell motility in T24 and 5637 cells. In conclusion, RNA methylation-related risk model can predict the prognosis, immune landscape and response to immunotherapy in BLCA. Among the 7-gene signature, FN1 is a pivotal gene that promotes the migration of bladder cancer cells.

Functions of METTL1/WDR4 and QKI as m7G modification - related enzymes in digestive diseases

N7-methylguanosine (m7G) modification is one of the most prevalent forms of chemical modification in RNA molecules, which plays an important role in biological processes such as RNA stability, translation regulation and ribosome recognition. Methyl-transferation of m7G modification is catalyzed by the enzyme complex of methyltransferase-like 1 (METTL1) and WD repeat domain 4 (WDR4), and Quaking (QKI) recognizes internal m7G methylated mRNA and regulates mRNA translation and stabilization. Recent studies have found that m7G modification - related enzymes are associated with the onset and progression of digestive cancer, such as colorectal cancer, liver cancer, and other digestive diseases such as ulcerative colitis. This review will focus on the latest research progress on the roles of m7G methyltransferase METTL1/WDR4 and recognized enzyme QKI in digestive diseases.

RNA modifications in cancer immune therapy: regulators of immune cells and immune checkpoints

RNA modifications are epigenetic changes that alter the structure and function of RNA molecules, playing a crucial role in the onset, progression, and treatment of cancer. Immune checkpoint inhibitor (ICI) therapies, particularly PD-1 blockade and anti-CTLA-4 treatments, have changed the treatment landscape of virous cancers, showing great potential in the treatment of different cancer patients, but sensitivity to these therapies is limited to certain individuals. This review offers a comprehensive survey of the functions and therapeutic implications of the four principal RNA modifications, particularly highlighting the significance of m6A in the realms of immune cells in tumor and immunotherapy. This review starts by providing a foundational summary of the roles RNA modifications assume within the immune cell community, focusing on T cells, NK cells, macrophages, and dendritic cells. We then discuss how RNA modifications influence the intricate regulatory mechanisms governing immune checkpoint expression, modulation of ICI efficacy, and prediction of ICI treatment outcomes, and review drug therapies targeting genes regulated by RNA modifications. Finally, we explore the role of RNA modifications in gene editing, cancer vaccines, and adoptive T cell therapies, offering valuable insights into the use of RNA modifications in cancer immunotherapy.

M7G-related tumor immunity: novel insights of RNA modification and potential therapeutic targets

RNA modifications play a pivotal role in regulating cellular biology by exerting influence over distribution features and molecular functions at the post-transcriptional level. Among these modifications, N7-methylguanosine (m7G) stands out as one of the most prevalent. Over recent years, significant attention has been directed towards understanding the implications of m7G modification. This modification is present in diverse RNA molecules, including transfer RNAs, messenger RNAs, ribosomal RNAs, and other noncoding RNAs. Its regulation occurs through a series of specific methyltransferases and m7G-binding proteins. Notably, m7G modification has been implicated in various diseases, prominently across multiple cancer types. Earlier studies have elucidated the significance of m7G modification in the context of immune biology regulation within the tumor microenvironment. This comprehensive review culminates in a synthesis of findings related to the modulation of immune cells infiltration, encompassing T cells, B cells, and various innate immune cells, all orchestrated by m7G modification. Furthermore, the interplay between m7G modification and its regulatory proteins can profoundly affect the efficacy of diverse adjuvant therapeutics, thereby potentially serving as a pivotal biomarker and therapeutic target for combinatory interventions in diverse cancer types.