Genome-wide identification and functional analysis of dysregulated alternative splicing profiles in sepsis

Comparative study of transcriptomic alterations in sepsis-induced acute liver injury: Deciphering the role of alternative splicing in mouse models

BACKGROUND

Sepsis represents a critical health crisis often leading to the failure of multiple organs, with the liver playing a pivotal role in controlling inflammation and defending against systemic infections. The exacerbation of liver damage can escalate sepsis severity, underscoring the necessity to delve into the molecular mechanisms underlying sepsis-induced acute liver injury (ALI). The role of alternative splicing (AS), a complex post-transcriptional mechanism, has been occasionally noted in relation to sepsis across different investigations.

OBJECTIVE

This research aimed to provide an extensive analysis of gene expression and alternative splicing variants in sepsis-induced ALI using mouse models, thus broadening the understanding of gene-level modulations during sepsis and pinpointing potential therapeutic targets.

METHODS

We employed mouse models of ALI induced via both cecal ligation and puncture (CLP) and lipopolysaccharides (LPS). An extensive evaluation was conducted to identify variances in gene expression and the occurrence of alternative splicing variants within the liver tissues of mice afflicted with sepsis.

RESULTS

The results of our study revealed significant alterations in the regulation of genes associated with RNA splicing and numerous pathways related to inflammation following exposure to CLP and LPS. We identified a total of 170 genes exhibiting both differential expression and splicing variations within the groups subjected to CLP and LPS interventions. Four key genes were specifically identified and validated, emphasizing their potential as treatment targets for ALI in sepsis. Among them, Nop58 was found to play a dual role in inflammation regulation, with intron retention linked to pro-inflammatory responses, while its full-length splicing variant exhibited anti-inflammatory properties. Furthermore, our data highlighted the potential role of specific splicing factors, such as Rbm3, Plrg1, and Snip1, in sepsis-induced liver abnormalities.

CONCLUSION

This study offers a comprehensive insight into the role of AS in sepsis-induced ALI, laying the groundwork for future therapeutic interventions. By demonstrating the functional relevance of specific splicing events, such as those involving Nop58, this work underscores the potential of targeting splicing mechanisms as innovative strategies to mitigate sepsis-induced liver injuries.

Genome-wide identification of alternative splicing related with transcription factors and splicing regulators in breast cancer stem cells responding to fasting-mimicking diet

Fasting-mimicking diet (FMD) can effectively inhibit the viability of breast cancer stem cells (CSCs). However, the molecular mechanisms underlying the inhibitory function of FMD on breast CSCs remain largely unknown. Elucidating the mechanisms by which FMD suppresses breast CSCs is beneficial to targeting breast CSCs. Herein, we systematically analyze alternative splicing and RNA binding protein (RBP) expression in breast CSCs during FMD. The analysis results show that a large number of regulated alternative splicing (RAS) and differentially expressed genes (DEGs) appear responding to FMD. Further studies show that there are potential regulatory relationships between transcription factors (TFs) with RAS (RAS-TFs) and their differentially expressed target genes (RAS-TF-DEGs). Moreover, differentially expressed RNA binding proteins (DERBPs) exhibit potential regulatory functions on RAS-TFs. In short, DERBPs potentially control the alternative splicing of TFs (RAS-TFs), regulating their target gene (RAS-TF-DEG) expression, which leads to the regulation of biological processes in breast CSCs during FMD. In addition, the alternative splicing and DEGs are compared between breast CSCs and differentiated cancer cells during FMD, providing new interpretations for the different responses of the two types of cells. Our studies will shed light on the understanding of the molecular mechanisms underlying breast CSC inhibition induced by FMD.

Landscape of multiple tissues' gene expression pattern associated with severe sepsis: Genetic insights from Mendelian randomization and trans-omics analysis

BACKGROUND

Sepsis, a systemic syndrome often culminating in multiple organ failure (MOF), poses a substantial global health threat. However, the gene expression pattern of various tissues associated with severe sepsis remains elusive.

METHODS

Applying the summary data-based Mendelian randomization (SMR) method, we integrated sepsis genome-wide association study (GWAS) data and expression quantitative trait loci (eQTLs) summaries. This facilitated the investigation of gene causality across 12 tissue types within 26 cohorts linked to adverse sepsis outcomes, including critical care and 28-day mortality. Additionally, trans-omics analyses, including blood transcriptome and single-cell RNA sequencing, were conducted to examine cellular origins and gene functions. The effects of ST7L on sepsis were validated in vivo and in vitro.

RESULTS

We identified 127 genes associated with severe sepsis across diverse tissues. Cross-tissue analysis highlighted ST7L as a significant pan-tissue risk factor for severe sepsis, displaying significance across 11 tissues for both critical care sepsis (meta OR 1.19, 95 % CI: 1.14-1.25, meta p < 0.0001) and 28-day-death sepsis (meta OR: 1.22, 95 % CI: 1.17-1.27, meta p < 0.0001). Notably, independent blood single-cell RNA sequencing data showed specific expression of ST7L in dendritic cells (DCs). ST7L+ DCs were elevated in non-surviving sepsis patients and exhibited an augmented inflammatory molecular pattern compared to ST7L- DCs. Both transcription and translation level of ST7L in DCs exhibited a dose-dependent pattern with LPS. Knocking down ST7L by siRNA was sufficient to alleviate the inflammation phenotype of DCs, including inhibiting p65/NF-kB pathway and inflammatory factors.

CONCLUSION

Our findings underscore ST7L as a pan-tissue risk factor for severe sepsis, specifically manifested in DCs and associated with an inflammatory phenotype. These results offer essential insights into the gene expression profiles across multiple tissues in severe sepsis, potentially identifying therapeutic targets for effective sepsis management.

A tagging polymorphism in fat mass and obesity-associated (FTO) gene is associated with sepsis status in children

INTRODUCTION

Sepsis is one of the most common causes of death in patients admitted to intensive care units (ICUs). The development of sepsis is significantly influenced by genetic predisposition. In this study, we highlight a potential association between a variant of the fat mass and obesity-associated (FTO) gene and risk of sepsis in children and adolescents.

METHODS

We investigated a first-intron tagging FTO polymorphism (rs17817449) by comparing a severe condition (SC) group, comprising 598 paediatric patients (ages 0-19 years) admitted to an ICU with fever, systemic inflammatory response syndrome (SIRS), sepsis, severe sepsis, septic shock, or multiple organ dysfunction syndrome (MODS), with a control group consisting of 616 healthy young adults.

RESULTS

We observed a lower prevalence (p < 0.01; OR = 0.59, 95% CI = 0.39-0.87) of the FTO TT genotype in febrile and SIRS patients compared to patients with severe illness. There was a borderline trend towards a lower prevalence of the FTO TT genotype in the control group compared to the SC group (p < 0.09, OR = 0.81, 95% CI = 0.62-1.06).

CONCLUSIONS

Our findings suggest that rs17817449, a common FTO polymorphism, may be a predictor of sepsis in paediatric patients, and that higher body weight is protective against this clinical complication.