Search Results (320)

Fanconi anemia (FA) is a DNA repair deficiency disorder associated with genomic and chromosomal instability and a high cancer risk. In a small percentage of cases, FA is caused by biallelic pathogenic variants (PVs) in the BRCA2/FANCD1 gene, defining the FA-D1 subtype. Experimental and epidemiologic data indicate that the complete absence of BRCA2 is incompatible with viability. Therefore, cells from individuals affected with FA caused by biallelic BRCA2 PVs must have a residual BRCA2 function. This activity may be maintained through hypomorphic missense mutations, translation termination–reinitiation associated with a translational stop mutation, or other non-canonical or uncommon translation initiation and elongation events. In some cases, however, residual BRCA2 function is provided by alternatively or aberrantly spliced BRCA2 transcripts. Here, we review and debate aspects of the contribution of splicing in the 5′ segment to BRCA2 functions in the context of PVs affecting this largely intrinsically disordered protein region, with a focus on recent findings in individuals with FA-D1. In this Perspective, we also discuss some of the broader biological implications and open questions that arise from considering 5′-terminal BRCA2 splicing in light of old and new findings from FA-D1 patients and beyond. Full article

Background/Objectives: Apolipoprotein E receptor-2 (apoER2) exists in various alternatively spliced forms, including variants that express apoER2 with or without exon 19 in the cytoplasmic domain. This study compared vascular response to endothelial denudation, as well as diet-induced atherosclerotic and metabolic diseases, between genetically modified mice that exclusively expressed the apoER2 splice variant with or without exon 19 to determine the impact of apoER2 exon 19 motif in cardiometabolic disease modulation. Methods: Vascular response to injury was assessed by measuring neointima area of the carotid arteries after endothelial denudation. The genetically modified mice were also fed a high-fat high-cholesterol diet for 16 weeks for the determination of body weight gain, glucose and insulin levels, glucose tolerance and insulin secretion. Additionally, adipose tissue inflammation was assessed by analysis of adipose gene expression, and atherosclerosis was characterized by measuring fatty lesion size in the whole aorta, as well as in the aortic roots. Results: The results showed that whereas the expression of either splice variant is sufficient to impede denudation-induced fibrotic neointima formation and complex necrotic atherosclerotic lesions, the expression of the apoER2 splice variant containing exon 19 is necessary for the complete protection of injury-induced neointima formation in the vessel wall. However, exclusive expression of either apoER2 cytoplasmic splice variant does not influence the early phase of atherogenesis. Additionally, the exclusive expression of apoER2 without exon 19 promotes adipocyte inflammation and accelerates diet-induced insulin resistance and glucose intolerance. Conclusions: These results indicate that the apoER2 cytoplasmic variants have distinct and cell type-specific roles in influencing cardiometabolic disease development. Full article

Synaptic plasticity is the key mechanism underlying learning and memory. Neurexins are pre-synaptic molecules that play a pivotal role in synaptic plasticity, interacting with many different post-synaptic molecules in the formation of neural circuits. Neurexins are alternatively spliced at different splice sites, yielding thousands of isoforms with different properties of interaction with post-synaptic molecules for a quick adaptation to internal and external inputs. The endocannabinoid system also plays a central role in synaptic plasticity, regulating key retrograde signaling at both excitatory and inhibitory synapses. This study aims at elucidating the crosstalk between alternative splicing of neurexin and the endocannabinoid system in the hippocampus. By employing an ex vivo hippocampal system, we found that pharmacological activation of cannabinoid receptor 1 (CB1) with the specific agonist ACEA led to reduced neurotransmission, associated with increased expression of the Nrxn1–3 spliced isoforms excluding the exon at splice site 4 (SS4−). In contrast, treatment with the CB1 antagonist AM251 increased glutamatergic activity and promoted the expression of the Nrxn variants including the exon (SS4+) Knockout of the involved splicing factor SLM2 determined the suppression of the exon splicing at SS4 and the expression only of the SS4+ variants of Nrxns1–3 transcripts. Interestingly, in SLM2 ko hippocampus, modulation of neurotransmission by AM251 or ACEA was abolished. These findings suggest a direct crosstalk between CB1-dependent signaling, neurotransmission and expression of specific Nrxns splice variants in the hippocampus. We propose that the fine-tuned regulation of Nrxn1–3 genes alternative splicing may play an important role in the feedback control of neurotransmission by the endocannabinoid system. Full article

Background: Canine oral melanoma (COM) is an aggressive and often fatal neoplasm in dogs, with clinical and molecular similarities to human melanoma. Despite its relevance as a comparative oncology model, the molecular mechanisms underlying COM remain poorly understood. This study aimed to characterize gene expression profiles in COM to identify differentially expressed genes (DEGs), potential biomarkers, and therapeutic targets. Methods: In this pilot study, we performed RNA sequencing (RNA-seq) on tumor and healthy oral tissue samples from dogs. Two independent analytical pipelines—Bowtie2-DESeq2 and HISAT-StringTie-Ballgown—were used to ensure robustness in DEG detection. We also conducted pathway enrichment and isoform-level analyses to investigate biological processes and alternative splicing events. Results: Both approaches identified a core set of 929 common DEGs. Key oncogenic pathways, including MAPK/ERK and cell cycle regulation, were significantly affected, with notable upregulation of BRAF, NRAS, CDK4, and MITF (log2FC = 2.86, p < 0.001). The transcription factor SOX10 and the cytokine IL-33, both previously implicated in melanoma progression, were consistently overexpressed. Additionally, NF1, a known RAS pathway inhibitor, was also upregulated. Isoform analysis revealed novel transcript variants, suggesting a complex layer of post-transcriptional regulation in COM. Many DEGs remained uncharacterized, and chromosomal distribution analysis highlighted potential genomic influences. Conclusions: Our findings provide new insights into the molecular landscape of COM, reinforcing its utility as a model for human melanoma. The identification of conserved oncogenic pathways and novel transcript variants opens avenues for further functional studies and the development of targeted therapies in both veterinary and human oncology. Full article

The existence of s-DAPK-1, an alternatively spliced variant of DAPK-1, adds complexity to our understanding of the proteins involved in the regulation of cell survival, apoptosis, and autophagy. DAPK-1 has been implicated in the regulation of these processes; however, it remains unclear whether s-DAPK-1 also plays a similar role or a separate function; thus, determining its involvement in these processes is challenging due to the limited understanding of its regulation, interacting partners, function, and three-dimensional (3D) structure. Hence, this study was aimed at (1) understanding the regulation of s-DAPK-1 by predicting its microRNA targets, (2) predicting the 3D structure of s-DAPK-1, (3) its physicochemical and thermodynamic properties, (4) its interacting partners, and (5) molecular functions using computational methods. To achieve this aim, various bioinformatics tools and in silico webservers, such as ProteinPrompt, ProtParam, ProtScale, ScooP, Hawkdock, Phyre2, I-TASSER, PSIPRED, SAVES, and PROCHECK, along with user-friendly databases, such as NCBI, TarBase, and Protein Data Bank (PDB), were employed. For miRNA prediction, we used TarBase, and identified the specific microRNAs targeting s-DAPK-1. Furthermore, the Phyre2 database demonstrated that s-DAPK-1 possesses 40% alpha helices and 4% beta strands, forming a stable 3D structure. Additionally, s-DAPK-1 demonstrated stability to withstand high temperatures, suggesting that it is a thermostable protein. Moreover, s-DAPK-1 was found to interact with a variety of proteins involved in tumor progression and gene regulation, including a prion protein and histone H2B type 2-E (H2B2E). This suggests that s-DAPK-1 may perform diverse molecular functions such as regulation of metabolic processes, nucleic acid binding, and mRNA splicing by interacting with different proteins. Full article

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. Full article

The crustacean hyperglycemic hormone (CHH) is a unique multifunctional neuroendocrine hormone superfamily in crustaceans, crucial for maintaining physiological homeostasis and stress adaptation. To explore the role of CHHs in shrimp metabolism and growth, we identified LvCHH Ia, a CHH family member who regulates glucose metabolism in the Pacific white shrimp (Litopenaeus vannamei), through CHH family gene classification, phylogenetic analysis, gene structure analysis, and transcription factor binding site (TFBS) prediction. Subsequently, we cloned two alternative splicing variants of this gene, LvCHH Ia-1 and LvCHH Ia-2, both expressed in the nervous system but with different expression levels, and LvCHH Ia-2 exhibiting a broader tissue distribution. Using interference (RNAi)-mediated gene silencing and recombinant protein injection, we investigated the functional similarities and differences between the two variants. Our results show that both variants affect glucose metabolism by modulating the expression of key enzyme genes involved in gluconeogenesis/glycolysis, such as HK, TPI, PCK1, ALD. Specifically, they likely regulate hemolymph glucose levels via the Wnt and PI3K-AKT signaling pathways, with LvCHH Ia-1 exerting a more sustained effect on glucose metabolism compared to LvCHH Ia-2. Furthermore, LvCHH Ia may also act as a molting inhibitory hormone by suppressing the expression of ecdysone synthesis-related genes, where LvCHH Ia-2 plays a more significant role. These findings deepen our understanding of CHH regulatory mechanisms in crustaceans and provide potential applications for shrimp physiological research and aquaculture. Full article

This study investigated whether exercise training improved cholesterol metabolism through modifying alternative splicing of the low-density lipoprotein receptor (LDLR). Blood lipids and expressions of LDLR splice variants were compared between exercise-trained and non-trained young adults with normal and high cholesterol. The expression of LDLR splice isoforms were examined using RT-PCR and the histone H3K36me3 by CHIP-assay in mouse liver following a 13-week normal or high-cholesterol-diet combined with or without 8 weeks of aerobic exercise-training. The influence of histone modifications on LDLR alternative splicing was examined in HepG2 cells (human liver cell-line). Expression levels of LDLR deletions in exons 4 and 12 (LDLR-∆Exon4 and LDLR-∆Exon12) were significantly higher in the obese adults with high-cholesterol. These LDLR splice variants were significantly lower in the exercise-trained than non-trained group with normal cholesterol. Thirteen weeks of high-cholesterol feeding increased LDLR-∆Exon14 expression in mice, which was diminished after 8 weeks of exercise training. When H3-K36me3 or the MORF-related gene on chromosomes 15 were overexpressed and interfered, the levels of LDLR-∆Exon4 and LDLR-∆Exon12 expression in HepG2 cells were significantly augmented and inhibited, respectively. Hypercholesterolemia was associated with augmented expressions of LDLR splice variants in obese adults and following high-cholesterol diet in mice. Aerobic exercise training prevented and reversed the dyslipidemia-related alternative splicing of LDLR pre-mRNA. The histone modifications contributed to the alternative splicing. Full article

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. Full article

Stargardt disease (STGD1), the most common retinal dystrophy caused by pathogenic variants of the biallelic ABCA4 gene, results in irreversible vision loss. This cross-sectional case series study analyzes 18 unrelated Stargardt disease (STGD1) patients from southeast China, examining clinical and genetic features. Ophthalmological assessments included BCVA, ophthalmoscopy, fundus photography, and autofluorescence, with ultra-widefield OCT angiography carried out on one patient. Genetic testing uses targeted exome sequencing for eye disease genes. The mean age of onset was 44.3 years for adult onset (6 patients) and 9.6 years for childhood/adolescent onset (12 patients). The mean logMAR visual acuity was 0.96 (right eye) and 0.91 (left eye). Eight novel ABCA4 variants were found, including two nonsense, two frameshift deletions, one copy number variant, one splice-site alternation, and two deep intronic variants. The genotypes are as follows: 77.8% (14/18) biallelic heterozygous, 16.7% (3/18) homozygous, and one patient with three variants. The study underscores STGD1’s phenotypic and genotypic diversity, expands the ABCA4 mutation spectrum, and offers insights into therapeutic strategies. Full article

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. Full article

(1) Background: Hippophae gyantsensis, a drought-tolerant plant native to the Tibetan Plateau, plays a crucial ecological and economic role. While its drought tolerance mechanisms have been extensively studied, the role of alternative splicing (AS) in drought resistance remains insufficiently explored. This study aims to elucidate how AS events regulate gene expression to enhance drought tolerance in H. gyantsensis under water-deficit conditions. (2) Methods: H. gyantsensis plants were subjected to progressive drought stress followed by rehydration. Physiological responses, transcriptomic data, and hormonal profiles were analyzed to investigate the plant’s adaptive mechanisms to drought stress, with a particular focus on abscisic acid (ABA) signaling-related genes. (3) Results: The results showed that H. gyantsensis maintained high leaf water content even under severe drought stress, emphasizing its strong drought resistance. A transcriptomic analysis revealed 11,962 differentially expressed genes, primarily enriched in hormone signaling and metabolic pathways. Notably, the accumulation of ABA was closely associated with AS events in ABA-related genes, such as ZEPs, ABCG, and PP2C. These genes produced multiple splice variants, indicating their role in modulating the ABA signaling pathway and enhancing drought tolerance. (4) Conclusions: This study highlights the pivotal role of AS in ABA signaling and drought tolerance in H. gyantsensis. It provides new insights into how AS contributes to plant adaptation to drought stress, bridging the knowledge gap in drought resistance mechanisms and emphasizing the importance of AS in plant stress responses. Full article

Resiniferatoxin (RTX), a potent capsaicin analog, is being investigated as a therapeutic agent for neurogenic conditions, particularly those affecting bladder control. However, the transcriptomic effects of RTX on the urinary bladder remain largely unexplored. This study aimed to characterize the transcriptomic changes in the porcine urinary bladder trigone region removed seven days post-treatment with intravesical RTX administration (500 nmol per animal in 60 mL of 5% aqueous solution of ethyl alcohol). High-throughput sequencing identified 126 differentially expressed genes (DEGs; 66 downregulated, 60 upregulated), 5 differentially expressed long non-coding RNAs (DELs), and 22 other RNAs, collectively involved in 175 gene ontology (GO) processes. Additionally, differential alternative splicing events (DASes) and single nucleotide variants (SNVs) were detected. RTX significantly modulated signaling pathways related to nerve growth and myelination. Changes in genes associated with synaptic plasticity and neuromodulation were observed, particularly within serotoninergic and cholinergic signaling. RTX altered the expression of immune-related genes, particularly those involved in chemokine signaling and immune regulation. Notably, altered gene expression patterns suggest a potential anti-cancer role for RTX. These findings provide new insights into RTX’s therapeutic effects beyond TRPV1 receptor interactions, filling a critical gap in our understanding of its molecular impact on bladder tissue. Full article

Interferon-gamma (IFN-γ) is a critical cytokine that plays a pivotal role in immune system regulation. It is a key mediator of both cellular defense mechanisms and antitumor immunity. As the sole member of the type II interferon family, IFN-γ modulates immune responses by activating macrophages, enhancing natural killer cell function, and regulating gene expression across multiple cellular processes. Alternative splicing is a post-transcriptional gene expression regulatory mechanism that generates multiple mature messenger RNAs from a single gene, dramatically increasing proteome diversity without the need of a proportional genome expansion. This process occurs in 90–95% of human genes, with alternative splicing events allowing for the production of diverse protein isoforms that can have distinct—or even opposing—functional properties. Alternative splicing plays a crucial role in cancer immunology, potentially generating tumor neoepitopes and modulating immune responses. However, how alternative splicing affects IFN-γ’s activity is still poorly understood. This review explores how alternative splicing regulates the expression and function of both upstream regulators and downstream effectors of IFN-γ, revealing complex mechanisms of gene expression and immune response modulation. Key transcription factors and signaling molecules of the IFN-γ pathway are alternatively spliced, and alternative splicing can dramatically alter IFN-γ signaling, immune cell function, and response to environmental cues. Specific splice variants can enhance or inhibit IFN-γ-mediated immune responses, potentially influencing cancer immunotherapy, autoimmune conditions, and infectious disease outcomes. The emerging understanding of these splicing events offers promising therapeutic strategies for manipulating immune responses through targeted molecular interventions. Full article

Otitis media is the most frequently diagnosed disease and a leading cause of hearing loss in young children. However, genetic contributors to susceptibility and pathogen–host–environment interactions in otitis media remain to be identified. Such knowledge would help identify at-risk individuals and effectively monitor, diagnose, and treat patients with otitis media. Through exome and Sanger sequencing, we identified a rare, deleterious splice variant SLPI c.394+1G>T co-segregating with otitis media in a large pedigree, with a genome-wide significant maximum LOD score of 4.59. Alternative splicing of SLPI was observed in saliva RNA of variant carriers. In bulk mRNA-seq data from an independent cohort of children with otitis media, SLPI was co-expressed with genes involved in infection, immune response, inflammation, and epithelial cell organization. After inoculation of non-typeable Haemophilus influenzae, Slpi was upregulated in polymorphonuclear leukocytes and epithelial cells of mouse middle ears. Furthermore, in the human middle ear, Haemophilus was significantly enriched in non-carriers, whereas Family-XI-Incertae-Sedis and Dialister were significantly enriched in variant carriers. Given the role of SLPI in immune modulation and host defense in mucosal epithelia, our findings support the SLPI variant as modulating susceptibility to otitis media. Full article