RNA splicing: Novel star in pulmonary diseases with a treatment perspective

Abstract

Alternative splicing (AS) serves as a fundamental regulatory mechanism in gene expression, contributing to proteomic diversity by generating an array of mRNA isoforms from precursor mRNA via distinct splice site combinations. In light of the limited therapeutic options currently available, the exploration of AS as a target for drug development is of paramount importance. This review offers an exhaustive analysis of the biological functions and underlying molecular mechanisms associated with various AS-induced splice variants, RNA-binding proteins, and cis-elements, highlighting their significance as clinical biomarkers. We place particular emphasis on the current therapeutic applications of AS in an array of lung diseases, including but not limited to lung cancer, cystic fibrosis, silicosis, acute respiratory distress syndrome, pneumonia, asthma, chronic obstructive pulmonary diseases, pulmonary arterial hypertension, and idiopathic pulmonary fibrosis. The review delves into the role of AS events in the diagnosis and treatment of lung diseases, focusing on the regulatory influence of splicing factors and RNA-binding proteins, while also enumerating the mutated components implicated in AS misregulation. Consequently, a comprehensive understanding of the intricate mechanisms governing these splicing events could potentially offer novel avenues for the development of splicing-targeted therapeutics and diagnostic tools for the prevention and treatment of lung diseases.

Keywords: Analysis method; Biomarkers; Lung diseases; RNA splicing; RNA-binding proteins; Splicing factor; Splicing variants; Therapeutic targets.

Graphical abstract

Figure 1

The inaugural documentation and evolutionary history of RNA alternative splicing in the context of pulmonary diseases.

Figure 2

An overview of the major spliceosome's role in pre-mRNA splicing. At the beginning of splicing, the 5′ splicing site interacts with U1snRNP, U2AF65 interacts with the polypyrimidine region, and U2AF35 binds to the 3′ splicing site. Subsequently, U2AF65 mediated the binding of Branchpoint Binding Protein (BBP) to branching sites, forming early complexes. Subsequently, U2AF mediates U2 to replace BBP and bind to the branching site, complementing and pairing with nucleotide bases near the branching site. However, due to the inability to pair adenosine at the branching site, protrusions will form, making it easy to undergo ester transfer reactions with the 5′ splicing site. Afterward, U4 and U6 are paired through base complementarity, while U5 is added to the complex through protein interactions. After releasing U1, U6 pairs with the 5′ splicing site. Then U4 is released, in which base complementary pairing occurs between U2 and U6, generating a catalytic active site, making the 5′ splice site close to the branching site, and completing the first transesterification reaction. U5 promotes the proximity of 5′ and 3′ junction sites, connecting the two exons, and finally releasing mature mRNA and snRNPs.

Figure 3

AS-related splicing factors and RBPs in lung diseases. AS, or alternative splicing, is a crucial process that takes place after transcription in gene expression. It allows for the production of multiple mRNA variants from a single gene, resulting in a wider range of protein diversity. RNA-binding proteins (RBPs) associated with AS play a significant role in determining the fate of mRNAs through various functional mechanisms. In particular, selective splicing and RBPs have been found to play important roles in a variety of lung diseases, including IPF, CF, PAH, ALI, lung cancer, PTB, COPD, asthma, and silicosis.

Figure 4

Application of RNA splicing in pulmonary diseases. (A) AS as a biomarker, can be used to differentiate between different types of tumors as well as subtypes of tumors and are associated with tumor staging and patient prognosis. Therefore, variable splicing has the potential to be used as a biomarker for specific clinical conditions. (B) AS and Drug Resistance: AS has been shown to play a role in tumor drug resistance. For instance, when the RNA-binding protein PRPF8 is specifically reduced, it can lead to the skipping of exon 3 in ERCC1, which in turn reduces the ability to repair DNA damage. This can result in increased resistance to cisplatin in lung cancer and also activate the cGAS–STING natural immune pathway. (C) As a therapeutic target, antisense nucleotides can be designed to target specific splicing events, thereby restoring the normal phenotype of cells. This approach is currently being evaluated in clinical trials. Additionally, small molecule complexes can be used to modulate splicing factors, potentially leading to varying effects depending on the type of tumor and the specific mutation of the splicing factor. (D) The spliceosome can serve as both a direct target for drugs and a tumor marker. For example, in some lung cancer patients, exon 14 jumps of the MET gene have been detected in the somatic cells. These patients are sensitive to MET-targeted therapies, making exon 14 jumps in the MET gene a potential secondary diagnostic marker.