Targeting serine- and arginine-rich splicing factors to rectify aberrant alternative splicing

Epigenetic Regulation and Therapeutic Targeting of Alternative Splicing Dysregulation in Cancer

Alternative splicing enables a single precursor mRNA to generate multiple mRNA isoforms, leading to protein variants with different structures and functions. Abnormal alternative splicing is frequently associated with cancer development and progression. Recent studies have revealed a complex and dynamic interplay between epigenetic modifications and alternative splicing. On the one hand, dysregulated epigenetic changes can alter splicing patterns; on the other hand, splicing events can influence epigenetic landscapes. The reversibility of epigenetic modifications makes epigenetic drugs, both approved and investigational, attractive therapeutic options. This review provides a comprehensive overview of the bidirectional relationship between epigenetic regulation and alternative splicing in cancer. It also highlights emerging therapeutic approaches aimed at correcting splicing abnormalities, with a special focus on drug-based strategies. These include epigenetic inhibitors, antisense oligonucleotides (ASOs), small-molecule compounds, CRISPR-Cas9 genome editing, and the SMaRT (splice-switching molecule) technology. By integrating recent advances in research and therapeutic strategies, this review provides novel insights into the molecular mechanisms of cancer and supports the development of more precise and effective therapies targeting aberrant splicing.

Establishment of an alternative splicing prognostic risk model and identification of FN1 as a potential biomarker in glioblastoma multiforme

Aberrant alternative splicing and abnormal alternative splicing events (ASEs) in glioblastoma multiforme (GBM) remain largely elusive. The prognostic-associated ASEs in GBM were identified and summarized into 123 genes using GBM and LGG datasets from ASCancer Atlas and TCGA. The eleven genes (C2, COL3A1, CTSL, EIF3L, FKBP9, FN1, HPCAL1, HSPB1, IGFBP4, MANBA, PRKAR1B) were screened to develop an alternative splicing prognostic risk score (ASRS) model through machine learning algorithms. The model was trained on the TCGA-GBM cohort and validated with four external datasets from CGGA and GEO, achieving AUC values of 0.808, 0.814, 0.763, 0.859, and 0.836 for 3-year survival rates, respectively. ASRS could be an independent prognostic factor for GBM patients (HR > 1.8 across three datasets) through multivariate Cox regression analysis. The high-risk group demonstrated poorer prognosis, elevated immune scores, increased levels of immune cell infiltration, and greater differences in drug sensitivity. We found that FN1, used for model construction, contained 4 abnormal ASEs resulting in high expression of non-canonical transcripts and the presence of premature termination codon. These abnormal ASEs may be regulated by tumour-related splicing factors according to the PPI network. Furthermore, both mRNA and protein levels of FN1 were highly expressed in GBM compared to LGG, correlating with poor prognosis in GBM. In conclusion, our findings highlight the role of ASEs in affecting the progression of GBM, and the model showed a potential application for prognostic risk of patients. FN1 may serve as a promising splicing biomarker for GBM, and mechanisms of processes of aberrant splicing need to be revealed in the future.

mRNA Transcript Variants Expressed in Mammalian Cells

Gene expression or gene regulation studies often assume one gene expresses one mRNA. However, contrary to the conventional idea, a single gene in mammalian cells can express multiple transcript variants translated into several different proteins. The transcript variants are generated through transcription from alternative start sites and alternative post-transcriptional processing of the precursor mRNA (pre-mRNA). In addition, gene mutations and RNA editing further enhance the diversity of the transcript variants. The transcript variants can encode proteins with various domains, expanding the functional repertoire of a single gene. Some transcript variants may not encode proteins but function as non-coding RNAs and regulate gene expression. The expression level of the transcript variants may vary between cell types or within the same cells under different biological conditions. Transcript variants are characteristic of cell differentiation in a particular tissue, and the variants may play a key role in normal development and aging. Studies also reported that some transcript variants may have roles in disease pathogenesis. The biological significances urge studying the complexity of gene expression at the transcript level. This article updates the molecular basis of transcript variants in mammalian cells, including the formation mechanisms and potential roles in host biology. Gaining insight into the transcript variants will not only identify novel mechanisms of gene regulation but also unravel the role of the variants in health and disease.

Functional evaluation of rare variants in complement factor I using a minigene assay

The regulatory serine protease, complement factor I (FI), in conjunction with one of its cofactors (FH, C4BP, MCP, or CR1), plays an essential role in controlling complement activity through inactivation of C3b and C4b. The functional impact by missense variants in the CFI gene, particularly those with minor allele frequencies of 0.01% to 0.1%, is infrequently studied. As such, these variants are typically classified as variants of uncertain significance (VUS) when they are identified by clinical testing. Herein, we utilized a minigene splicing assay to assess the functional impact of 36 ultra-rare variants of CFI. These variants were selected based on their minor allele frequencies (MAF) and their association with low-normal FI levels. Four variants lead to aberrant splicing-one 5' consensus splice site (NM_000204.5: c.1429G>C, p.Asp477His) and three exonic changes (c.355G>A, p.Gly119Arg; c.472G>A, p.Gly158Arg; and c.950G>A, p.Arg317Gln)-enabling their reclassification to likely pathogenic (LP) or pathogenic (P) based on ACMG guidelines. These findings underscore the value of functional assays, such as the minigene assay, in assessing the clinical relevance of rare variants in CFI.