Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution. Mol Cell. 2019;76:329-345. [PMID: 31626751 DOI: 10.1016/j.molcel.2019.09.017]

Alternative splicing of the Snap23 microexon is regulated by MBNL, QKI, and RBFOX2 in a tissue-specific manner and is altered in striated muscle diseases

The reprogramming of alternative splicing networks during development is a hallmark of tissue maturation and identity. Alternative splicing of microexons (small, genomic regions ≤ 51 nucleotides) functionally regulate protein-protein interactions in the brain and is altered in several neuronal diseases. However, little is known about the regulation and function of alternatively spliced microexons in striated muscle. Here, we investigated alternative splicing of a microexon in the synaptosome-associated protein 23 (Snap23) encoded gene. We found that inclusion of this microexon is developmentally regulated and tissue-specific, as it occurs exclusively in adult heart and skeletal muscle. The alternative region is highly conserved in mammalian species and encodes an in-frame sequence of 11 amino acids. Furthermore, we showed that alternative splicing of this microexon is mis-regulated in mouse models of heart and skeletal muscle diseases. We identified the RNA-binding proteins (RBPs) quaking (QKI) and RNA binding fox-1 homolog 2 (RBFOX2) as the primary splicing regulators of the Snap23 microexon. We found that QKI and RBFOX2 bind downstream of the Snap23 microexon to promote its inclusion, and this regulation can be escaped when the weak splice donor is mutated to the consensus 5' splice site. Finally, we uncovered the interplay between QKI and muscleblind-like splicing regulator (MBNL) as an additional, but minor layer of Snap23 microexon splicing control. Our results are one of the few reports detailing microexon alternative splicing regulation during mammalian striated muscle development.

The regulation and function of post-transcriptional RNA splicing

Eukaryotic RNA transcripts undergo extensive processing before becoming functional messenger RNAs, with splicing being a critical and highly regulated step that occurs both co-transcriptionally and post-transcriptionally. Recent analyses have revealed, with unprecedented spatial and temporal resolution, that up to 40% of mammalian introns are retained after transcription termination and are subsequently removed largely while transcripts remain chromatin-associated. Post-transcriptional splicing has emerged as a key layer of gene expression regulation during development, stress response and disease progression. The control of post-transcriptional splicing regulates protein production through delayed splicing and nuclear export, or nuclear retention and degradation of specific transcript isoforms. Here, we review current methodologies for detecting post-transcriptional splicing, discuss the mechanisms controlling the timing of splicing and examine how this temporal regulation affects gene expression programmes in healthy cells and in disease states.

Alternative splicing in autism spectrum disorder: Recent insights from mechanisms to therapy

Alternative splicing (AS) is a vital and highly dynamic RNA regulatory mechanism that allows a single gene to generate multiple mRNA and protein isoforms. Dysregulation of AS has been identified as a key contributor to the pathogenesis of autism spectrum disorders (ASD). A comprehensive understanding of aberrant splicing mechanisms and their functional consequences in ASD can help uncover the molecular basis of the disorder and facilitate the development of therapeutic strategies. This review focuses on the major aberrant splicing events and key splicing regulators associated with ASD, highlighting their roles in linking defective splicing to ASD pathogenesis. In addition, a discussion of how emerging technologies, such as long-read sequencing, single-cell sequencing, spatial transcriptomics and CRISPR-Cas systems are offering novel insights into the role and mechanisms of AS in ASD is presented. Finally, the RNA splicing-based therapeutic strategies are evaluated, emphasizing their potential to address unmet clinical needs in ASD treatment.

EFTUD2 Regulates Cortical Morphogenesis via Modulation of Caspase-3 and Aifm1 Splicing Pathways

Elongation Factor Tu GTP-Binding Domain Containing 2 (EFTUD2), a core spliceosomal GTPase associated with Mandibulofacial Dysostosis with Microcephaly (MFDM), plays a mechanistically undefined role in cerebral development. To investigate its pathophysiological contributions, murine models are generated through conditional Eftud2 ablation and in utero electroporation of human pathogenic EFTUD2 variants into cortical neural stem cells (NSCs). Embryonic NSC-specific Eftud2 knockout resulted in cortical disorganization and microcephaly, while pathogenic variants led to significant neuronal loss. Integrative transcriptomic and immunofluorescence analyses revealed that Eftud2 deficiency triggers apoptotic pathways, contributing to cortical malformations. Mechanistic studies using RNA co-immunoprecipitation and full-length transcriptome sequencing demonstrated that Eftud2 directly interacts with Caspase3 and Aifm1 transcripts, regulating their alternative splicing to generate pro-apoptotic isoforms. Splicing assays functionally validated this regulatory mechanism, showing its role in activating cell death pathways and disrupting neurodevelopmental homeostasis. These findings elucidate EFTUD2's critical role in maintaining apoptotic balance during corticogenesis and identify defective splicing regulation as the molecular basis of MFDM. This study provides insights for advancing diagnostic frameworks and therapeutic strategies for neurodevelopmental disorders.

Alternative splicing in aging and aging-related diseases: From pathogenesis to therapy

Aging is a complex biological process associated with nearly all diseases. Alternative splicing is increasingly recognized as an important contributor to aging and a key research pathway for extending human lifespan. In this review, we highlight the findings of alternative splicing in the hallmarks of aging including key processes such as genomic instability, telomere length, protein stability, autophagy processes, etc., as well as antagonistic hallmarks of aging such as various metabolic signals, energy metabolism, clearance of senescent cells, stem cell self-renewal, cell communication and inflammatory process, etc. We also discuss the roles of alternative splicing in age-related diseases, including neurodegenerative diseases, cardiovascular diseases, skeletal muscle-related diseases, metabolic disorders, cancer, sensory degeneration, and chronic inflammation, etc. These studies suggest that new anti-aging therapies could be developed by regulating key splicing proteins or specific splicing events.

RNA processing in innate immunity: regulation by RNA-binding proteins

RNA processing is an important but often overlooked process in determining protein expression. Alternative polyadenylation and regulated mRNA stability control the amount and duration of protein expression, while alternative splicing also controls protein identity and function. Much work in innate immunity has focused on the activation of transcription factors and the downstream consequences in gene expression. However, there is increasing evidence indicating that regulation of RNA processing by RNA-binding proteins (RBPs) contributes significantly to tuning the innate immune response. Herein we review work highlighting the impact of RNA processing in innate immunity and describe the RBPs and mechanisms driving this regulation. We conclude with a discussion of unanswered questions to motivate continued research in this important and understudied field.

TaPP2C-a5 fine-tunes wheat seed dormancy and germination with a Triticeae-specific, alternatively spliced transcript

INTRODUCTION

The sessile plants often experience environmental conditions not ideal for growth, and therefore have evolved strategies to survive and adapt to stress conditions. Abscisic acid (ABA) regulates plant development and abiotic stress response. Clade A type 2C protein phosphatases (PP2Cs), act as co-receptors of ABA, negatively regulate ABA signalling. However, the biological function and detailed molecular mechanism of clade A PP2Cs in ABA signalling pathway remain to be elucidated in wheat.

OBJECTIVES

To analyze the mechanisms of stress response and development mediated by ABA signal precisely regulated by TaPP2C-a5 at the post-transcriptional level in wheat, providing candidate genes for wheat improvement.

METHODS

Based on our previous results of TaPP2Cs gene family analysis, the function and detailed regulation mechanisms of TaPP2C-a5 gene in seed dormancy and germination as well as drought response mediated by ABA signaling pathway were explored through reverse genetics technology.

RESULTS

We found that class A TaPP2C-a5 underwent alternative splicing (AS) to produce two transcripts encoding TaPP2C-a5.1 and TaPP2C-a5.2, respectively. Both TaPP2C-a5.1 and TaPP2C-a5.2 were highly expressed in mature seeds, and were upregulated by exogenous ABA in seedlings. Overexpression of TaPP2C-a5.1 and TaPP2C-a5.2 coordinately negatively regulated seed dormancy and ABA-mediated seed germination as well as post-germination developmental arrest in wheat. TaPP2C-a5.1 negatively regulated drought stress response, while TaPP2C-a5.2 did not participate in drought stress response. The homologous genes of TaPP2C-a5 underwent the same AS as TaPP2C-a5 in tetraploid wheat, but not in rice.

CONCLUSION

Our results revealed that TaPP2C-a5 gene underwent AS and was involved in the regulation of seed dormancy and germination, as well as drought stress response mediated by the ABA signaling at the post-transcriptional level. Our work not only provide a potential target gene to improve PHS resistance, but also emphasize alternative splicing as a strategy with evolution contexts to fine-tune ABA signaling and its involvement in certain biological process.

Alternative Splicing of BnABF4L Mediates Response to Abiotic Stresses in Rapeseed (Brassica napus L.)

ABRE BINDING FACTOR 4 (ABF4) is a pivotal regulatory gene in the abscisic acid (ABA) signaling pathway, and changes in its expression levels can modulate the plant's stress resistance. To further explore the specific regulatory mechanisms of alternative splicing (AS) in the ABA signaling pathway and to identify new breakthroughs for breeding high stress-resistant varieties of Brassica napus, we identified 17 homologous genes of ABF4 in the genome. Utilizing bioinformatics techniques, we analyzed their motifs, conserved domains, and cis-acting elements of their promoters. Through transcriptome data from the stress-tolerant dwarf strain ndf2 and its parental line 3529, we uncovered a significantly differentially expressed ABF4 gene, which we named BnABF4L. Subsequently, we analyzed the AS events of BnABF4L under normal growth conditions and different abiotic stresses, as well as the impact of different transcript variants' 5' untranslated region (5'UTR) on gene translation. BnABF4L undergoes alternative 3' splice site (A3SS) selection to produce three transcripts (V1-V3) with divergent 5'UTRs. While V1 translation is suppressed by upstream ORFs (uORFs), V2/V3 exhibit enhanced translational efficiency. Under stress, ndf2 shifts splicing toward V3, circumventing uORF-mediated repression to upregulate stress-adapted isoforms. We validated the inhibitory effect of upstream open reading frames (uORFs) on protein-coding open reading frame (pORFs) and, based on the collective experimental results, proposed the flexible regulatory mechanism of AS events of BnABF4L in response to stress. Our findings provide new insights for future studies on stress resistance in rapeseed as well as for research on the regulation of alternative splicing mechanisms in the ABA signaling pathway.

Alternative Splicing and CaV-Associated Channelopathies

Voltage-gated calcium channels (VGCCs) are multi-subunit ion channel proteins that control and regulate a wide array of physiological processes. Their dysfunction has been implicated in several neurological, cardiac, psychiatric, endocrine, oncogenic, and muscular disorders. The diverse and specialized cellular functions involving VGCC-mediated calcium signaling stem from two primary mechanisms: differential and cell-specific expression of pore-forming (α1) and auxiliary subunit genes, and extensive alternative splicing of their pre-mRNA. All the 10 α1-encoding genes undergo alternative splicing to generate a wide array of cell-specific CaV variants with distinct biophysical, pharmacological, and protein-protein interaction properties. This proteomic diversity and the associated cell-specific expression signature of CaV splice variants are tightly regulated by trans-acting splicing factors-RNA-binding proteins that control the inclusion or skipping of alternatively spliced exons during post-transcriptional pre-mRNA processing. The discovery that several channelopathies are caused by aberrant splicing due to genetic mutations in either cis-acting binding elements on the pre-mRNA or in core splicing machinery components highlights the crucial role of alternative splicing in VGCC-related pathologies. These insights have opened new therapeutic avenues, as targeting the alternative splicing of disease-associated specific exons has recently emerged as a novel, promising treatment for neurodevelopmental disorders and channelopathies associated with splicing dysfunction.

The splicing factor SRRM2 modulates two S6K kinases to promote colorectal cancer growth

The mechanistic target of rapamycin (mTOR) pathway plays a critical role in cell growth and metabolic homeostasis. The ribosomal protein S6 kinases S6K1 and S6K2 are the major effectors of the mTOR pathway key to translation efficiency, but the underlying regulatory mechanisms remain largely unclear. In this study, we searched for mTOR regulators and found that the splicing factor SRRM2 modulates the levels of S6K1 and S6K2, thereby activating the mTOR-S6K pathway. Interestingly, SRRM2 facilitates the expression of S6K2 by modulating alternative splicing, and enhances the stability of the S6K1 protein by regulating the E3 ubiquitin ligase WWP2. Moreover, SRRM2 is highly expressed in colorectal cancer (CRC) tissues and is associated with a poor prognosis. SRRM2 promotes CRC growth in vitro and in vivo. Combined, these data reveal an oncogenic role of SRRM2 in CRC through activating the mTOR-S6K pathway by two different approaches, further suggesting SRRM2 as a potential therapeutic target for CRC.

Alternative spliceosomal protein Eftud2 mediated Kif3a exon skipping promotes SHH-subgroup medulloblastoma progression

Alternative splicing plays a pivotal role in various facets of organogenesis, immune response, and tumorigenesis. Medulloblastoma represents a prevalent childhood brain tumor, with approximately one-third classified as the Sonic Hedgehog (SHH) subgroup. Nevertheless, the contribution of alternative splicing to medulloblastoma oncogenesis remains elusive. This investigation delineated an upregulation of the spliceosomal protein Eftud2 in the SHH-subgroup medulloblastoma mouse model and human medulloblastoma patients. Targeted ablation of Eftud2 in granule precursor cells (GNPs) within the cerebellum prolonged the survival of SHH-subgroup medulloblastoma mice, indicating a putative association between Eftud2 expression and medulloblastoma prognosis. Functional assays unveiled that EFTUD2 depletion in human medulloblastoma cells significantly curtailed cellular proliferation by impeding the activation of the SHH signaling pathway. Through multi-omics sequencing analysis, it was discerned that Eftud2 influences exons 10-11 skipping of Kif3a, a kinesin motor critical for primary cilia formation. Notably, exons 10-11 skipping in Kif3a augmented human medulloblastoma cell proliferation by potentiating the transcriptional activity of Gli2. These findings underscore a robust correlation between Eftud2 and SHH-subgroup medulloblastoma, emphasizing its regulatory role in modulating downstream transcription factors through the alternative splicing of pivotal genes within the SHH signaling pathway, thereby propelling the aggressive proliferation of SHH-subgroup medulloblastoma.

The impact of an RNA-binding protein group on regulating the RSPO-LGR4/5-ZNRF3/RNF43 module and the immune microenvironment in hepatocellular carcinoma

BACKGROUND

Hepatocellular carcinoma (HCC) is a leading cause of cancer mortality. RNA-binding proteins (RBPs) are potential therapeutic targets because of their role in tumor progression. This study investigated the interactions between specific HCC progression-associated RBPs (HPARBPs), namely, ILF3, PTBP1, U2AF2, NCBP2, RPS3, and SSB, in HCC and their downstream targets, as well as their impact on the immune microenvironment and their clinical value.

METHODS

Tissue samples from human HCC, collected from 28 patients who experienced recurrence following postoperative adjuvant therapy were examined. The mRNA levels of RBPs and their prospective targets were quantified through RNA isolation and quantitative real-time PCR. Data from two public datasets were scrutinized for both expression and clinical relevance. Through Student's t test and logistic regression, HPARBPs were identified. Enhanced cross-linking immunoprecipitation (eCLIP) experiments revealed RBP-RNA interactions in HepG2 cells. For functional enrichment, Metascape was used, whereas CIBERSORT was used to characterize the immune microenvironment.

RESULTS

Public database analysis confirmed widespread RBP expression abnormalities in HCC (false discovery rate < 0.00001 and fold change ≥ 1.15 or ≤ 0.85), leading to the identification of 42 HPARBPs and core modules. eCLIP data analysis revealed the specificity of downstream target genes and binding site features for core HPARBPs (signal value > 3, P value < 0.01). Four core HPARBPs may bind to RNAs of genes in the RSPO-LGR4/5-ZNRF3/RNF43 module, affecting the Wnt pathway and HCC progression. Immunoinfiltration analysis revealed changes in the HCC immune microenvironment due to altered expression of relevant genes.

CONCLUSION

In our study, we identified core HPARBPs that might contribute to HCC progression by binding to RNAs in the RSPO-LGR4/5-ZNRF3/RNF43 module. Changes in the expression of HPARBPs affect the HCC immune microenvironment. Our findings offer novel insights into the regulatory network of Wnt pathway-related RBPs and their potential clinical value in HCC.

Targeting the RBM39-MEK5 axis synergizes with bortezomib to inhibit the malignant growth of multiple myeloma

ABSTRACT

Aberrant alternative splicing is one of the hallmarks of cancer and is potentially based on upregulated expression-of-splicing factors in some types of cancer. Our previous study suggested that the splicing factor RBM39 is significantly upregulated in multiple myeloma (MM) and that its upregulation is positively associated with poor prognosis. Here, we further demonstrate that the survival and proliferation of MM cells rely on RBM39 and that RBM39 knockdown inhibits the malignant growth of MM. Indisulam, a "molecular glue" that mediates the proteasomal degradation of RBM39, has potent suppressive effects on MM both in vitro and in vivo. Deletion of RBM39 results in extensively altered splicing, with mis-splicing of MEK5 verified to inhibit the malignant growth of MM. Full-length MEK5 plays a vital role in maintaining MM cell survival, whereas aberrant MEK5 isoforms with exon loss exhibit loss of function and a propensity for proteasomal degradation. Targeting RBM39 or MEK5 synergistically increases the cytotoxicity of bortezomib in MM cells via the inhibition of p65. Our study validates the specific mechanism of RBM39 in MM, providing an approach for broader targeting and optimized therapeutic strategies for MM.

Alternative Splicing in Lung Adenocarcinoma: From Bench to Bedside

Lung adenocarcinoma (LUAD) is a highly heterogeneous tumor and the most prevalent pathological type of lung cancer. The alternative splicing (AS) of mRNA enables the generation of multiple protein products from a single gene. This is a tightly regulated process that significantly contributes to the proteome diversity in eukaryotes. Recent multi-omics studies have delineated the splicing profiles that underline LUAD tumorigenesis from initiation to metastasis. Such progress holds robust promise to facilitate the development of screening strategies and individualized therapies. Perturbed AS fosters the emergence of novel neoantigen resources and disturbances in the immune microenvironment, which allow new investigations into modulatory targets for LUAD immunotherapy. This review presents an update on the landscape of dysregulated splicing events in LUAD and the associated mechanisms and theranostic perspectives with unique insights into AS-based immunotherapy, such as Chimeric Antigen Receptor T cell therapy. These AS variants can be used in conjunction with current therapeutic modules in LUAD, allowing bench to bedside translation to combat this highly malignant cancer.

Direct RNA sequencing reveals chicken post-transcriptional modifications in response to Campylobacter jejuni inoculation

BACKGROUND

Campylobacter jejuni (C. jejuni), is a leading cause of food-borne pathogen, poses significant threats to poultry industry and public health. Post-transcriptional modifications play crucial roles in regulating the immune system and cell functions. However, the epigenetic regulation in response to C. jejuni inoculation in chicken remains elusive.

RESULTS

The RNA transcriptional profiles and base modification alterations in the chicken cecum following C. jejuni inoculation were characterized using direct RNA sequencing and analyzed by bio-informatics and expression analysis. We identified 40,755 transcripts and 23,877 genes following C. jejuni inoculation in the chicken cecum. Of which, 10,503 novel transcripts across 8,560 genes were identified. The number of significantly differential alternative splicing events and poly(A) tails was 192 and 426, respectively (P < 0.05). Particularly, 121 significantly differentially expressed transcripts which were enriched in defense response to gram-negative bacteria, positive regulation of interleukin-6 production, innate immune response, macrophage activation (P < 0.05). Among these, 29 transcripts contained m5C sites, and 37 transcripts contained m6A sites. The transcripts containing m6A/m5C modifications displayed higher expression levels and shorter poly(A) tails than those without modifications. Functional analysis of these modules including differentially expressed transcripts (DETs), transcripts with differentially significant poly(A) tail length, m5C modified DETs, and m6A modified DETs showed that the negative regulation of interferon-beta production was enriched (P < 0.05). Specially, ENSGALT00000020390 (novel transcript), and ENSGALT00000053962 (IFIH1-202) were significantly enriched.

CONCLUSIONS

This study provided a post-transcriptional modification profile in the chicken cecum post C. jejuni inoculation, including alternative splicing, poly(A) tail length, m6A and m5C modifications. ENSGALG00000012480 and IFIH1 could be potential candidate genes as epigenetic markers following C. jejuni inoculation. The findings provide new insights into the complexity of expression regulation and data resource of the epitranscriptome, enhancing our understanding on epigenetic modification regulating C. jejuni inoculation.

Multi-Omics Analysis of Survival-Related Splicing Factors and Identifies CRNKL1 as a Therapeutic Target in Esophageal Cancer

Background: RNA alternative splicing represents a pivotal regulatory mechanism of eukaryotic gene expression, wherein splicing factors (SFs) serve as key regulators. Aberrant SF expression drives oncogenic splice variant production, thereby promoting tumorigenesis and malignant progression. However, the biological functions and potential targets of SFs remain largely underexplored. Methods: Through multi-omics analysis, we identified survival-related splicing factors (SFs) in esophageal cancer and elucidated their biological regulatory networks. To further investigate their downstream splicing targets, we combined alternative splicing events resulting from SF knockdown with those specific to esophageal cancer. Finally, these splicing events were validated through full-length RNA sequencing and confirmed in cancer cells and clinical specimens. Result: We identified six SFs that are highly expressed in esophageal cancer and correlate with poor prognosis. Further analysis revealed that these factors are significantly associated with immune infiltration, cancer stemness, tumor heterogeneity, and drug resistance. CRNKL1 was identified as a hub SFs. The target genes and pathways regulated by these SFs showed substantial overlap, suggesting their coordinated roles in promoting cancer stemness and metastasis. Specifically, alternative splicing of key markers, such as CD44 and CTTN, was regulated by most of these SFs and correlated with poor prognosis. Conclusions: Our study unveils six survival-related SFs that contribute to the aggressiveness of esophageal cancer and CTTN and CD44 alternative splicing may act as common downstream effectors of survival-related SFs. This study provides mechanistic insights into SF-mediated tumorigenesis and highlight novel therapeutic vulnerabilities in esophageal cancer.

Next-Generation Mapping of the ACINUS-Mediated Alternative Splicing Machinery and Its Regulation by O-glycosylation in Arabidopsis

Alternative splicing (AS) is a key mechanism of gene regulation, but the full repertoire of proteins involved and the regulatory mechanisms governing this process remain poorly understood. Using TurboID-based proximity labeling coupled with mass spectrometry (PL-MS), we comprehensively mapped the Arabidopsis AS machinery, focusing on the evolutionarily conserved splicing factor ACINUS, its paralog PININ, and the stable interactor SR45. We identified 298 high-confidence components, including both established and novel interactors, providing strong evidence that alternative splicing is coupled to transcription and that multiple RNA processing steps occur simultaneously in plants. Bioinformatic analysis reveals high redundancy, conserved mechanisms, and unique plant-specific features. Selected known and novel interactors were validated by AS readouts and phenotypic analysis, which also revealed a coordinated influence on splicing. Furthermore, a systematic evaluation of O-glycosylation double mutants revealed that SECRET AGENT (O-GlcNAc transferase) and SPINDLY (O-fucose transferase) modulate AS through both ACINUS-dependent and -independent pathways. Our results reveal the conserved as well as plant-specific AS regulatory network and highlight the global role of sugar modification in RNA processing.

Molecular epidemiological study of exosomes circZNF609, circPUM1, IGF2 with ischemic stroke

BACKGROUND

Ischemic stroke (IS) is a common cardiovascular disease (CVD). Insulin-like growth factor 2 (IGF2), circZNF609, and circPUM1 are involved in metabolic regulation, vascular health, neuroprotection, and inflammation modulation and are relevant to IS mechanisms. This study investigated the effects of plasma exosomal expression of circZNF609, circPUM1, and IGF2 on IS.

METHODS

The expression of circZNF609, circPUM1, and IGF2 mRNA in exosomes was detected in 145 patients with IS and 290 controls using real-time qPCR in a cross-sectional study. Q1-Q4 represents the quartile groups based on the target gene expression levels.

RESULTS

There was no significant difference in the expression levels of circZNF609 and circPUM1 in the plasma exosomes between the IS and control groups (P > 0.05). However, a nonlinear relationship between the expression levels of circZNF609 in the IS group (P < 0.05). Exosomal IGF2 mRNA expression in the IS group was significantly lower than that in the control group (P = 0.043). The multifactorial adjusted results showed that in the case-control study of IS, circZNF609 in plasma exosomes was associated with a reduced risk of disease in group Q2 (adjusted OR: 0.565; P = 0.035) compared to that in group Q1, the low-expression group. In plasma exosomes, circZNF609 expression in group Q4 was associated with a reduced risk of disease in group Q1 (adjusted OR: 0.654; P = 0.004) compared to that in group Q1 (low expression). Plasma exosomes with IGF2 showed a reduced risk in the Q4 group with high IGF2 expression compared to that in the Q1 group with low IGF2 expression (adjusted OR: 0.543; P = 0.042).

CONCLUSIONS

This study suggests that the low expression of circZNF609, circPUM1, and IGF2 in peripheral blood plasma exosomes could pose a potential risk for IS and serve as biomarkers for clinical treatment.

Clusters of deep intronic RbFox motifs embedded in large assembly of splicing regulators sequences regulate alternative splicing

The RbFox RNA binding proteins regulate alternative splicing of genes governing mammalian development and organ function. They bind to the RNA sequence (U)GCAUG with high affinity but also non-canonical secondary motifs in a concentration dependent manner. However, the hierarchical requirement of RbFox motifs, which are widespread in the genome, is still unclear. Here we show that deep intronic, tightly clustered RbFox1 motifs cooperate and are important regulators of alternative exons splicing. Bioinformatic analysis revealed that (U)GCAUG-clusters are widely present in both mouse and human genes and are embedded in sequences binding the large assembly of splicing regulators (LASR). Integrative data analysis from eCLIP and RNAseq experiments showed a global increase in RNA isoform modulation of genes with Rbfox1 eCLIP-peaks associated with these clusters. Experimentally, by employing recombineering mutagenesis in a bacterial artificial chromosome containing the NTrk2 mouse region subjected to alternative splicing we showed that tightly clustered (U)GCAUG motifs in the middle of 50 Kb introns are necessary for RbFox1 regulation of NTrk2 gene isoforms expression. Moreover, clustered (U)GCAUG-motifs promote the recruitment of RbFox1 proteins to form a Rbfox1/LASR complex required for splicing. These data suggest that clustered, distal intronic Rbfox-binding motifs embedded in LASR binding sequences are important determinants of RbFox1 function in the mammalian genome and provide a target for identification of pathogenic mutations.

Pathogenicity analysis of ATP7B in pediatric patients with Wilson's disease and functional verification of alternative splice variants

BACKGROUND

Wilson's disease (WD) is an autosomal recessive inherited disease caused by ATP7B gene mutations. Some mutations in ATP7B are presumed to be pathogenic by altering pre-mRNA splicing, while most have not been functionally verified. This study aimed to perform functional studies to verify the pathogenicity of variants that may affect pre-mRNA splicing.

METHODS

We recruited 42 pediatric patients who were clinically diagnosed with WD (Leipzig score ≥ 4) and underwent ATP7B gene sequencing. We leveraged in silico analysis and prioritized seven splice genic variants in ATP7B. Minigene assays were used to evaluate the effects of the selected variants on transcript splicing. Total RNA was extracted from peripheral blood mononuclear cells (PBMCs), and Reverse Transcription-Polymerase Chain Reaction (RT-PCR) was performed on samples from several patients to verify the splicing alterations.

RESULTS

This study screened 42 distinct mutations for their potential effects on splicing based on in silico analysis and functional verification. Five intronic variants (c.1286-1delG, c.1543 + 1G > T, c.1708-1G > C, c.1870-8A > G, and c.2121 + 3A > T) and one missense variant (c.2120A > G) were proved to alter the splicing of ATP7B transcription by minigene assays. The transcript assays demonstrated splicing changes in vivo in patient PBMCs for c.3993 T > G. The altered transcription products resulting from c.2570_2572del were confirmed by sequencing.

CONCLUSIONS

This study adds experimental evidence to genetic diagnosis based on assessing the genetic defects of 42 pediatric WD patients and provides new insights into the pathogenicity of the splicing variants.

Inverted Alu repeats in loop-out exon skipping across hominoid evolution

Background

Changes in RNA splicing over the course of evolution have profoundly diversified the functional landscape of the human genome. While DNA sequences proximal to intron-exon junctions are known to be critical for RNA splicing, the impact of distal intronic sequences remains underexplored. Emerging evidence suggests that inverted pairs of intronic Alu elements can promote exon skipping by forming RNA stem-loop structures. However, their prevalence and influence throughout evolution remain unknown.

Results

Here, we present a systematic analysis of inverted Alu pairs across the human genome to assess their impact on exon skipping through predicted RNA stem-loop formation and their relevance to hominoid evolution. We found that inverted Alu pairs, particularly pairs of AluY-AluSx1 and AluSz-AluSx, are enriched in the flanking regions of skippable exons genome-wide and are predicted to form stable stem-loop structures. Exons defined by weak 3' acceptor and strong 5' donor splice sites appear especially prone to this skipping mechanism. Through comparative genome analysis across nine primate species, we identified 67,126 hominoid-specific Alu insertions, primarily from AluY and AluS subfamilies, which form inverted pairs enriched across skippable exons in genes of ubiquitination-related pathways. Experimental validation of exon skipping among several hominoid-specific inverted Alu pairs further reinforced their potential evolutionary significance.

Conclusion

This work extends our current knowledge of the roles of RNA secondary structure formed by inverted Alu pairs and details a newly emerging mechanism through which transposable elements have contributed to genomic innovation across hominoid evolution at the transcriptomic level.

Integration of proteomics profiling data to facilitate discovery of cancer neoantigens: a survey

Cancer neoantigens are peptides that originate from alterations in the genome, transcriptome, or proteome. These peptides can elicit cancer-specific T-cell recognition, making them potential candidates for cancer vaccines. The rapid advancement of proteomics technology holds tremendous potential for identifying these neoantigens. Here, we provided an up-to-date survey about database-based search methods and de novo peptide sequencing approaches in proteomics, and we also compared these methods to recommend reliable analytical tools for neoantigen identification. Unlike previous surveys on mass spectrometry-based neoantigen discovery, this survey summarizes the key advancements in de novo peptide sequencing approaches that utilize artificial intelligence. From a comparative study on a dataset of the HepG2 cell line and nine mixed hepatocellular carcinoma proteomics samples, we demonstrated the potential of proteomics for the identification of cancer neoantigens and conducted comparisons of the existing methods to illustrate their limits. Understanding these limits, we suggested a novel workflow for neoantigen discovery as perspectives.

The Rbfox1/LASR complex controls alternative pre-mRNA splicing by recognition of multipart RNA regulatory modules

The Rbfox proteins regulate alternative pre-mRNA splicing by binding to the RNA element GCAUG. In the nucleus, most of Rbfox is bound to the large assembly of splicing regulators (LASR), a complex of RNA-binding proteins that recognize additional RNA motifs. However, it remains unclear how the different subunits of the Rbfox/LASR complex act together to bind RNA and regulate splicing. We used a nuclease protection assay to map the transcriptome-wide footprints of Rbfox1/LASR on nascent cellular RNA. In addition to GCAUG, Rbfox1/LASR binds RNA motifs for LASR subunits hnRNPs M, H/F, and C and Matrin3. These elements are often arranged in tandem, forming multipart modules of RNA motifs. To distinguish contact sites of Rbfox1 from the LASR subunits, we analyzed a mutant Rbfox1(F125A) that has lost RNA binding but remains associated with LASR. Rbfox1(F125A)/LASR complexes no longer interact with GCAUG but retain binding to RNA elements for LASR. Splicing analyses reveal that in addition to activating exons through adjacent GCAUG elements, Rbfox can also stimulate exons near binding sites for LASR subunits. Minigene experiments demonstrate that these diverse elements produce a combined regulatory effect on a target exon. These findings illuminate how a complex of RNA-binding proteins can decode combinatorial splicing regulatory signals by recognizing groups of tandem RNA elements.

ESRP2-microRNA-122 axis promotes the postnatal onset of liver polyploidization and maturation

Hepatocyte polyploidy and maturity are critical to acquiring specialized liver functions. Multiple intracellular and extracellular factors influence ploidy, but how they cooperate temporally to steer liver polyploidization and maturation or how post-transcriptional mechanisms integrate into these paradigms is unknown. Here, we identified an important regulatory hierarchy in which postnatal activation of epithelial splicing regulatory protein 2 (ESRP2) stimulates processing of liver-specific microRNA (miR-122) to facilitate polyploidization, maturation, and functional competence of hepatocytes. By determining transcriptome-wide protein-RNA interactions in vivo and integrating them with single-cell and bulk hepatocyte RNA-seq data sets, we delineated an ESRP2-driven RNA processing program that drives sequential replacement of fetal-to-adult transcript isoforms. Specifically, ESRP2 binds the primary miR-122 host gene transcript to promote its processing/biogenesis. Combining constitutive and inducible ESRP2 gain- and loss-of-function mouse models with miR-122 rescue experiments, we demonstrated that timed activation of ESRP2 augments the miR-122-driven program of cytokinesis failure, ensuring the proper onset and extent of hepatocyte polyploidization.

Post-Transcriptional Regulation of Gene Expression and the Intricate Life of Eukaryotic mRNAs

In recent years, there has been a growing appreciation for how regulatory events that occur either co- or post-transcriptionally contribute to the control of gene expression. Messenger RNAs (mRNAs) are extensively regulated throughout their metabolism in a precise spatiotemporal manner that requires sophisticated molecular mechanisms for cell-type-specific gene expression, which dictates cell function. Moreover, dysfunction at any of these steps can result in a variety of human diseases, including cancers, muscular atrophies, and neurological diseases. This review summarizes the steps of the central dogma of molecular biology, focusing on the post-transcriptional regulation of gene expression.

The main sources of molecular organization in the cell. Atlas of self-organized and self-regulated dynamic biostructures

One of the most important goals of contemporary biology is to understand the principles of the molecular order underlying the complex dynamic architecture of cells. Here, we present an overview of the main driving forces involved in the cellular molecular complexity and in the emergent functional dynamic structures, spanning from the most basic molecular organization levels to the complex emergent integrative systemic behaviors. First, we address the molecular information processing which is essential in many complex fundamental mechanisms such as the epigenetic memory, alternative splicing, regulation of transcriptional system, and the adequate self-regulatory adaptation to the extracellular environment. Next, we approach the biochemical self-organization, which is central to understand the emergency of metabolic rhythms, circadian oscillations, and spatial traveling waves. Such a complex behavior is also fundamental to understand the temporal compartmentalization of the cellular metabolism and the dynamic regulation of many physiological activities. Numerous examples of biochemical self-organization are considered here, which show that practically all the main physiological processes in the cell exhibit this type of dynamic molecular organization. Finally, we focus on the biochemical self-assembly which, at a primary level of organization, is a basic but important mechanism for the order in the cell allowing biomolecules in a disorganized state to form complex aggregates necessary for a plethora of essential structures and physiological functions. In total, more than 500 references have been compiled in this review. Due to these main sources of order, systemic functional structures emerge in the cell, driving the metabolic functionality towards the biological complexity.

STING in cancer immunoediting: Modeling tumor-immune dynamics throughout cancer development

Cancer immunoediting is a dynamic process of tumor-immune system interaction that plays a critical role in cancer development and progression. Recent studies have highlighted the importance of innate signaling pathways possessed by both cancer cells and immune cells in this process. The STING molecule, a pivotal innate immune signaling molecule, mediates DNA-triggered immune responses in both cancer cells and immune cells, modulating the anti-tumor immune response and shaping the efficacy of immunotherapy. Emerging evidence has shown that the activation of STING signaling has dual opposing effects in cancer progression, simultaneously provoking and restricting anti-tumor immunity, and participating in every phase of cancer immunoediting, including immune elimination, equilibrium, and escape. In this review, we elucidate the roles of STING in the process of cancer immunoediting and discuss the dichotomous effects of STING agonists in the cancer immunotherapy response or resistance. A profound understanding of the sophisticated roles of STING signaling pathway in cancer immunoediting would potentially inspire the development of novel cancer therapeutic approaches and overcome the undesirable protumor effects of STING activation.

Physiological and pathological roles of the transcriptional kinases CDK12 and CDK13 in the central nervous system

The cyclin-dependent kinases 12 (CDK12) and 13 (CDK13) govern several steps of gene expression, including transcription, RNA processing and translation. The main target of CDK12/13 is the serine 2 residue of the carboxy-terminal domain of RNA polymerase II (RNAPII), thus influencing the directionality, elongation rate and processivity of the enzyme. The CDK12/13-dependent regulation of RNAPII activity influences the expression of selected target genes with important functional roles in the proliferation and viability of all eukaryotic cells. Neuronal cells are particularly affected by the loss of CDK12/13, as result of the high dependency of neuronal genes on RNAPII processivity for their expression. Deregulation of CDK12/13 activity strongly affects brain physiology by influencing the stemness potential and differentiation properties of neuronal precursor cells. Moreover, mounting evidence also suggest the involvement of CDK12/13 in brain tumours. Herein, we discuss the functional role(s) of CDK12 and CDK13 in gene expression regulation and highlight similarities and differences between these highly homologous kinases, with particular attention to their impact on brain physiology and pathology. Lastly, we provide an overview of CDK12/13 inhibitors and of their efficacy in brain tumours and other neoplastic diseases.

TDP-43/ALKBH5-mediated m6A modification of CDC25A mRNA promotes glioblastoma growth by facilitating G1/S cell cycle transition

Glioblastoma (GBM) exhibits significant intratumor heterogeneity (ITH), indicating the presence of tumor cells with diverse growth rates. Here, we aimed to identify fast-growing cells in GBM and elucidate the underlying mechanisms. Precisely targeting these cells could offer an improved treatment option. Our results found that targeting ALKBH5 expression impaired GBM proliferation and tumor stemness. Nuclear but not overall expression of ALKBH5 differs between monoclonal cells derived from the same patient with different proliferation rates. Mechanistically, ALKBH5 interacted with TAR DNA-binding protein 43 (TDP-43) in fast-growing cells. Furthermore, TDP-43 facilitated the nuclear localization of ALKBH5 and its binding to cell division cycle 25A (CDC25A) pre-mRNA. The TDP-43/ALKBH5 complex regulates CDC25A mRNA splicing via N6-methyladenosine (m6A) demethylation to maintain the expression of its oncogenic isoform (CDC25A-1), ultimately promoting the G1/S phase transition and growth of GBM cells. TRAD01 selectively targeted the interaction between TDP-43 and ALKBH5, leading to significant antitumor effects both in vitro and in vivo. Our study identified a novel epigenetic mechanism by which TDP-43/ALKBH5 contributes to GBM growth via m6A modification and alternative splicing. Therefore, targeting the TDP-43/ALKBH5 axis might be a promising therapeutic strategy for GBM patients.

From computational models of the splicing code to regulatory mechanisms and therapeutic implications

Since the discovery of RNA splicing and its role in gene expression, researchers have sought a set of rules, an algorithm or a computational model that could predict the splice isoforms, and their frequencies, produced from any transcribed gene in a specific cellular context. Over the past 30 years, these models have evolved from simple position weight matrices to deep-learning models capable of integrating sequence data across vast genomic distances. Most recently, new model architectures are moving the field closer to context-specific alternative splicing predictions, and advances in sequencing technologies are expanding the type of data that can be used to inform and interpret such models. Together, these developments are driving improved understanding of splicing regulatory mechanisms and emerging applications of the splicing code to the rational design of RNA- and splicing-based therapeutics.

Characterization of aberrant splicing in pediatric central nervous system tumors reveals CLK1 as a candidate oncogenic dependency

Pediatric brain cancer is the leading cause of disease-related mortality in children, and many aggressive tumors still lack effective treatment strategies. We characterized aberrant alternative splicing across pediatric brain tumors, identifying pediatric high-grade gliomas (HGGs) among the most heterogeneous. Annotating these events with UniProt, we identified 11,940 splice events in 5,368 genes leading to potential protein function changes. We discovered CDC-like kinase 1 (CLK1) is aberrantly spliced to favor exon 4 inclusion, resulting in a gain of two phosphorylation sites and subsequent activation. Inhibition of CLK1 with Cirtuvivint significantly decreased both cell viability and proliferation in the pediatric HGG KNS-42 cell line. Morpholino-mediated depletion of CLK1 exon 4 splicing reduced RNA expression, protein abundance, and cell viability with concurrent differential expression of 78 cancer genes and differential splicing at functional sites in 193 cancer genes. Our findings highlight a dependency of pediatric HGGs on CLK1 and represent a promising therapeutic strategy.

RNA gain-of-function mechanisms in short tandem repeat diseases

As adaptors, catalysts, guides, messengers, scaffolds, and structural components, RNAs perform an impressive array of cellular regulatory functions often by recruiting RNA-binding proteins (RBPs) to form ribonucleoprotein complexes (RNPs). While this RNA-RBP interaction network allows precise RNP assembly and the subsequent structural dynamics required for normal functions, RNA motif mutations may trigger the formation of aberrant RNP structures that lead to cell dysfunction and disease. Here, we provide our perspective on one type of RNA motif mutation, RNA gain-of-function mutations associated with the abnormal expansion of short tandem repeats (STRs) that underlie multiple developmental and degenerative diseases. We first discuss our current understanding of normal polymorphic STR functions in RNA processing and localization followed by an assessment of the pathogenic roles of STR expansions in the neuromuscular disease myotonic dystrophy. We also highlight ongoing questions and controversies focused on STR-based insights into the regulation of nuclear RNA processing and export as well as the relevance of the RNA gain-of-function pathomechanism for other STR expansion disorders in both coding and noncoding genes.

Alternative splicing factors and cardiac disease: more than just missplicing?

Alternative splicing (AS) is the process wherein the exons from a single gene are joined in different combinations to produce nonidentical, albeit related, RNA transcripts. This process is important for the development and physiological function of many organs and is particularly important in the heart. Notably, AS has been implicated in cardiac disease and failure, and a growing number of genetic variants in AS factors have been identified in association with cardiac malformation and/or disease. With the field poised to interrogate how these variants affect cardiac development and disease, an understandable point of emphasis will undoubtedly be on downstream target gene missplicing. In this Perspective article, we would like to encourage consideration not only of the potential for novel disease mechanisms, but also for contributions from disruption of the ever-expanding list of nonsplicing functions ascribed to many AS factors. We discuss the emergence of a novel cardiac disease mechanism based on pathogenic RNA granules and speculate on the generality of such a mechanism among localization-disrupting AS factor genetic variants. We also highlight emerging nonsplicing functions attributed to several AS factors with cardiac disease-associated genetic variants in the hopes of pointing to avenues for exploration of mechanisms that may contribute to disease alongside target gene missplicing.

DHX9 helicase impacts on splicing decisions by modulating U2 snRNP recruitment in Ewing sarcoma cells

Ewing sarcomas (ESs) are biologically aggressive tumours of bone and soft tissues caused by chromosomal translocations yielding in-frame fusion proteins driving the neoplastic transformation. The DNA/RNA helicase DHX9 is an important regulator of cellular processes often deregulated in cancer. Using transcriptome profiling, our study reveals cancer-relevant genes whose splicing is modulated by DHX9. Immunodepletion experiments demonstrate that DHX9 impacts on the recruitment of U2 small nuclear RNP (snRNP) onto the pre-mRNA. Analysis of structure and sequence features of DHX9 target exons reveal that DHX9-sensitive exons display shorter flanking introns and contain HNRNPC and TIA1 consensus motifs. A prominent target of DHX9 is exon 11 in the Cortactin (CTTN) gene, which is alternatively spliced to generate isoforms with different activities in cell migration and tumour invasion. Alternative inclusion of the exon 11 in CTTN gene is one of the most recurrent isoform switches in multiple cancer types, thus highlighting the pivotal role of DHX9 in defining the tumour phenotype. Biochemical analyses reveal that DHX9 binding promotes the recruitment of U2snRNP, SF3B1, and SF3A2 to the splice sites flanking exon 11. These findings uncover a new role of DHX9 in the control of co-transcriptional splicing in ES, which may represent a new druggable target to counteract ES malignancy.

The changes in the ratio of Dicer1 transcripts can participate in the neuronal hypoxic response by regulating miR-29b

The nervous system is highly dependent on the supply of oxygen and nutrients, so when demand for oxygen exceeds its supply, hypoxia is induced. The hippocampus is very important in the nervous system. It has the ability to control human behavior, memory, emotion, and so on. Therefore, when the hippocampus is damaged by hypoxia, it may cause nervous system diseases such as Alzheimer's disease, Parkinson's disease, and stroke. Alternative splicing plays an important regulatory role in the processes of growth and disease occurrence and development. However, the function of hypoxia-induced alternative splicing in neurological diseases needs to be further studied. Therefore, we performed hypoxia stress on mouse hippocampal neuron HT22 cells and then analyzed differentially expressed genes and differential alternative splicing events by next-generation sequencing. Through bioinformatics analysis and verification, it was found that hypoxia stress regulated the expression of Rbm15 and the ratio of Dicer1 transcripts in HT22 cells. The change in the ratio of Dicer1 transcripts may be related to the upregulation of miR-29b under hypoxia stress. This study can provide multiple time point sequencing results and a theoretical basis for the study of hypoxia-related gene alternative splicing.

A special focus on polyadenylation and alternative polyadenylation in neurodegenerative diseases: A systematic review

Neurodegenerative diseases (NDDs) are one of the prevailing conditions characterized by progressive neuronal loss. Polyadenylation (PA) and alternative polyadenylation (APA) are the two main post-transcriptional events that regulate neuronal gene expression and protein production. This systematic review analyzed the available literature on the role of PA and APA in NDDs, with an emphasis on their contributions to disease development. A comprehensive literature search was performed using the PubMed, Scopus, Cochrane, Google Scholar, Embase, Web of Science, and ProQuest databases. The search strategy was developed based on the framework introduced by Arksey and O'Malley and supplemented by the inclusion and exclusion criteria. The study selection was performed by two independent reviewers. Extraction and data organization were performed in accordance with the predefined variables. Subsequently, quantitative and qualitative analyses were performed. Forty-seven studies were included, related to a variety of NDDs, namely Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. Disease induction was performed using different models, including human tissues, animal models, and cultured cells. Most investigations were related to PA, although some were related to APA or both. Amyloid precursor protein (APP), Tau, SNCA, and STMN2 were the major genes identified; most of the altered PA patterns were related to mRNA stability and translation efficiency. This review particularly underscores the key roles of PA and APA in the pathogenesis of NDDs through their mechanisms that contribute to gene expression dysregulation, protein aggregation, and neuronal dysfunction. Insights into these mechanisms may lead to new therapeutic strategies focused on the modulation of PA and APA activities. Further research is required to investigate the translational potential of targeting these pathways for NDD treatment.

Emerging roles of cohesin-STAG2 in cancer

Cohesin, a crucial regulator of genome organisation, plays a fundamental role in maintaining chromatin architecture as well as gene expression. Among its subunits, STAG2 stands out because of its frequent deleterious mutations in various cancer types, such as bladder cancer and melanoma. Loss of STAG2 function leads to significant alterations in chromatin structure, disrupts transcriptional regulation, and impairs DNA repair pathways. In this review, we explore the molecular mechanisms underlying cohesin-STAG2 function, highlighting its roles in healthy cells and its contributions to cancer biology, showing how STAG2 dysfunction promotes tumourigenesis and presents opportunities for targeted therapeutic interventions.

Comprehensive Omics Analysis Reveals Cold-Induced Metabolic Reprogramming and Alternative Splicing in Dendrobium officinale

Dendrobium officinale is an economically important orchid species that is sensitive to cold stress. Understanding the molecular and metabolic mechanisms underlying its response to cold is crucial for developing strategies to improve its cold tolerance. In this study, we constructed a comprehensive cold stress response dataset for D. officinale and characterized its regulatory landscape in response to varying cold stress conditions. The glycine metabolism-related genes Dca003913 and Dca022726 play pivotal roles in both cold and drought stress adaptation, and their expression is not upregulated by hormones or fungi infection. Carbohydrate metabolism showed specific dynamic changes in freezing injury cells, which involved a variety of hormonal responses. The abundance of sphingolipids was notably higher in the freezing treatment (FT) compared to the freezing recovery (FR) plants, indicating specialized metabolic adaptations at different cold intensities. An alternative splicing (AS) analysis identified 368 DAS genes, with spliceosome pathways significantly enriched. Three key ubiquitination proteins (PKU64802, XP_020672210, and PKU75555) were found to regulate splicing factors, which showed increased abundance in cold stress. This study highlights the roles of metabolic reprogramming and RNA splicing in cold adaptation, revealing a complex molecular network activated in response to cold stress.

Targeting RNA splicing modulation: new perspectives for anticancer strategy?

The excision of introns from pre-mRNA is a crucial process in the expression of the majority of genes. Alternative splicing allows a single gene to generate diverse mRNA and protein products. Aberrant RNA splicing is recognized as a molecular characteristic present in almost all types of tumors. Therefore, identifying cancer-specific subtypes from aberrant processing offers new opportunities for therapeutic development. Numerous splicing modulators, each utilizing different mechanisms, have been developed as promising anticancer therapies, some of which are in clinical trials. In this review, we summarize the splice-altered signatures of cancer cell transcriptomes and the contributions of splicing aberrations to tumorigenesis and progression. Especially, we discuss current and emerging RNA splicing-targeted strategies for cancer therapy, including pharmacological approaches and splice-switching antisense oligonucleotides (ASOs). Finally, we address the challenges and opportunities in translating these findings into clinical practice.

The Establishment of Artificial RNA Cascade Circuits for Gene Regulation Based on Doxycycline-Induced Pre-mRNA Alternative Splicing

This study developed an artificial chimeric intron module with an RNA riboswitch and TetR aptamer that were integrated into essential gene exons. Doxycycline can modulate Pre-mRNA alternative splicing, modify the exon reading frame, and dynamically regulate gene expression. By shifting the aptamer 2 base pair within the switch, we unexpectedly obtained the "on-switch" CTM and "off-switch" C2ITetR>4A, which possess thoroughly contrasting regulatory functions. The CTM module can conditionally induce tumor cell apoptosis and regulate genes reversibly and sustainably following doxycycline induction. We integrated the C2ITetR>4A/CTM switches with the L7Ae/k-turn module to create an intron-spliced double-switched RNA cascade system. The system can both activate and inhibit the splicing mechanism utilizing the same ligand to minimize crosstalk among aptamer switching elements, control target gene leakage, and enhance the dynamic range of gene expression. We analyzed numerous factors affecting Pre-mRNA splicing to identify the optimal equilibrium point for switch regulation. This will enable precise predictions of dynamic regulatory efficiency and the rational design of genetic modules, thereby providing a valuable instrument for mammalian synthetic biology.

Hybrid exons evolved by coupling transcription initiation and splicing at the nucleotide level

Exons within transcripts are traditionally classified as first, internal or last exons, each governed by different regulatory mechanisms. We recently described the widespread usage of 'hybrid' exons that serve as terminal or internal exons in different transcripts. Here, we employ an interpretable deep learning pipeline to dissect the sequence features governing the co-regulation of transcription initiation and splicing in hybrid exons. Using ENCODE data from human tissues, we identified 80 000 hybrid first-internal exons. These exons often possess a relaxed chromatin state, allowing transcription initiation within the gene body. Interestingly, transcription start sites of hybrid exons are typically centered at the 3' splice site, suggesting tight coupling between splicing and transcription initiation. We identified two subcategories of hybrid exons: the majority resemble internal exons, maintaining strong 3' splice sites, while a minority show enrichment in promoter elements, resembling first exons. Diving into the evolution of their sequences, we found that human hybrid exons with orthologous first exons in other species usually gained 3' splice sites or whole exons upstream, while those with orthologous internal exons often gained promoter elements. Overall, our findings unveil the intricate regulatory landscape of hybrid exons and reveal stronger connections between transcription initiation and RNA splicing than previously acknowledged.

Alternative Splicing at the Crossroad of Inflammatory Bowel Diseases and Colitis-Associated Colon Cancer

The risk of developing colorectal cancer (CRC) is increased in ulcerative colitis patients compared to the general population. This increased risk results from the state of chronic inflammation, a well-known tumour-promoting condition. This review explores the pathologic and molecular characteristics of colitis-associated colon cancer (CAC), emphasizing the distinct features from sporadic CRC. We focus on the key signalling pathways involved in the transition to CAC, highlighting the emerging role of alternative splicing in these processes, namely on how inflammation-induced alternative splicing can significantly contribute to the increased CRC risk observed among UC patients. This review calls for more transcriptomic studies to elucidate the molecular mechanisms through which inflammation-induced alternative splicing drives CAC pathogenesis. A better understanding of these splicing events is crucial as they may reveal novel biomarkers for disease progression and have the potential to target changes in alternative splicing as a therapeutic strategy.

hnRNPU-mediated pathogenic alternative splicing drives gastric cancer progression

BACKGROUND

Alternative splicing (AS) is a process that facilitates the differential inclusion of exonic sequences from precursor messenger RNAs, significantly enhancing the diversity of the transcriptome and proteome. In cancer, pathogenic AS events are closely related to cancer progression. This study aims to investigate the role and regulatory mechanisms of AS in gastric cancer (GC).

METHODS

We analyzed AS events in various tumor samples and identified hnRNPU as a key splicing factor in GC. The effects of hnRNPU on cancer progression were assessed through in vitro and in vivo experiments. Gene knockout models and the FTO inhibitor (meclofenamic acid) were used to validate the interaction between hnRNPU and FTO and their impact on AS.

RESULTS

We found that hnRNPU serves as a key splicing factor in GC, and its high expression is associated with poor clinical prognosis. Genetic depletion of hnRNPU significantly reduced GC progression. Mechanistically, the m6A demethylase FTO interacts with hnRNPU transcripts, decreasing the m6A modification levels of hnRNPU, which leads to exon 14 skipping of the MET gene, thereby promoting GC progression. The FTO inhibitor meclofenamic acid effectively inhibited GC cell growth both in vitro and in vivo.

CONCLUSION

The FTO/hnRNPU axis induces aberrant exon skipping of MET, thereby promoting GC cell growth. Targeting the FTO/hnRNPU axis may interfere with abnormal AS events and provide a potential diagnostic and therapeutic strategy for GC.

Downregulation of hnRNPA1 inhibits hepatocellular carcinoma cell progression by modulating alternative splicing of ZNF207 exon 9

Introduction

Hepatocellular carcinoma (HCC) is the most prevalent liver cancer and a leading cause of cancer-related deaths worldwide. Heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) plays a critical role in RNA metabolism, including alternative splicing, which is linked to cancer progression. Our study investigated the role of hnRNPA1 in HCC and its potential as a therapeutic target.

Methods

We analyzed hnRNPA1 expression in HCC tissues compared to non-tumor tissues using RNA-seq and immunohistochemistry. hnRNPA1 was knocked down in Hep G2 cells to assess its impact on cell proliferation, migration, and apoptosis using scratch assays, flow cytometry, qPCR, and Western blot. We also explored the interaction between hnRNPA1 and ZNF207, as well as its splicing effects and downstream signaling pathways by RIP assay, bioinformatics, qPCR and Western blot.

Results

hnRNPA1 was significantly upregulated in HCC tissues compared to normal tissues, correlating with poor patient survival. hnRNPA1 knockdown reduced Hep G2 cell proliferation and migration while increasing apoptosis. We identified that hnRNPA1 bound to ZNF207 and regulated its exon 9 skipping, influencing ZNF207 splicing and the PI3K/Akt/mTOR pathway, key regulators of cell growth and survival.

Conclusion

Our findings demonstrate that hnRNPA1 promotes HCC progression by regulating ZNF207 splicing and the PI3K/Akt/mTOR pathway. hnRNPA1-ZNF207 interaction represents a potential therapeutic target for HCC, providing insights into the molecular mechanisms underlying HCC progression.

CircSugp1 interacts with CPSF6 to modulate intestinal mucosa repair by regulating alternative polyadenylation-mediated shortening of the Wdr89 3'UTR

Circular RNAs are a single-stranded non-coding RNAs and play an important role in the development of many diseases. Alternative polyadenylation (APA) regulates the gene 3'UTR length for controlling gene expressions. Although the APA mechanism has been widely studied in the development of diseases, there is no data on its role in the burned intestinal mucosa. We thus herein assessed the role of the circSugp1-initiating APA mechanism in the burned intestinal mucosa. CircSugp1 was downregulated in the intestinal mucosa of burned mice. CircSugp1 promoted proliferation and migration in vitro and in vivo. CircSugp1 promotes the expression of CPSF6; the overexpression of CPSF6 can shorten the gene 3'UTR within the transcript APA range. The promoting effect of circSugp1 on value-added migration was mediated by the APA regulation of the Wdr89 short 3'UTR isoform. CircSugp1 targeted the upregulation of the expression of CPSF6, followed by upregulation of the expression of Wdr89 through APA, promoting the repair of intestinal mucosal damage in burned mice.

Mis-splicing of a neuronal microexon promotes CPEB4 aggregation in ASD

The inclusion of microexons by alternative splicing occurs frequently in neuronal proteins. The roles of these sequences are largely unknown, and changes in their degree of inclusion are associated with neurodevelopmental disorders1. We have previously shown that decreased inclusion of a 24-nucleotide neuron-specific microexon in CPEB4, a RNA-binding protein that regulates translation through cytoplasmic changes in poly(A) tail length, is linked to idiopathic autism spectrum disorder (ASD)2. Why this microexon is required and how small changes in its degree of inclusion have a dominant-negative effect on the expression of ASD-linked genes is unclear. Here we show that neuronal CPEB4 forms condensates that dissolve after depolarization, a transition associated with a switch from translational repression to activation. Heterotypic interactions between the microexon and a cluster of histidine residues prevent the irreversible aggregation of CPEB4 by competing with homotypic interactions between histidine clusters. We conclude that the microexon is required in neuronal CPEB4 to preserve the reversible regulation of CPEB4-mediated gene expression in response to neuronal stimulation.

Comprehensive Analysis of Prognostic Alternative Splicing Signatures in Tumor Immune Infiltration in Bladder Cancer

BACKGROUND

Bladder cancer exhibits substantial heterogeneity encompassing genetic expressions and histological features. This heterogeneity is predominantly attributed to alternative splicing (AS) and AS-regulated splicing factors (SFs), which, in turn, influence bladder cancer development, progression, and response to treatment.

OBJECTIVE

This study aimed to explore the immune landscape of aberrant AS in bladder cancer and establish the prognostic signatures for survival prediction.

METHODS

Bladder cancer-related RNA-Seq, transcriptome, and corresponding clinical information were downloaded from The Cancer Genome Atlas (TCGA). Gene set enrichment analysis (GSEA) was used to identify significantly enriched pathways of cancer-related AS events. The underlying interactions among differentially expressed genes (DEGs) and cancer-related AS events were assessed by a protein-protein interaction network. Univariate and multivariate Cox regression analyses were performed to identify crucial prognostic DEGs that co-occurred with cancer-related AS events (DEGAS) for overall survival. The area under the curve (AUC) of receiver operating characteristic (ROC) curves was used to assess the efficiency of the prognostic signatures. The CIBERSORT algorithm was used to explore the abundance of immune infiltrating cells.

RESULTS

A total of 3755 cancer-related AS events and 3110 DEGs in bladder cancer were identified. Among them, 379 DEGs co-occurred with cancer-related AS events (DEGAS), of which 102 DEGAS were associated with 14 dysregulated SFs. GSEA and KEGG analysis showed that cancer-related AS events were predominantly enriched in pathways related to immunity, tumorigenesis, and treatment difficulties of bladder cancer. Multivariate Cox regression analysis identified 8 DEGAS (CABP1, KCNN2, TNFRSF13B, PCDH7, SNRPA1, APOLD1, CX3CL1, and DENND5A) significantly associated with OS, and they were further integrated into the prediction model with good AUCs at 3-year, 5-year and 7-year ROC curves (all>0.7). Immune infiltration analysis revealed the significant enrichment of three immune cell types (B cells naïve, dendritic cells resting, and dendritic cell activated) in high-risk bladder cancer patients.

CONCLUSION

This study not only unveiled comprehensive prognostic signatures of AS events in bladder cancer but also established a robust prognostic model based on survival-related DEGAS. These aberrant AS events, dysregulated SFs, and the identified 8 DEGAS may have significant clinical potential as therapeutic targets for bladder cancer.

RNA splicing: a split consensus reveals two major 5' splice site classes

The established consensus sequence for human 5' splice sites masks the presence of two major splice site classes defined by preferential base-pairing potentials with either U5 snRNA loop 1 or the U6 snRNA ACAGA box. The two 5' splice site classes are separable in genome sequences, sensitized by specific genotypes and associated with splicing complexity. The two classes reflect the commitment to 5' splice site usage occurring primarily during 5' splice site transfer to U6 snRNA. Separating the human 5' splice site consensus into its two major constituents can help us understand fundamental features of eukaryote genome architecture and splicing mechanisms and inform treatment design for diseases caused by genetic variation affecting splicing.

Evolutionarily Developed Alternatively Spliced Exons Containing Translation Initiation Sites

Alternative splicing is essential for the generation of various protein isoforms that are involved in cell differentiation and tissue development. In addition to internal coding exons, alternative splicing affects the exons with translation initiation codons; however, little is known about these exons. Here, we performed a systematic classification of human alternative exons using coding information. The analysis showed that more than 5% of cassette exons contain translation initiation codons (alternatively skipped exons harboring a 5' untranslated region and coding region, 5UC-ASEs) although their skipping causes the deletion of translation initiation sites essential for protein synthesis. The splicing of 5UC-ASEs is under the repressive control of MATR3, a DNA/RNA-binding protein associated with neurodegeneration, and is distinctly regulated particularly in the human brain, muscle, and testis. Interestingly, MATR3 represses its own translation by skipping a 5UC-ASE in MATR3 to autoregulate its expression level. 5UC-ASEs are larger than other types of alternative exons. Furthermore, evolutionary analysis revealed that 5UC-ASEs have already appeared in cartilaginous fishes, have increased in amphibians, and are concentrated in the genes involved in transcription in mammals. Taken together, our analysis identified a unique set of alternative exons, 5UC-ASEs, that have evolutionarily acquired a repression mechanism for gene expression through association with MATR3.

Identification of RBP binding sites using RNA deaminases

RNA-binding proteins (RBPs) are critical regulators of gene expression and RNA processing. Identification of their binding sites has important implications for their physiological and disease-related functions. Crosslinking and immunoprecipitation, followed by sequencing (CLIP-seq) and its derivatives, are the most commonly used methods to identify RBP binding sites, but are laborious and require a large amount of starting material. Recent advancements harnessing RNA deaminases in fusion to any RBP of interest, allow for the profiling of RBP binding sites from low-input samples in simpler procedures. Among these efforts, we developed STAMP (Surveying Targets by APOBEC-Mediated Profiling), which efficiently detects RBP-RNA interactions. This chapter describes the detailed protocol for the STAMP method, including plasmid construction, delivery and sorting, library preparation and bioinformatic data analysis.