rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

Caloric restriction alters NCOA2 splicing to regulate lipid metabolism in subcutaneous white adipose tissue

Caloric restriction (CR) promotes longevity and metabolic health by modulating gene expression and cellular processes. However, the role of alternative mRNA splicing in CR-induced metabolic adaptation remains underexplored. In this study, we analyzed RNA sequencing data from the subcutaneous white adipose tissue of CR mice. We identified 6058 differentially expressed genes, with significant upregulation of lipid metabolism pathway genes, such as Elovl6, Fasn, and Srebp1c. We also detected 400 CR-associated alternative splicing events, with the skipped exon and retained intron events predominantly affecting lipid biosynthesis and energy metabolism. Among these events, Ncoa2, a nuclear receptor coactivator involved in lipid metabolism, exhibited increased exon 13 inclusion under CR, favoring the expression of the full-length isoform. Functional assays revealed that full-length NCOA2 enhanced PPARγ-mediated transcriptional activation, while the truncated Δ-NCOA2 isoform exhibited altered coactivator activity. Δ-NCOA2 was found to lack an LXXL motif critical for nuclear receptor interactions, potentially modifying its function. Taken together, these findings indicate that CR-induced alternative splicing fine-tunes metabolic and transcriptional networks, thereby contributing to lipid homeostasis and energy adaptation. Our study highlights a novel regulatory layer by which CR modulates metabolism through coordinated transcriptional and splicing alterations, offering new insights into the molecular mechanisms underlying the beneficial effects of CR on aging and metabolic health. Further investigations are warranted to determine the tissue-specificity of the CR-induced splicing changes and their potential implications for metabolic disorders and lifespan extension.

Alternative splicing in addiction

Addiction is a chronic and relapsing medical condition characterized by the compulsive use of drugs or alcohol despite harmful consequences. While transcriptional regulation has long been recognized for its role in addiction, recent genome-wide analyses have uncovered widespread alternative splicing changes that shift protein isoform diversity in multiple brain reward regions central to addiction. In this review, we discuss emerging research and evidence that alternative splicing is dysregulated in cocaine, alcohol, and opioid use disorders.

Transcriptomic analysis of the response of Spodoptera frugiperda (Lepidoptera: Noctuidae) to short-term low-temperature stress

Spodoptera frugiperda is a major invasive pest that poses a serious threat to crops worldwide. Low temperature is a key factor limiting the survival and reproduction for this pest. To study the responses of S. frugiperda to low-temperature stress, high-throughput sequencing was used to perform transcriptomic analysis on the 6th instar larvae under low-temperature stress at 5 °C and 10 °C, along with 25 °C as a control. As a result, 215 differentially expressed genes (DEGs) were identified under different low-temperature stresses. Upon functional annotation of the DEGs in KEGG and GO databases, the number of DEGs annotated in control vs. LT10 comparison was the largest (n = 150), whereas fewer DEGs (n = 89) were annotated in control vs. LT5 comparison. This discrepancy suggested that S. frugiperda might adopt different strategies to cope with low-temperature stress. The DEGs in the GO database were particularly associated with cell catalytic activity, cell anatomical entity process, cell apoptosis, and cell binding channel. KEGG annotation analysis of the different low-temperature stresses showed that most of the enriched pathways were related to carbon metabolism, oxidative phosphorylation, and lipid metabolism. The results will be the basis for mastering the cold tolerant mechanism of S. frugiperda, and is of great significance for its prevention.

Rbm39 ameliorates metabolic dysfunction-associated steatotic liver disease by regulating Apob and Fabp4

Excessive hepatic lipid accumulation is the hallmark of metabolic dysfunction-associated steatotic liver disease (MASLD), yet its underlying mechanisms still not fully understood. In this study, we identified RNA binding motif protein 39 (Rbm39) as a key modulator of hepatic lipid homeostasis during MASLD progression. To establish in vivo MASLD model, mice were fed either a high-fat diet (HFD) or a Gubra-Amylin NASH (GAN) diet. We employed adeno-associated virus to manipulate Rbm39 expression levels to assess its role in MASLD. Transcriptome analysis was conducted to pinpoint the genes targeted by Rbm39. Western blot, RT-PCR, dual-luciferase reporter gene assays, and alternative splicing analysis were utilized to delve into the molecular mechanisms. Our results showed that Rbm39 expression was notably decreased in the livers of MASLD mice. Knockdown of hepatic Rbm39 aggravated HFD-induced hepatic steatosis and GAN diet-induced MASH, along with a notable decrease in serum lipid levels. Conversely, overexpression of Rbm39 attenuated MASLD development and progression. RNA sequencing data analysis indicated that Rbm39 regulated the expression of apolipoprotein B (Apob) and fatty acid-binding protein 4 (Fabp4), both of which are crucial for lipid transport. Mechanistically, Rbm39 enhanced the transcription of Apob by upregulating hepatocyte nuclear factor 4α (Hnf4α), while it suppressed Fabp4 transcription by regulating alternative splicing of hypoxia inducible factor-1α (Hif-1α). These findings highlight the pivotal role of Rbm39 in maintaining hepatic lipid homeostasis and suggest its potential as a therapeutic target for MASLD.

TCF4 expansion-associated loss of FN1 intron retention drives extracellular matrix accumulation in Fuchs endothelial corneal dystrophy

Fuchs endothelial corneal dystrophy (FECD), which is characterized by excessive extracellular matrix (ECM) accumulation and corneal endothelial cell degeneration, has trinucleotide repeat expansion in TCF4 as a major genetic risk factor. While aberrant splicing has been implicated in FECD pathogenesis, the mechanistic link between splicing abnormalities and disease-specific features remains unclear. Here, we investigated the intron retention (IR) patterns in corneal endothelial cells from FECD patients with TCF4 expansion. Initial RNA-Seq analysis using rMATS identified 486 upregulated and 89 downregulated IR events in expansion-positive FECD compared to controls. Subsequent analysis with the more stringent IRFinder algorithm revealed 10 upregulated IR events distributed across nine genes and, notably, 6 downregulated events exclusively localized within FN1, a major component of corneal guttae. While DEXSeq analysis showed reduced expression across FN1 gene regions in FECD samples, subsequent qPCR validation in an independent cohort demonstrated significantly elevated FN1 expression in both expansion-positive and expansion-negative FECD samples compared to controls. This paradoxical finding suggests that the loss of normal IR-mediated regulation may contribute to pathological FN1 overexpression in FECD. Gene ontology analysis of IR-associated genes revealed enrichment in RNA splicing and ECM-related pathways, supporting a role for IR in disease pathogenesis. Our findings reveal an association between TCF4 expansion and reduced FN1 intron retention, which correlates with ECM accumulation, suggesting a potential link between RNA processing alterations and hallmark features of FECD. These results suggest that targeting IR-mediated regulation could represent a therapeutic strategy for preventing disease progression.

XRCC1 is linked to poor prognosis in adenocarcinoma of the esophagogastric junction after radiotherapy: transcriptome and alternative splicing events analysis

PURPOSE

This study aimed to (i) investigate the relationship between X-ray repair cross-complementing protein 1 gene (XRCC1) and prognosis in patients with adenocarcinoma of the esophagogastric junction (AEG), and (ii) analyze the roles of XRCC1 in human gastric adenocarcinoma (AGS) cells following X-ray radiation.

METHODS

A total of 46 AEG patients were enrolled and examined for XRCC1 protein by immunohistochemistry. XRCC1 was knocked down in AGS cells by transfection, and AGS cells were subsequently exposed to 6 Gy of X-ray radiation. XRCC1 mRNA and protein expression was examined via quantitative real-time PCR (qRT-PCR) and Western blot analysis. The apoptosis of AGS cells was examined by flow cytometer. RNA-sequencing technology was used to identified differentially expressed genes and alternative splicing events following XRCC1 knockdown and radiation exposure.

RESULTS

XRCC1 positivity was strongly associated with distant metastasis, pathological tumor-node-metastasis (pTNM) classification, and radiotherapy resistance in AEG patients. A significant difference in progression-free survival was observed between AEG patients with low and high XRCC1 protein expression. The knockdown of XRCC1 notably exacerbated the effects of X-ray radiation on apoptosis in AGS cells. Additionally, X-ray radiation modified the expression of genes related to apoptosis and immune response in XRCC1-knockdown AGS cells. Furthermore, the generation of splice variants was influenced by XRCC1 knockdown in AGS cells.

CONCLUSION

XRCC1 may serve as a key oncogene that elucidates the role of alternative splicing events in the progression of AEG following X-ray treatment.

Alternative mRNA splicing in anthracycline-induced cardiomyopathy - a COG-ALTE03N1 report

BACKGROUND

Anthracycline-induced cardiomyopathy is a well-established adverse consequence in childhood cancer survivors. Altered mRNA expression in the peripheral blood has been found at the level of genes and pathways among anthracycline-exposed childhood cancer survivors with and without cardiomyopathy. However, the role of aberrant alternative splicing in anthracycline-induced cardiomyopathy remains unexplored. The present study examined if transcript-specific events, due to alternative splicing occur in anthracycline-exposed childhood cancer survivors with and without cardiomyopathy.

METHODS

Participants were anthracycline-exposed childhood cancer survivors with cardiomyopathy (cases) matched with anthracycline-exposed childhood cancer survivors without cardiomyopathy (controls; matched on primary cancer diagnosis, year of diagnosis, and race/ethnicity). mRNA sequencing was performed on total RNA from peripheral blood in 32 cases and 32 matched controls. Event-level splicing tool, rMATS (replicate Multivariate Analysis of Transcript Splicing) was used for quantitative profiling of alternative splicing events.

RESULTS

A total of 45 alternative splicing events in 36 genes were identified. Using a prioritization strategy to filter the alternative splicing events, intron retention in RPS24 and skipped exon of PFND5 showed differential expression of altered transcripts.

CONCLUSIONS

We identified specific alternative splicing events in anthracycline-exposed childhood cancer survivors with and without cardiomyopathy. Our findings suggest that differential alternative splicing events can provide additional insight into the peripheral blood transcriptomic landscape of anthracycline-induced cardiomyopathy.

U1 snRNP regulates alternative promoter activity by inhibiting premature polyadenylation

Emerging evidence indicates that splicing factors mediate the close link between transcription and splicing. However, the mechanisms underlying this coupling remain unclear. U1 small nuclear ribonucleoprotein particle (U1 snRNP) not only initiates splicing but also plays a crucial role in preventing premature cleavage and polyadenylation, facilitating long-distance transcriptional elongation. Here, we show that U1 snRNP regulates alternative promoter activity in human cells by inhibiting premature polyadenylation. In genes carrying premature polyadenylation sites between two promoters, U1 snRNP inhibition with antisense oligonucleotides leads to a significant decrease in downstream promoter activity. Conversely, restoring U1 snRNP activity or inhibiting premature polyadenylation rescues downstream promoter activity. Mechanistically, U1 snRNP inhibition correlates with reduced chromatin accessibility, decreased RNA polymerase II serine 5 phosphorylation, and increased promoter-proximal pause at downstream promoters. Our findings support a model in which U1 snRNP favors productive elongation from upstream promoters, triggering downstream promoter activation by destabilizing nucleosomes and promoting promoter escape.

Integrated Metabolomic and Transcriptomic Analyses of Mouse Liver Reveals the In Vivo Toxicity and Mechanisms of Individual and Combined Toxicants Formed in the Thermal Processing of High-Fat Diets

As a part of a continuous 90 day subchronic toxicology study, integrated metabolomic and transcriptomic approaches were applied to assess the metabolic network changes in the livers of Kunming mice exposed to three typical thermally induced food toxicants, including oxidative derivatives of triacylglycerols (ox-TGs), aldehydes, and 3-monochloropropane-1,2-diol esters (3-MCPDE), as well as their mixtures. Results showed lipid metabolic dysregulation through impaired purine metabolism, PPAR signaling, and bile acid metabolism. Ox-TGs emerged as the most hazardous compound, altering over 10 genes/enzymes. 3-MCPDE exhibited gender-specific effects, significantly upregulating fatty acid metabolism and gluconeogenesis genes in males. Interestingly, toxicant mixtures attenuated the adverse metabolic effects caused by individual compounds, demonstrating complex regulatory mechanisms in fatty acid biosynthesis and oxidation. The metabolomic and transcriptomic analyses conducted in this study revealed that combined exposure to multiple toxicants generated during lipid thermal processing may induce more complex toxicity effects than the simple additive effects of individual toxicants. Certain antagonistic effects were observed when comparing individual toxicants to their mixtures, highlighting the need for further mechanistic verifications in this area.

Alternative splicing analysis of stress tolerance to Al and flg22 in Vitis quinquangularis

MAIN CONCLUSION

Alternative splicing of transcriptomes after Al and flg22 treatment for 12 h in response to plant defense of Chinese wild Vitis quinquangularis: genes related to stress resistance and splicing factors were identified in response to Al and flg22 treatment. Alternative splicing (AS) is one of the major post-transcriptional regulation processes that potentially regulates the response to biotic and abiotic stresses in plants. So far, the insight into potential roles of AS in grapevine response to aluminium (Al) and flagellin 22 (flg22) stresses remains poorly understood. We performed transcriptome sequencing of grape leaves before and after Al treatment and flg22 treatment, respectively, to identify AS genes. In this study, a total of 11,805 AS events were identified in Al treatment, of which the skipped exon (SE; 88.72%) type was the most frequent. 9156 AS events were identified under flg22 treatment, of which the SE (88.52%) type was the most frequent. Compared with Al-treated and flg22-treated 0 h, there were 42 and 147 differential alternative splicing (DAS) genes differentially expressed (DASEGs) in Al-treated and flg22-treated 12 h, respectively. Functional analysis showed that DASEGs after Al treatment were mainly enriched in glutathione metabolism pathway; DASEGs after flg22 treatment were enriched in MAPK signaling and plant hormone signal transduction. We further verified seven resistance-related DASEGs with up-regulated expression in Al-treated 12 h, including beta-glucosidase, calcineurin B-like protein, synaptotagmin-3, cysteine synthase and glutathione reductase. Several genes function as leucine-rich repeats receptor-like serine/threonine protein kinase, BRI1 associated receptor kinase 1 and receptor-like protein kinase were also verified by RT-qPCR. We also verified four serine/arginine (SR)-rich proteins SCL30A, SCL28, RS2Z32 and SR45A, which were up-regulated in both Al and flg22 stresses. In conclusion, this study provides an in-depth analysis of the correlation between alternative splicing and grapevine stress tolerance, which helps to identify potential candidate genes for useful traits, provides a theoretical basis for grapevine breeding in plant stress tolerance, and offers new perspectives for understanding grapevine environmental adaptation strategies.

Clinical response to azacitidine in MDS is associated with distinct DNA methylation changes in HSPCs

Hypomethylating agents are frontline therapies for myelodysplastic neoplasms (MDS), yet clinical responses remain unpredictable. We conducted a phase 2 trial comparing injectable and oral azacitidine (AZA) administered over one or three weeks per four-week cycle, with the primary objective of investigating whether response is linked to in vivo drug incorporation or DNA hypomethylation. Our findings show that injection results in higher drug incorporation, but lower DNA demethylation per cycle, while global DNA methylation levels in mononuclear cells are comparable between responders and non-responders. However, hematopoietic stem and progenitor cells (HSPCs) from responders exhibit distinct baseline and early treatment-induced CpG methylation changes at regulatory regions linked to tissue patterning, cell migration, and myeloid differentiation. By cycle six-when clinical responses typically emerge-further differential hypomethylation in responder HSPCs suggests marrow adaptation as a driver of improved hematopoiesis. These findings indicate that intrinsic baseline and early drug-induced epigenetic differences in HSPCs may underlie the variable clinical response to AZA in MDS.

Alternative splicing fine-tunes prey shift of Coccinellini lady beetles to non-target insect

BACKGROUND

Coccinellini lady beetles have been applied as biological control agent of aphids, however, not all of these species are obligately aphidophagous. Thus, a comprehensive understanding of the molecular mechanisms behind predaceous specificity of Coccinellini lady beetles can provide important clues for evaluating their performance and ecological risk assessment in biological control. Post-transcriptional regulations act a key role in shaping organisms' rapid adaptation to changing environment, yet, little is known about their role in the acclimation of Coccinellini lady beetles to non-target preys.

RESULTS

In this study, we conducted a genome-wide investigation to alternative splicing (AS) dynamics in three Coccinellini species Propylea japonica, Coccinella septempunctata and Harmonia axyridis in response to feeding shift from natural prey bean aphids (Megoura japonica) to non-target insect citrus mealybugs (Planococcus citri). Compared to aphid-feeding, all three lady beetles were subject to substantial splicing changes when preying on mealybugs. Most of these differentially spliced genes (DSGs) were not differentially expressed, and regulated different pathways from differentially expressed genes, indicating the functionally nonredundant role of AS. The DSGs were primarily associated with energy derivation, organ formation and development, chemosensation and immune responses, which may promote tolerance of lady beetles to nutrient deprivation and pathogen challenges induced by prey shift. The lady beetles feeding on mealybugs moreover downregulated the generation of splicing products containing premature termination codons (PTCs) for the genes involved in energy derivation and stimulus responses, to fine-tune their protein expression and rationalize energy allocation.

CONCLUSION

These findings unraveled the functional significance of AS reprogramming in modulating acclimation of Coccinellini lady beetles to prey shift from aphids to non-target insects and provided new genetic clues for evaluating their ecological safety as biological control agents.

Transcriptomic analysis of AhAHL23-mediated root development and space-induced mutations in peanut (Arachis hypogaea L.)

Peanut seedling development encompasses four distinct tissues (leaf, stem, hypocotyl, root) with largely uncharacterized transcriptional regulatory networks, so we conducted RNA-seq on the space mutant line ZHM112. Transcriptome analysis showed that differentially expressed genes (DEGs) in peanut seedlings were enriched in basic biosynthesis and physiological metabolism pathways, with photosynthetic metabolism prominent in leaves and hormone metabolism in roots. The weighted gene co-expression network analysis (WGCNA) identified eight modules related to the four tissues. By integrating differential expression and co-expression analyses, we found 1190 key genes in leaves, 133 in stems, 72 in hypocotyls, and 1472 in roots. Further, screening these genes led to the identification of 154 core transcription factors and the construction of a transcriptional regulatory network. Notably, the root-specific transcription factor AhAHL23 was found to enhance root development in Arabidopsis by modulating auxin and cytokinin pathways upon ectopic expression. These findings elucidate the transcriptional regulatory networks of peanut seedling development, providing a molecular basis for understanding genetic improvements in space breeding and their applications in peanut cultivation.

Effects of λ-cyhalothrin on the behavior and physiology of Leschenault's rousette bat (Rousettus leschenaultii)

In addition to exerting direct toxic effects, pesticides disrupt the complex physiology and behavioral patterns of bats. Previous studies have focused on quantifying pesticide residues in bats. However, limited studies have examined the effects of pesticides on acoustic behavior, auditory health, and gene expression in bats. This study examined the effects of λ-cyhalothrin on vocalization, auditory health, and gene expression in Rousettus leschenaultii by integrating behavioral, cochlear pathological, and transcriptomic analyses. Exposure to low and high concentrations of λ-cyhalothrin increased the frequencies of social calls in R. leschenaultii. Histological analysis revealed that λ-cyhalothrin induced tympanic canal bleeding, Reissner's membrane rupture, and cell shedding in the tectorial membrane and the organ of Corti. Transcriptomic analysis revealed that λ-cyhalothrin significantly altered the enrichment of genes in Gene Ontology entries, especially those related to actin, transport protein for sodium-potassium ion channel, and the calcium pathway. These results suggest that λ-cyhalothrin exposure alters social calls in R. leschenaultii by inducing pathological damage and dysregulating gene expression in the cochlea. Thus, there is an urgent need to develop sustainable agricultural practices to mitigate pesticide impacts on bats and their ecological roles.

Targeting PSMD14 combined with arachidonic acid induces synthetic lethality via FADS1 m6A modification in triple-negative breast cancer

Dysregulation of deubiquitination is essential for cancer growth. However, the role of 26S proteasome non-ATPase regulatory subunit 14 (PSMD14) in the progression of triple-negative breast cancer (TNBC) remains to be determined. Gain- and loss-of-function experiments showed that silencing PSMD14 notably attenuated the growth, invasion, and metastasis of TNBC cells in vitro and in vivo. Overexpression of PSMD14 produced the opposite results. Mechanistically, PSMD14 decreased K63-linked ubiquitination on SF3B4 protein to de-ubiquitin and stabilize SF3B4 protein. Then, SF3B4/HNRNPC complex bound to FADS1 mRNA and promoted exon inclusion in the target mRNA through m6A site on FADS1 mRNA recognized by HNRNPC, thereby up-regulating the expression of FADS1 and activating Akt/mTOR signaling. Exogenous arachidonic acid supplementation combined with PSMD14 knockdown induced synthetic lethality, which was further confirmed in TNBC organoid (PDO) and TNBC patient-derived xenograft (PDX) mouse models. Overall, our findings reveal an oncogenic role of PSMD14 in TNBC progression, which indicates a potential biomarker and ferroptosis-mediated therapeutic strategy for TNBC.

Multi-omics insights into growth and fruiting body development in the entomopathogenic fungus Cordycepsblackwelliae

Cordycepsblackwelliae is an entomopathogenic fungus with significant potential for research and development due to its ease of cultivation. However, the lack of omics-based studies has limited our understanding of the molecular mechanisms governing its growth and fruiting body development. This study employed a multi-omics approach, integrating genomic, transcriptomic and metabolomic analyses. Utilising both Illumina and Nanopore sequencing technologies, we assembled a 31.06 Mb nuclear genome comprising 11 scaffolds, with telomere presence at one or both ends in eight scaffolds and annotated 8,138 identified genes (8,136 from genome prediction and two from local BLAST searches). Transcriptomic analysis identified 2,078 differentially expressed genes across three developmental stages: liquid culture mycelia, wheat culture mycelia and fruiting bodies. Amongst these, 745 genes were up-regulated in fruiting bodies, primarily associated with biosynthetic and catabolic pathways. Metabolomic analysis identified 1,161 metabolites, with 1,014 showing significant variations across developmental stages. Integrated transcriptomic and metabolomic analyses uncovered 17 genes positively correlated with 34 metabolites, which are likely crucial regulators of fruiting body development. These findings provide new insights into the molecular networks underlying C.blackwelliae growth and fruiting body formation.

Chronic hypoxia induces alternative splicing of transcripts in the goldfish brain

Several species evolved mechanisms to tolerate periods of severe environmental hypoxia and anoxia. Among them, goldfish are unique as they do not enter a comatose state under such conditions. Taking advantage of the recently published and annotated goldfish genome, we had previously profiled the transcriptomic response of the goldfish brain under normoxic (21 kPa oxygen saturation, N) and hypoxic conditions (2.1 kPa oxygen saturation) after 1 and 4 weeks (1WH, 4WH). Using the RNA-Seq data, we report the occurrence of alternative mRNA splicing (skipped exon, retained intron, alternative 3' or 5' splice sites, and mutually exclusive exons). At 1WH/N, 1004 significant alternative splicing events on 769 gene loci were identified, increasing to 1187 on 963 loci at 4WH/N. There were 305 loci with alternatively spliced transcripts common to both 1WH/N and 4WH/N, 221 of which exhibited the same precise location and splicing mechanism. Specific gene transcripts affected by alternative splicing events were almost entirely different from previously identified differentially expressed genes under chronic hypoxia. GO-term enrichment analyses of gene loci of alternatively spliced transcripts, however, did include similar pathways as previously identified for DEGs. These include epigenetic machinery, ion channel activity (1WH/N), glutamate signaling (4WH/N), endothelial cell function, and ATP hydrolyzation pathways (1WH/N + 4WH/N). We describe selected examples of alternatively spliced transcripts to discuss possible functional relevance in the goldfish brain response to chronic hypoxia. Together, our data identified an additional layer of regulation in brain pathways relevant to hypoxia tolerance in goldfish, which complement previously reported gene expression changes.

Snord67 promotes breast cancer metastasis by guiding U6 modification and modulating the splicing landscape

Previously considered "housekeeping" genes, small nucleolar RNAs (snoRNAs) are increasingly understood to have wide-ranging functions in cancer, yet their role in metastasis has been less well studied. Here, we identify the snoRNA Snord67 as a regulator of lymph node (LN) metastasis in breast cancer. Snord67 expression is enriched in LN metastases in an immune-competent mouse model of female breast cancer. In an orthotopic breast cancer model, loss of Snord67 decreases LN metastasis. In a model of lymphatic metastasis, Snord67 loss decreases LN tumor growth and distant metastases. In breast cancer cell lines, Snord67 knockout results in loss of targeted 2'-O-methylation on U6 small nuclear RNA, as well as widespread changes in splicing. Together, these results demonstrate that Snord67 regulates splicing and promotes the growth of LN metastases and subsequent spread to distant metastases. SnoRNA-guided modifications of the spliceosome and regulation of splicing may represent a potentially targetable pathway in cancer.

A critical genetic interaction between Gemin3/Ddx20 and translation initiation factor NAT1/eIF4G2 drives development

Gemin3 (Gem3) or DEAD-box RNA helicase 20 (Ddx20) has been mostly implicated in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs) as part of the SMN-Gemins complex. Nonetheless, several studies have hinted at its participation in diverse snRNP-independent activities. Here, we utilised a narrow unbiased genetic screen to discover novel Gem3 interactors in Drosophila with the aim of gaining better insights on its function in vivo. Through this approach, we identified a novel genetic interaction between Gem3 and NAT1, which encodes the Drosophila orthologue of translational regulator eIF4G2. Despite lack of a physical association, loss of NAT1 function was found to downregulate Gem3 mRNA levels. Extensive convergence in transcriptome alterations downstream of Gem3 and NAT1 silencing further supports a functional relationship between these factors in addition to showing a requirement for both in actin cytoskeleton organisation and organism development, particularly neurodevelopment. In confirmation, flies with either Gem3 or NAT1 depletion exhibited brain growth defects and reduced muscle contraction. Severe delays in developmental progression were also observed in a newly generated Gem3 hypomorphic mutant. Our data linking Gemin3 to a key component of the translational machinery support an emerging role for Gemin3 in translation that is also critical during organism development.

Tripartite phosphorylation of SPT5 by CDK9 times pause release and tunes elongation rate of RNA polymerase II

The RNA polymerase II (RNAPII) transcription cycle is regulated throughout its duration by protein phosphorylation. Previously, two regions phosphorylated by cyclin-dependent kinase 9 (CDK9) in elongation factor SPT5-the linker between Kyrpides-Ouzounis-Woese (KOW) x-4 and 5 domains and carboxy-terminal repeat (CTR) 1-were implicated in promoter-proximal pausing and termination, respectively. Here, we show that phosphorylations in the linker, CTR1, and a third region, CTR2, coordinately control pause release, elongation speed, and termination in HCT116 human colon cancer cells. Pausing was unaffected or increased by mutations preventing CTR1 or CTR2 phosphorylation, respectively, but attenuated when both CTRs were mutated. Whereas loss of CTR1 phosphorylation slowed elongation and repressed nascent transcription, simultaneous CTR2 mutation partially reversed both effects. Nevertheless, mutating both CTRs had additive effects on splicing, termination, steady-state mRNA levels, and cell proliferation. Therefore, tripartite SPT5 phosphorylation times pause release and tunes RNAPII elongation rate to ensure productive transcription and cell viability.

A novel splicing graph allows a direct comparison between exon-based and splice junction-based approaches to alternative splicing detection

There are primarily two computational approaches to alternative splicing (AS) detection using short reads: splice junction-based and exon-based approaches. Despite their shared goal of addressing the same biological problem, these approaches have not been reconciled before. We devised a novel graph structure and algorithm aimed at mapping between the exonic parts and splicing events detected by the two different methods. Through simulations, we demonstrated disparities in sensitivity and specificity between splice junction-based and exon-based methods. When applied to empirical data, there were large discrepancies in the results, suggesting that the methods are complementary. With the discrepancies localized to individual events and exonic parts, we were able to gain insights into the strengths and weaknesses inherent in each approach. Finally, we integrated the results to generate a comprehensive list of both common and unique AS events detected by both methodologies.

irCLIP-RNP and Re-CLIP reveal patterns of dynamic protein assemblies on RNA

RNA-binding proteins (RBPs) control varied processes, including RNA splicing, stability, transport and translation1-3. Dysfunctional RNA-RBP interactions contribute to the pathogenesis of human disease1,4,5; however, characterizing the nature and dynamics of multiprotein assemblies on RNA has been challenging. Here, to address this, non-isotopic ligation-based ultraviolet-light-induced cross-linking and immunoprecipitation6 was combined with mass spectrometry (irCLIP-RNP) to identify RNA-dependent associated proteins (RDAPs) co-bound to RNA with any RBP of interest. irCLIP-RNP defined landscapes of multimeric protein assemblies on RNA, revealing patterns of RBP-RNA associations, including cell-type-selective combinatorial relationships between RDAPs and primary RBPs. irCLIP-RNP also defined dynamic RDAP remodelling in response to epidermal growth factor (EGF), revealing that EGF-induced recruitment of UPF1 adjacent to HNRNPC promotes splicing surveillance of cell proliferation mRNAs. To identify the RNAs simultaneously co-bound by multiple studied RBPs, a sequential immunoprecipitation irCLIP (Re-CLIP) method was also developed. Re-CLIP confirmed binding relationships observed in irCLIP-RNP and identified HNRNPC and UPF1 RBP co-binding on RND3 and DDX3X mRNAs. irCLIP-RNP and Re-CLIP provide a framework to identify and characterize dynamic RNA-protein assemblies in living cells.

Identification of NIBAN2-Regulated RUNX2 Alternative Splicing Presents Novel Strategies for Antagonizing Osteoporosis

Osteoporosis is characterized by excessive bone resorption and/or defects in bone formation. Identification of factors promoting osteoblast differentiation may provide potential targets for osteoporosis therapy. Through integral analyses of multiple datasets, NIBAN2 is found to be tightly associated with bone formation and osteoporosis. Indeed, NIBAN2 promotes osteoblast differentiation, and conditional Niban2 knockout in osteoblasts caused bone loss and insufficient mineralization. Mechanistically, NIBAN2 interacts with the HNRNPU-cored spliceosome complex and alters its components to regulate the alternative splicing of RUNX2, which ultimately cause an increase in functional RUNX2 (nuclear localization sequence complete) but a decrease in dysfunctional RUNX2 (exon 6 exclusive) to reinforce osteoblast differentiation. Most importantly, NIBAN2 expression level negatively correlates with RUNX2 spliced isoforms and bone loss in osteoporosis patients. NIBAN2 overexpression rescues bone loss in ovariectomized mice. Thus, this research identifies NIBAN2-regulated RUNX2 alternative splicing as a potential mechanism of osteoblast differentiation that may present strategies for antagonizing osteoporosis.

The splicing factor U2AF65B regulates cytosine methylation through interacting with DEFECTIVE IN MERISTEM SILENCING 3 in Arabidopsis

U2AF65B is one of the splicing factors that are involved in the recognition of the 3' splicing site and it plays an important role in plant development and stress response through its mRNA splicing function. However, it is not clear whether U2AF65B regulates gene expression in a splicing-independent manner. Through mutant screening and map-based cloning, protein-protein interaction, transcriptomic sequencing, whole-genome bisulfite sequencing and chromatin immunoprecipitation analysis, we investigated the function of U2AF65B in gene silencing in Arabidopsis thaliana. We found in the u2af65b mutant that the exogenous transgene 35S::HYG is activated in expression with decreased DNA methylation on the 35S core-promoter compared with that in the wild-type. Loss of U2AF65B function also globally decreased the methylation of CG, CHG and CHH with a profound effect on CHH methylation in transposons and intergenic sequences. Among the hypomethylated non-CG cytosines in u2af65b, nearly half of them are also hypomethylated in the dms3 mutant. Interestingly, U2AF65B interacts with the RNA-directed DNA methylation (RdDM) pathway component DMS3, and loss of U2AF65B function significantly decreased the enrichment of DMS3 on the targets, including the 35S::HYG transgene and endogenous RdDM loci. Our findings suggest that U2AF65B is a crucial player in RdDM-mediated DNA methylation, partially through promoting the RdDM pathway by interacting with and recruiting DMS3 to the target sequences.

Interrogation of mirror-image l-RNA-protein interactions reveals key mechanisms of single-stranded G-rich l-RNA cytotoxicity and a potential mitigation strategy

l-Oligonucleotides (ONs), the synthetic enantiomers of native d-nucleic acids, are being increasingly utilized in the development of diverse biomedical technologies, including molecular imaging tools, diagnostic biosensors, and aptamer-based therapeutics. Nevertheless, our understanding of how l-ONs behave in living systems falls far short of native d-ONs. In particular, despite the potential for an abundant l-ON-protein interactome, the extent to which l-ONs bind to endogenous proteins and the consequences of these interactions are unknown, posing a major hurdle towards engineering functional l-ONs with predictable intracellular behaviours. Towards closing this knowledge gap, we now report the first l-ON-protein interactome, revealing that a wide-range of nuclear proteins have the potential to bind l-RNA. Importantly, by focusing our study on cytotoxic single-stranded G-rich l-RNA sequences, our data reveal key protein interactions that contribute to the cytotoxicity of these sequences. Furthermore, we show that introducing 2'-O-methyl modifications into single-stranded G-rich l-RNA can decrease its cytotoxicity through reducing l-RNA-protein interactions, thereby demonstrating that a well-established strategy for mitigating the cytotoxic effects of antisense ONs may translate across the chiral mirror. Overall, these findings greatly deepen our understanding of the intracellular behavior of l-ONs and provide valuable guidance for the future development of safe and effective l-ON-based biomedical technologies.

Identification and validation of diagnostic alternative splicing events in tumor-educated platelets for non-small cell lung cancer in patients with ground-glass opacity: a multicenter study

Background

The diagnostic potential of tumor-educated platelets (TEPs) across various cancer types has gained increasing recognition; however, the relationship between alternative splicing (AS) events in TEPs and tumor development remains understudied. Early detection of non-small cell lung cancer (NSCLC) in ground-glass opacities (GGOs) is critical for improving patient outcomes, yet current methods lack sufficient accuracy. Our research identified diagnostic-related alternative splicing events (DASEs) in TEPs, revealing several promising biomarkers for NSCLC, specifically in patients presenting with GGOs.

Methods

Patients with GGOs from two hospitals were prospectively enrolled [Hospital 1-Platelet (H1-P) and Hospital 2-Tissue (H2-T) in the validation cohort; Hospital 2-Platelet (H2-P) in the test cohort]. Benign/malignant diagnosis of GGOs was confirmed by pathological examination according to the World Health Organization (WHO) classification. TEPs from the H1-P cohort were collected for transcriptome sequencing and AS analysis. Chi-square tests, least absolute shrinkage and selection operator (LASSO) regression analysis, and protein-protein interaction (PPI) network were used for the preliminary screening of DASEs. Pathological tissue from the H2-T cohort was collected to validate the diagnostic efficacy of hub DASEs in NSCLC against the pathological gold standard. Moreover, TEPs from the H2-P cohort were used to assess the predictive performance of hub DASEs for GGOs using receiver operating characteristic (ROC) curves. Decision curve analysis (DCA) was used to determine whether diagnosing NSCLC in the GGOs population via hub DASEs could benefit patients.

Results

A total of 285 patients with GGOs were enrolled, including 151 NSCLC and 128 inflammatory nodules confirmed by pathological examination. Thirteen DASEs were screened with the chi-square test and LASSO regression analysis to identify diagnostic TEP AS markers for GGOs NSCLC. The PPI network identified four hub diagnostic-related alternative splice genes (DASGs) (TMEM219, MPV17, FIBP, and VPS28). Pathological tissues and platelets were collected to validate the four hub DASEs of these four hub DASGs. MXE-32112-TMEM219 yielded an area under the curve (AUC) of 0.82 [95% confidence interval (CI): 0.729-0.902], with a sensitivity of 83.33% and a specificity of 80.00%; RI-3259-VPS28 yielded an AUC of 0.77 (95% CI: 0.677-0.870) with a sensitivity of 93.33% and a specificity of 78.33%; and RI-3641-MPV17 yielded an AUC of 0.82 (95% CI: 0.728-0.901) with a sensitivity of 90.00% and a specificity of 80.00%. The DCA results suggested that using hub DASEs in diagnosing NSCLC in individuals with GGOs could provide benefits.

Conclusions

The specific diagnostic AS events (MXE-32112-TMEM219, RI-3259-VPS28, and RI-3641-MPV17) identified in TEP samples demonstrated high sensitivity and specificity for diagnosing NSCLC in patients with GGOs. These findings suggest that TEP-related AS events may serve as non-invasive biomarkers to guide biopsy decisions for NSCLC in GGOs, reducing unnecessary procedures.

A Novel Role for Coilin in Vertebrate Innate Immunity

Coilin is a protein localized in the nucleus, where it plays a role in the assembly of the Cajal Body and is involved in ribonucleoprotein biogenesis. Our recent research has uncovered new roles for coilin, including its involvement in producing microRNAs and in modifying other proteins through phosphorylation and SUMOylation. We also proposed that coilin could respond to stress signals. In plants, coilin has been shown to help regulate immune genes and activate defense mechanisms, especially in response to stress. In this study, we used two vertebrate models to study coilin function: a human primary foreskin fibroblast cell line deficient in coilin through RNA interference and a newly created zebrafish line with a mutation in the coilin gene generated by CRISPR-Cas9. Transcriptomic analysis in these two models of coilin deficiency revealed dysregulation of immunity-related genes in both species. To phenotypically validate the transcriptomic results, we challenged zebrafish coilin mutants with lipopolysaccharide (LPS), which triggers an innate immune response, and identified an attenuated response to LPS in vivo in the zebrafish coilin mutants. Our results support a vital novel function for coilin in vertebrates in regulating the expression of immunity-related genes. Moreover, these findings could lead to more research on how coilin regulates innate immunity in animals and humans.

Transcriptomic analysis reveals the molecular mechanisms of heterosis in low-temperature tolerance in the hybrids of Argopecten scallops

The F1 hybrid of Argopecten irradians irradians (♀) × A. purpuratus (♂) exhibits significant heterosis in growth performance and mid-parent heterosis in low-temperature tolerance. This study presents a comparative transcriptomic analysis of A. irradians irradians (Ai), A. purpuratus (Ap), and the hybrid A. irradians irradians♀ × A. purpuratus♂ (Aip) to explore the mechanisms underlying low-temperature tolerance heterosis in Aip. A total of 33,376 differentially expressed genes (DEGs) were identified between F1 hybrids and purebreds under cold stress. In Aip, 80.32 % of DEGs exhibited non-additive expression patterns, with over-dominant expression observed in 30.65 % of these genes. Pairwise comparisons among the transcriptomes of Ai, Ap, and Aip revealed 14,959 alternative splicing events, affecting 8169 genes. KEGG pathway analysis indicated substantial enrichment of overlapping genes from common DEGs and non-additively expressed genes (NAGs) in apoptosis, longevity regulation, ABC transporters, and spliceosome pathways. Furthermore, analysis of DEGs, DAGs (Differentially Alternative Splicing genes), and NAGs identified 6 genes undergoing alternative splicing. These pathways and genes may be crucial in Aip's response to low-temperature stress and offer insights for advancing scallop cross-breeding strategies.

FTDC1/2, oocyte-specific cofactors of DNMT1 required for epigenetic regulation and embryonic development

The unique epigenetic patterns during gametogenesis and embryonic development indicate the existence of specialized methylation machinery. In the present study, we describe the discovery of two oocyte-specific cofactors of DNA methyltransferase 1 (DNMT1), encoded by uncharacterized genes, ferritin domain containing 1 and 2 (Ftdc1 and Ftdc2). Genetic ablation of Ftdc1 or Ftdc2 causes midgestation defects and female infertility. FTDC1 or FTDC2 depletion induces the progressive loss of DNA methylation including imprinted regions in early embryos. This loss correlates with a marked reduction in DNMT1 protein due to increased degradation, likely via the ubiquitin-proteasome pathway. Mechanistically, we find that FTDC1, FTDC2 and DNMT1 form a complex by direct interactions, thereby stabilizing each other. Surprisingly, knockout of Ftdc1 or Ftdc2 displayed stronger DNA demethylation phenotypes and earlier embryonic lethality than the Dnmt1-null mutant, implying their unique functions. These data suggest that FTDC1/2 are crucial players specifically involved in maintaining genomic methylation during embryogenesis, offering new insights into the epigenetic control of mammalian development.

Comprehensive analysis of splicing variants in corneal endothelial cells of patients with Fuchs endothelial corneal dystrophy

Trinucleotide repeat (TNR) expansion in the transcription factor 4 (TCF4) gene represents the most prevalent genetic risk factor for Fuchs endothelial corneal dystrophy (FECD) and may cause dysfunction of splicing regulators. We investigated differential alternative splicing (DAS) events in corneal endothelial cells (CECs) from FECD patients with and without TCF4 TNR expansion through RNA-Seq analysis. We identified distinct splicing profiles among control subjects, FECD patients with TNR expansion, and FECD patients without TNR expansion. Skipped Exon events constituted approximately 50% of all DAS events across all comparisons, with the remaining events distributed among alternative 3' splice site, alternative 5' splice site, mutually exclusive exon, and retained intron categories. Motif analysis in FECD patients with TNR expansion revealed several RNA-binding proteins, including MBNL1, as potential regulators of these splicing alterations. Computational analysis demonstrated that 34% of Skipped Exon events in the TNR expansion group significantly impacted protein structure. This comprehensive analysis revealed distinct alternative splicing signatures in FECD, particularly in cases with TNR expansion, suggesting a crucial role for aberrant splicing in FECD pathogenesis.

Alternative splicing categorizes organ development by stage and reveals unique human splicing variants linked to neuromuscular disorders

Alternative splicing (AS) diversifies protein expression and contributes to species-specific differences in organ development. Here, we focused on stage-specific splicing variants and their correlation with disease in human compared to mouse during brain and heart development. Temporal transcriptomic analysis revealed that splicing factors (SFs) can accurately classify organ developmental stages, and 5 SFs were identified specifically upregulated in human during organogenesis. Additionally, inter-stage splicing variations were identified across analogous human and mouse developmental stages. Developmentally dynamic alternative splicing genes (devASGs) were enriched in various neurodevelopmental disorders in both species, with the most significant changes observed in human newborn brain and 16 weeks post-conception heart. Intriguingly, diseases specifically enriched in humans were primarily associated with neuro-muscular dysfunction, and human-specific neuromuscular devASGs were linked to mannose glycosylation and ciliary motility. These findings highlight the significance of SFs and AS events in organogenesis, and inform the selection of appropriate models for translational research.

The splicing factor Acin1 is essential for embryonic development but has limited effects on muscle structure and homeostasis

Apoptotic chromatin condensation inducer 1 (Acin1) is an RNA-binding protein involved in the regulation of alternative splicing, but its physiological function remains unclear. Global deletion of Acin1 causes embryonic lethality around E11.5, with mutants exhibiting developmental delays and increased apoptosis. Using conditional knockout mice, we found that skeletal muscle myofiber-specific Acin1 knockout mice (Acin1 MKO) are viable and fertile and that Acin1 MKO mice show enlarged myofibers and ongoing muscle damage and regeneration, characterized by increased central nuclei and embryonic myosin heavy chain expression. RNA-seq analysis revealed that Acin1 deletion altered the expression and splicing patterns of genes crucial for muscle function. Notable changes included modified splicing of genes associated with muscle disease and mitochondrial function, often resulting in the expression of gene variants typical of immature or diseased muscle. These findings suggest that Acin1 is essential for embryonic development and has limited effects on muscle structure and homeostasis via its regulation of gene expression and alternative splicing.

SFSWAP is a negative regulator of OGT intron detention and global pre-mRNA splicing

O-GlcNAcylation is the reversible post-translational addition of β-N-acetylglucosamine to serine and threonine residues of nuclear and cytoplasmic proteins. It plays an important role in several cellular processes through the modification of thousands of protein substrates. O-GlcNAcylation in humans is mediated by a single essential enzyme, O-GlcNAc transferase (OGT). OGT, together with the sole O-GlcNAcase OGA, form an intricate feedback loop to maintain O-GlcNAc homeostasis in response to changes in cellular O-GlcNAc using a dynamic mechanism involving nuclear retention of its fourth intron. However, the molecular mechanism of this dynamic regulation remains unclear. Using an O-GlcNAc responsive GFP reporter cell line, we identify SFSWAP, a poorly characterized splicing factor, as a trans-acting factor regulating OGT intron detention. We show that SFSWAP is a global regulator of retained intron splicing and exon skipping that primarily acts as a negative regulator of splicing. In contrast, knockdown of SFSWAP leads to reduced inclusion of a 'decoy exon' present in the OGT retained intron which may mediate its role in OGT intron detention. Global analysis of decoy exon inclusion in SFSWAP and UPF1 double knockdown cells indicate altered patterns of decoy exon usage. Together, these data indicate a role for SFSWAP as a global negative regulator of pre-mRNA splicing and positive regulator of intron retention.

IKAROS levels are associated with antigen escape in CD19- and CD22-targeted therapies for B-cell malignancies

Antigen escape relapse is a major challenge in targeted immunotherapies, including CD19- and CD22-directed chimeric antigen receptor (CAR) T-cell for B-cell acute lymphoblastic leukemia (B-ALL). To identify tumor-intrinsic factors driving antigen loss, we perform single-cell analyses on 61 B-ALL patient samples treated with CAR T cells. Here we show that low levels of IKAROS in pro-B-like B-ALL cells before CAR T treatment correlate with antigen escape. IKAROSlow B-ALL cells undergo epigenetic and transcriptional changes that diminish B-cell identity, making them resemble progenitor cells. This shift leads to reduced CD19 and CD22 surface expression. We demonstrate that CD19 and CD22 expression is IKAROS dose-dependent and reversible. Furthermore, IKAROSlow cells exhibit higher resistance to CD19- and CD22-targeted therapies. These findings establish a role for IKAROS as a regulator of antigens targeted by widely used immunotherapies and in the risk of antigen escape relapse, identifying it as a potential prognostic target.

HAND1, partially mediated through ape-specific LTR binding, is essential for human extra-embryonic mesenchyme derivation from iPSCs

The specification of extra-embryonic mesenchyme (ExMC) is a prime example of developmental divergence between mouse and human. Derived from definitive mesoderm during mouse gastrulation, the human ExMC first appears at peri-implantation prior to gastrulation and therefore its human cellular origin, still unknown, must differ. In a human pluripotent stem cell model, we report that ExMC shares progenitor cells with trophoblast, suggesting a trophectoderm origin. This ability to form ExMC appears to extend to human trophoblast stem cell lines. We define HAND1 as an essential regulator of ExMC specification, with null cells remaining in the trophoblast lineage. Bound by HAND1, ape-specific, endogenous retrovirus-derived LTR2B contributes to unique features of ExMC. Additionally, ExMC supports the maintenance of pluripotent stem cells, possibly reflecting a role in maintaining epiblast pluripotency through peri-implantation development. Our data emphasize the nascent evolutionary innovation in human early development and provide a cellular system to study this.

Autism-related traits in myotonic dystrophy type 1 model mice are due to MBNL sequestration and RNA mis-splicing of autism-risk genes

Genome-wide enrichment of gene-specific tandem repeat expansions has been linked to autism spectrum disorder. One such mutation is the CTG tandem repeat expansion in the 3' untranslated region of the DMPK gene, which is known to cause myotonic muscular dystrophy type 1. Although there is a clear clinical association between autism and myotonic dystrophy, the molecular basis for this connection remains unknown. Here, we report that sequestration of MBNL splicing factors by mutant DMPK RNAs with expanded CUG repeats alters the RNA splicing patterns of autism-risk genes during brain development, particularly a class of autism-relevant microexons. We demonstrate that both DMPK-CTG expansion and Mbnl null mouse models recapitulate autism-relevant mis-splicing profiles, along with social behavioral deficits and altered responses to novelty. These findings support our model that myotonic dystrophy-associated autism arises from developmental mis-splicing of autism-risk genes.

Transcriptomic profiling of severe and critical COVID-19 patients reveals alterations in expression, splicing and polyadenylation

Coronavirus disease 2019 (COVID-19) is a multi-systemic illness that became a pandemic in March 2020. Although environmental factors and comorbidities can influence disease progression, there is a lack of prognostic markers to predict the severity of COVID-19 illness. Identifying these markers is crucial for improving patient outcomes and appropriately allocating scarce resources. Here, an RNA-sequencing study was conducted on blood samples from unvaccinated, hospitalized patients divided by disease severity; 367 moderate, 173 severe, and 199 critical. Using a bioinformatics approach, we identified differentially expressed genes (DEGs), alternative splicing (AS) and alternative polyadenylation (APA) events that were severity-dependent. In the severe group, we observed a higher expression of kappa immunoglobulins compared to the moderate group. In the critical cohort, a majority of AS events were mutually exclusive exons and APA genes mostly had longer 3'UTRs. Interestingly, multiple genes associated with cytoskeleton, TUBA4A, NRGN, BSG, and CD300A, were differentially expressed, alternatively spliced and polyadenylated in the critical group. Furthermore, several inflammation-related pathways were observed predominantly in critical vs. moderate. We demonstrate that integrating multiple downstream analyses of transcriptomics, from moderate, severe, and critical patients confers a significant advantage in identifying relevant dysregulated genes and pathways.

Mechanical control of the alternative splicing factor PTBP1 regulates extracellular matrix stiffness induced proliferation and cell spreading

Cells sense mechanical cues and convert them into biochemical responses to regulate biological processes such as embryonic development, aging, cellular homeostasis, and disease progression. In this study, we introduce a large-scale, systematic approach to identify proteins with mechanosensitive nuclear localization, highlighting their potential roles in mechanotransduction. Among the proteins identified, we focus here on the splicing factor PTBP1. We demonstrate that its nuclear abundance is regulated by mechanical cues such as cell density, size, and extracellular matrix (ECM) stiffness and that PTBP1 medicates the mechanosensitive alternative splicing of the endocytic adapter protein Numb. Furthermore, we show that PTBP1 and Numb alternative splicing is critical for ECM stiffness-induced epithelial cell spreading and proliferation as well as for mesenchymal stem cell differentiation into osteoblasts on a stiff matrix. Our results underscore the emerging role of alternative splicing in mechanotransduction and provide novel mechanistic insights into how matrix stiffness modulates cellular mechanoresponses.

Nuclear accumulation of YTHDF1 regulates mRNA splicing in the DNA damage response

YTH domain-containing family protein 1 (YTHDF1), a reader of N6-methyladenosine (m6A), has been implicated in regulating RNA metabolism in the cytosol. Here, we report a role of YTHDF1 within the nucleus in response to genotoxic stress. Upon radiation, YTHDF1 is phosphorylated at serine-182 in an ataxia telangiectasia and Rad3-related-dependent manner. This phosphorylation inhibits exportin 1-mediated nuclear export of YTHDF1, resulting in its accumulation within the nucleus. Nuclear YTHDF1 enhances the binding capacity of serine- and arginine-rich splicing factor 2 to a group of m6A-modified exons, leading to increased exon inclusion. Specifically, YTHDF1 promotes splicing and expression of DNA repair genes, such as BRCA1 and TP53BP1, thereby mitigating excessive DNA damage. Depletion of YTHDF1 sensitizes cancer cells to radiation treatment. Together, our study reveals a crucial role of YTHDF1 in m6A-mediated messenger RNA splicing in the DNA damage response, proposing it as a potential target for radiation therapy.

Multi-omics landscape of alternative splicing in diffuse midline glioma reveals immune- and neural-driven subtypes with implications for spliceosome-targeted therapy

Introduction

H3K27-altered diffuse midline glioma (DMG) is a highly aggressive glioma subtype, accounting for approximately 60% of pediatric high-grade gliomas, with a median survival of less than 12 months. Due to its predominant localization in the brainstem, conventional surgical resection is often unfeasible, underscoring the urgent need for alternative therapeutic strategies. While previous studies on DMG have primarily focused on regulatory mechanisms at the protein level, the role of alternative splicing in DMG remains largely unexplored. Given its potential impact on gene regulation and tumor progression, a comprehensive analysis of alternative splicing could provide novel insights into targeted or immune therapeutic strategies, complementing existing transcriptomic studies of DMG.

Methods

To investigate the alternative splicing landscape of DMG, we performed transcriptome sequencing (RNA-seq) on patient-derived H3WT and H3K27-altered DMG cell lines, integrating these data with RNA-seq and single-cell transcriptomic (scRNA-seq) datasets from published sources. This comprehensive approach enabled us to delineate the alternative splicing landscape of H3K27-altered DMG and validate its distinct features at the cellular level.

Results

Our multi-omics analysis revealed significant transcriptional alterations in H3K27-altered DMG compared to H3WT DMG, particularly in pathways related to neuro-regulation, metabolism, and immunity. Further in-depth analysis identified extensive alternative splicing changes in H3K27-altered DMG, predominantly associated with RNA modifications and key alterations in extracellular matrix and nucleotide metabolism. Integrating these findings, we characterized five RNA-associated proteins that enabled a binary classification of DMG into neural and immune subtypes, with each subtype exhibiting distinct prognostic and transcriptomic features. Notably, we identified RALYL as a potential key regulator in DMG progression.

Discussion

Our findings indicate that H3K27-altered DMG exhibits significant alternative splicing alterations, which play crucial roles in tumorigenesis and progression. Additionally, our study identified an RNA-binding protein-based classification of DMG and characterized RALYL as a potential regulatory factor, highlighting its potential as a novel therapeutic target.

Pentatricopeptide repeat protein targeting CUG repeat RNA ameliorates RNA toxicity in a myotonic dystrophy type 1 mouse model

Myotonic dystrophy type 1 (DM1) is an autosomal dominant multisystemic disorder caused by the expansion of a CTG-triplet repeat in the 3' untranslated region of the dystrophia myotonica protein kinase (DMPK) gene. It results in the transcription of toxic RNAs that contain expanded CUG repeats (CUGexp). Splicing factors, such as muscleblind-like 1 (MBNL1), are sequestered by CUGexp, thereby disrupting the normal splicing program that is essential for various cellular functions. Pentatricopeptide repeat (PPR) proteins, originally found in plants, regulate RNA in organelles by binding in a sequence-specific manner. Here, we designed PPR proteins that specifically bind to the hexamer of CUG repeat RNAs (CUG-PPRs) and showed that CUG-PPR1 could ameliorate RNA toxicity induced by CUGexp in cell models of DM1. A single systemic recombinant adeno-associated virus (AAV9) vector-mediated gene delivery of CUG-PPR1 demonstrated long-term therapeutic effects on myotonia and restored splicing activity in a mouse model of DM1. These results highlight the potential of PPR molecules to target pathogenic RNA sequences in DM1 and potentially other RNA-mediated disorders.

Invention of an oral medication for cardiac Fabry disease caused by RNA mis-splicing

Pathogenic RNA splicing variants have emerged as promising therapeutic targets due to their role in disease while preserving coding sequences. In this study, we developed RECTAS-2.0, a small molecule designed to correct RNA mis-splicing caused by the GLA c.639+919G>A mutation, which leads to the inclusion of a 57-nucleotide poison exon, resulting in later-onset Fabry disease, particularly prevalent in East Asia. RECTAS-2.0 restored normal GLA mRNA splicing and α-galactosidase activity in patient-derived B-lymphoblastoid cell lines and induced pluripotent stem cell-derived cardiomyocytes. Furthermore, oral administration of RECTAS-2.0 effectively corrected splicing in a transgenic mouse model, demonstrating its substantial splice-switching activity and safety for clinical application. RECTAS-2.0 demonstrated potential applicability to other genetic disorders that involve similar exon competition. These findings underscore the therapeutic potential of RECTAS-2.0 for Fabry disease and highlight its broader implications for RNA splicing-targeted therapies in genetic disorders.

Perturbation of mRNA splicing in liver cancer: insights, opportunities and challenges

Perturbation of mRNA splicing is commonly observed in human cancers and plays a role in various aspects of cancer hallmarks. Understanding the mechanisms and functions of alternative splicing (AS) not only enables us to explore the complex regulatory network involved in tumour initiation and progression but also reveals potential for RNA-based cancer treatment strategies. This review provides a comprehensive summary of the significance of AS in liver cancer, covering the regulatory mechanisms, cancer-related AS events, abnormal splicing regulators, as well as the interplay between AS and post-transcriptional and post-translational regulations. We present the current bioinformatic approaches and databases to detect and analyse AS in cancer, and discuss the implications and perspectives of AS in the treatment of liver cancer.

Effects of acute PM2.5 purification on cognitive function and underlying mechanisms: Evidence from integrating alternative splicing into multi-omics

The relationship between fine particulate matter (PM2.5) and cognition has been extensively investigated. However, the causal impact of acute PM2.5 purification on cognition improvement and the underlying biological mechanisms remain relatively opaque. Our double-blinded randomized controlled trial assessed the impact of acute PM2.5 purification on executive function, underpinned by multi-omics approaches including alternative splicing (AS) analysis. A total of 93 participants experienced a two-hour exposure to either reduced and normal PM2.5 levels. We measured the cognition of healthy young adults, collected peripheral blood before and after intervention, and performed multi-omics analysis including transcriptomics, metabolomics, and proteomics. Results indicated that reducing PM2.5 by 1 μg/m3 was associated with a 0.10 % (95 % CI: [0.18 %, 0.01 %]; p = 0.031) improvement in executive function. Notably, we identified 96 AS events without concurrent transcriptional amount alterations. Multi-layered omics analyses revealed disrupted pathways in hypoxia, mitochondrial function and energy metabolism, and immune responses, validated by ELISA and biochemical assay. These findings demonstrated short-term improvements of cognition following PM2.5 purification and provide mechanistic understandings of PM2.5-induced cognition alterations. This study underscores the significance of incorporating AS in the molecular framework of multi-omics research by exploring variable exon splicing, which could enrich multi-omics analysis methodologies and expose to broader audience.

5-ethynyluridine perturbs nuclear RNA metabolism to promote the nuclear accumulation of TDP-43 and other RNA binding proteins

TDP-43, an essential nucleic acid binding protein and splicing regulator, is broadly disrupted in neurodegeneration. TDP-43 nuclear localization and function depend on the abundance of its nuclear RNA targets and its recruitment into large ribonucleoprotein complexes, which restricts TDP-43 nuclear efflux. To further investigate the interplay between TDP-43 and nascent RNAs, we aimed to employ 5-ethynyluridine (5EU), a widely used uridine analog for 'click chemistry' labeling of newly transcribed RNAs. Surprisingly, 5EU induced the nuclear accumulation of TDP-43 and other RNA-binding proteins and attenuated TDP-43 mislocalization caused by disruption of the nuclear transport apparatus. RNA FISH demonstrated 5EU-induced nuclear accumulation of polyadenylated and GU-repeat-rich RNAs, suggesting increased retention of both processed and intronic RNAs. TDP-43 eCLIP confirmed that 5EU preserved TDP-43 binding at predominantly GU-rich intronic sites. RNAseq revealed significant 5EU-induced changes in alternative splicing, accompanied by an overall reduction in splicing diversity, without any major changes in RNA stability or TDP-43 splicing regulatory function. These data suggest that 5EU may impede RNA splicing efficiency and subsequent nuclear RNA processing and export. Our findings have important implications for studies utilizing 5EU and offer unexpected confirmation that the accumulation of endogenous nuclear RNAs promotes TDP-43 nuclear localization.

MCTASmRNA: A deep learning framework for alternative splicing events classification

Alternative splicing (AS) plays crucial post-transcriptional gene function regulation roles in eukaryotic. Despite progress in studying AS at the RNA level, existing methods for AS event identification face challenges such as inefficiency, lengthy processing times, and limitations in capturing the complexity of RNA sequences. To overcome these challenges, we evaluated 10 AS detection tools and selected rMATS for dataset construction. We then developed a multi-scale convolutional and Transformer-based model (MCTASmRNA) to classify AS events in mRNA sequences without relying on a reference genome. To handle the problem of large intra-class and small inter-class difference in AS event sequences, we incorporated an efficient channel attention mechanism and designed a new joint loss function to optimize MCTASmRNA training. MCTASmRNA outperformed baseline models, with an accuracy improvement and exhibited enhanced cross-species generalizability. This model provides valuable support for AS research across different organisms. Future work will focus on optimizing and expanding the model to further explore the complex mechanisms underlying AS.

PRMT5-regulated splicing of DNA repair genes drives chemoresistance in breast cancer stem cells

Breast cancer stem cells (BCSCs) are a rare cell population that is responsible for tumour initiation, metastasis and chemoresistance. Despite this, the mechanism by which BCSCs withstand genotoxic stress is largely unknown. Here, we uncover a pivotal role for the arginine methyltransferase PRMT5 in mediating BCSC chemoresistance by modulating DNA repair efficiency. Mechanistically, we identify PRMT5 as a major regulator of DNA damage response (DDR) gene splicing in BCSCs, particularly those integral to the Fanconi Anaemia and homologous recombination pathways, with PRMT5 inhibition synergising with chemotherapy to promote BCSC apoptosis. A comparison of BCSCs and their bulk cell progeny identified some shared (ATM, DDX11, EXO1, FAN1, SLX4) but many unique (ATR, RAD17, RAD51D, RUVBL1) PRMT5-dependent alternative DDR splicing events. Surprisingly, these skipped exons and retained intron events rarely lead to substantial gene expression repression, suggesting that PRMT5 inhibition predominantly results in nuclear detention of intron-containing transcripts and the production of non-canonical isoforms with compromised protein function. Since many genes within the same DDR pathway undergo deregulated splicing, this study thus reveals additional points of vulnerability and alternative combination drug strategies that could improve the therapeutic efficacy of PRMT5 inhibitors to promote BCSC eradication.

Evaluation of GFM1 mutations pathogenicity through in silico tools, RNA sequencing and mitophagy pahtway in GFM1 knockout cells

GFM1 is a nuclear gene that plays a role in mitochondrial function. In recent decades, various homozygous and compound heterozygous mutations have been identified, leading to significant health issues in patients and often resulting in early death. There is a few experimental research on this gene, particularly regarding its pathogenicity through in silico methods and RNA sequencing and experimental validation in GFM1 knockout cells. This study aims to explore how high-risk pathogenic variants affect protein stability and function using a comprehensive bioinformatics approach. Analyses with Align-GVGD, PolyPhen-2, MupRo, and SIFT indicated that most variants are likely to be highly pathogenic and destabilize the protein structure. The variants were consistently classified as high-risk by Align-GVGD and were deemed "probably damaging" or "possibly damaging" by PolyPhen-2. MupRo analysis suggested a reduction in protein stability, while SIFT indicated functional impacts for all variants. Further analysis with MetaRNN and structural assessments showed that these variants affect protein size, charge, and hydrophobicity, which may disrupt inter-domain interactions and hinder protein function. Differential gene expression analysis in GFM1 knockout HK2 and 293 T cells revealed significant changes in gene expression, particularly in areas related to translation, mitochondrial function, and cellular responses. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses indicated that the affected genes are linked to neurodegenerative diseases, cancer, and various signaling pathways. GFM1 knockout cells displayed notable pathway changes, including those related to oxidative phosphorylation and neurodegenerative diseases (e.g., Parkinson's, Alzheimer's, Huntington's). Upregulation of mitochondrial electron transport chain components (COX17, NDUFB1, ATP5MC1) suggests a compensatory mechanism in response to impaired mitochondrial function. Disruptions in proteostasis and protein synthesis were highlighted by dysregulated proteasome and ribosomal pathways. Markers of mitophagy, such as increased HSP90 and decreased TOMM20 levels, along with changes in PINK1 protein, emphasize GFM1's involvement in mitophagy. Protein-protein interaction analysis connected GFM1 to key mitophagy proteins (e.g., OPTN, Park2/Parkin). Functional experiments confirmed increased mitophagy, indicating a protective response. These results highlight the negative impact of high-risk pathogenic variants on protein stability and cellular function, shedding light on their potential roles in disease progression. This study offers valuable insights into the pathogenic mechanisms linked to GFM1 mutations, underscoring its critical role in mitochondrial function and cellular balance. The findings highlight the gene's involvement in mitophagy, oxidative phosphorylation, and neurodegenerative pathways, laying the groundwork for future research into therapeutic approaches targeting GFM1-related dysfunctions.

Global profiling of alternative splicing in non-small cell lung cancer reveals novel histological and population differences

Lung cancer is one of the most frequently diagnosed cancers in the US. African-American (AA) men are more likely to develop lung cancer with higher incidence and mortality rates than European-American (EA) men. Herein, we report high-confidence alternative splicing (AS) events from high-throughput, high-depth total RNA sequencing of lung tumors and non-tumor adjacent tissues (NATs) in two independent cohorts of patients with adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC). We identified novel AS biomarkers with notable differential percent spliced in (PSI) values between lung tumors and NATs enriched in the AA and EA populations, which were associated with oncogenic signaling pathways. We also uncovered tumor subtype- and population-specific AS events associated with cell surface proteins and cancer driver genes. We highlighted significant AS events in SYNE2 specific to LUAD in both populations, as well as those in CD44 from EAs and TMBIM6 from AAs specific to LUAD. Here, we also present the validation of cancer signatures based on direct high-throughput reverse transcription-PCR. Our large survey of lung tumors presents a rich data resource that may help to understand molecular subtypes of lung tumor between AAs and EAs and reveal new therapeutic vulnerabilities that potentially advance health equity.