Splicing factor SRSF6 mediates pleural fibrosis

Angiogenic factor AGGF1 is a general splicing factor regulating angiogenesis and vascular development by alternative splicing of SRSF6

AGGF1 encodes an angiogenic factor that causes vascular disease Klippel-Trenaunay syndrome when mutated. AGGF1 also acts at the top of the genetic regulatory hierarchy for mesodermal differentiation of hemangioblasts, multipotent stem cells for differentiation of blood cells and vascular cells. Alternative splicing (AS) is a post-transcriptional process that generates multiple mature mRNAs from a single primary transcript (pre-mRNA), producing protein diversity. Deregulation of AS leads to many human diseases. The physiological role and mechanism of AGGF1 in AS are not clear. Full-length transcriptome sequencing of human pulmonary artery endothelial cells (HPAECs) with AGGF1 silencing revealed 63 121 genes, including 1144 new unannotated genes, and showed that AGGF1 is a general splicing factor regulating AS of 436 genes, including SRSF6 regulating AS of many target genes. AGGF1 promoted the skipping of exon 3 that produces the full-length SRSF6 protein, an evolutionarily conserved AS event. Overexpression of full-length SRSF6 reversed the reduced cell proliferation, migration, and capillary tube formation of HPAECs with AGGF1 silencing. Knockdown of SRSF6 and overexpression of the shorter, alternatively spliced isoform of SRSF6 both inhibited HPAEC proliferation, migration, and capillary tube formation, whereas opposite results were obtained for overexpression of full-length SRSF6. Knockdown of srsf6 impaired development of ISVs in zebrafish, whereas overexpression of srsf6 enhanced vascular development and partially rescued impaired ISV development in zebrafish embryos with aggf1 knockdown. Overall, our findings reveal that AGGF1 is a general splicing factor, and that AGGF1-mediated exon 3 skipping of SRSF6 pre-mRNA is important for endothelial cell functions, angiogenesis, and vascular development.

Renal Tubular Epithelial Cell-Derived hsa_circ_0008925 From Urine Is Related to Chronic Renal Fibrosis

Renal fibrosis (RF) is a crucial pathological factor in the progression of chronic kidney disease (CKD) to end-stage renal failure, and accurate and noninvasive assays to monitor the progression of renal fibrosis are needed. Circular RNAs (circRNAs) are noncoding RNAs that can be used as diagnostic biomarkers and therapeutic targets for human diseases. In this study, we analysed the expression of hsa_circ_0008925 in human urinary renal tubular cells and investigated its role in renal fibrosis. Urinary samples were collected from CKD patients with varying degrees of renal fibrosis; renal tubular epithelial cells were isolated from the urinary samples using magnetic bead sorting. In patients with moderate-severe renal fibrosis, the expression of hsa_circ_0008925 in urinary renal tubular epithelial cells was elevated compared to that in patients with no renal fibrosis to mild renal fibrosis. Spearman correlation analysis indicated that the hsa_circ_0008925 expression was positively correlated with serum creatinine (Scr, rs = 0.424, p = 0.031). The expression of hsa_circ_0008925 was elevated in TGF-β1-treated HK-2 cells in vitro. Silencing of hsa_circ_0008925 using siRNA inhibited TGF-β1-induced fibrosis in HK2 cells. RNA pull-down and mass spectrometric analyses indicated that serine/arginine-rich splicing factor 6 (SRSF6) is the downstream of hsa_circ_0008925. Silencing mmu_circ_0002215 and inhibiting SRSF6 alleviated renal fibrosis in a UUO model in vivo. Inhibiting hsa_circ_0008925/SRSF6 alleviated renal fibrosis in vitro and in vivo. These findings suggest that targeting the hsa_circ_0008925/SRSF6 pathway could hold promise as a potential therapeutic strategy for treating renal fibrosis.

Proteomic profiling of neutrophils and plasma in community-acquired pneumonia reveals crucial proteins in diverse biological pathways linked to clinical outcome

Introduction

Neutrophils play a dichotomous role in community-acquired pneumonia (CAP), providing protection and potentially causing damage. Existing research on neutrophil function in CAP relies on animal studies, leaving a gap in patient-centered investigations.

Methods

We used mass spectrometry to characterize the neutrophil proteome of moderately ill CAP patients at general ward admission and related the proteome to controls and clinical outcomes.

Results

We prospectively included 57 CAP patients and 26 controls and quantified 3482 proteins in neutrophil lysates and 386 proteins in concurrently collected plasma. The extensively studied granule-related proteins in animal models did not drive the neutrophil proteome changes associated with human CAP. Proteome alterations were primarily characterized by an increased abundance of proteins related to (aerobic) metabolic activity and (m)RNA translation/processing, concurrent with a diminished presence of cytoskeletal organization-related proteins (all pathways p<0.001). Higher and lower abundances of specific proteins, primarily constituents of these pathways, were associated with prolonged time to clinical stability in CAP. Moreover, we identified a pronounced presence of platelet-related proteins in neutrophil lysates of particularly viral CAP patients, suggesting the existence of neutrophil-platelet complexes in non-critically ill CAP patients. Of the proteins measured in neutrophils, 4.3% were detected in plasma.

Discussion

Our study presents new perspectives on the neutrophil proteome associated with CAP, laying the groundwork for forthcoming patient-centred investigations. Our results could pave the way for targeted strategies to fine-tune neutrophil responses, potentially improving CAP outcomes.

SRSF6 modulates histone-chaperone HIRA splicing to orchestrate AR and E2F activity in prostate cancer

Despite novel therapeutic strategies, advanced-stage prostate cancer (PCa) remains highly lethal, pointing out the urgent need for effective therapeutic strategies. While dysregulation of the splicing process is considered a cancer hallmark, the role of certain splicing factors remains unknown in PCa. This study focuses on characterizing the levels and role of SRSF6 in this disease. Comprehensive analyses of SRSF6 alterations (copy number/mRNA/protein) were conducted across eight well-characterized PCa cohorts and the Hi-MYC transgenic model. SRSF6 was up-regulated in PCa samples, correlating with adverse clinical parameters. Functional assays, both in vitro (cell proliferation, migration, colony, and tumorsphere formation) and in vivo (xenograft tumors), demonstrated the impact of SRSF6 modulation on critical cancer hallmarks. Mechanistically, SRSF6 regulates the splicing pattern of the histone-chaperone HIRA, consequently affecting the activity of H3.3 in PCa and breast cancer cell models and disrupting pivotal oncogenic pathways (AR and E2F) in PCa cells. These findings underscore SRSF6 as a promising therapeutic target for PCa/advanced-stage PCa.

CTCF and BORIS-mediated autophagy regulation via alternative splicing of BNIP3L in breast cancer

Autophagy is a pivotal regulatory and catabolic process, induced under various stressful conditions, including hypoxia. However, little is known about alternative splicing of autophagy genes in the hypoxic landscape in breast cancer. Our research unravels the hitherto unreported alternative splicing of BNIP3L, a crucial hypoxia-induced autophagic gene. We showed that BNIP3L, under hypoxic condition, forms two isoforms, a full-length isoform (BNIP3L-F) and a shorter isoform lacking exon 1 (BNIP3L-Δ1). The hypoxia-induced BNIP3L-F promotes autophagy, while under normoxia, the BNIP3L-Δ1 inhibits autophagy. We discovered a novel dimension of hypoxia-mediated epigenetic modification that regulates the alternative splicing of BNIP3L. Here, we showed differential DNA methylation of BNIP3L intron 1, causing reciprocal binding of epigenetic factor CCCTC-binding factor (CTCF) and its paralog BORIS. Additionally, we highlighted the role of CTCF and BORIS impacting autophagy in breast cancer. The differential binding of CTCF and BORIS results in alternative splicing of BNIP3L forming BNIP3L-F and BNIP3L-Δ1, respectively. The binding of CTCF on unmethylated BNIP3L intron 1 under hypoxia results in RNA Pol-II pause and inclusion of exon 1, promoting BNIP3L-F and autophagy. Interestingly, the binding of BORIS on methylated BNIP3L intron 1 under normoxia also results in RNA Pol-II pause but leads to the exclusion of exon 1 from BNIP3L mRNA. Finally, we reported the critical role of BORIS-mediated RNA Pol-II pause, which subsequently recruits SRSF6, redirecting the proximal splice-site selection, promoting BNIP3L-Δ1, and inhibiting autophagy. Our study provides novel insights into the potential avenues for breast cancer therapy by targeting autophagy regulation, specifically under hypoxic condition.

Extracellular Matrix-Derived Damage-Associated Molecular Patterns (DAMP): Implications in Systemic Sclerosis and Fibrosis

Damage-associated molecular patterns (DAMPs) are intracellular molecules released under cellular stress or recurring tissue injury, which serve as endogenous ligands for toll-like receptors (TLRs). Such DAMPs are either actively secreted by immune cells or passively released into the extracellular environment from damaged cells or generated as alternatively spliced mRNA variants of extracellular matrix (ECM) glycoproteins. When recognized by pattern recognition receptors (PRRs) such as TLRs, DAMPs trigger innate immune responses. Currently, the best-characterized PRRs include, in addition to TLRs, nucleotide-binding oligomerization domain-like receptors, RIG-I-like RNA helicases, C-type lectin receptors, and many more. Systemic sclerosis (SSc) is a chronic autoimmune condition characterized by inflammation and progressive fibrosis in multiple organs. Using an unbiased survey for SSc-associated DAMPs, we have identified the ECM glycoproteins fibronectin-containing extra domain A and tenascin C as the most highly upregulated in SSc skin and lung biopsies. These DAMPs activate TLR4 on resident stromal cells to elicit profibrotic responses and sustained myofibroblasts activation resulting in progressive fibrosis. This review summarizes the current understanding of the complex functional roles of DAMPs in the progression and failure of resolution of fibrosis in general, with a particular focus on SSc, and considers viable therapeutic approaches targeting DAMPs.

Towards understandings of serine/arginine-rich splicing factors

Serine/arginine-rich splicing factors (SRSFs) refer to twelve RNA-binding proteins which regulate splice site recognition and spliceosome assembly during precursor messenger RNA splicing. SRSFs also participate in other RNA metabolic events, such as transcription, translation and nonsense-mediated decay, during their shuttling between nucleus and cytoplasm, making them indispensable for genome diversity and cellular activity. Of note, aberrant SRSF expression and/or mutations elicit fallacies in gene splicing, leading to the generation of pathogenic gene and protein isoforms, which highlights the therapeutic potential of targeting SRSF to treat diseases. In this review, we updated current understanding of SRSF structures and functions in RNA metabolism. Next, we analyzed SRSF-induced aberrant gene expression and their pathogenic outcomes in cancers and non-tumor diseases. The development of some well-characterized SRSF inhibitors was discussed in detail. We hope this review will contribute to future studies of SRSF functions and drug development targeting SRSFs.

Advances in The Study of RNA-binding Proteins in Diabetic Complications

Background

It has been reported that diabetes mellitus affects 435 million people globally as a primary health care problem. Despite many therapies available, many diabetes remains uncontrolled, giving rise to irreversible diabetic complications that pose significant risks to patients’ wellbeing and survival.

Scope of Review

In recent years, as much effort is put into elucidating the posttranscriptional gene regulation network of diabetes and diabetic complications; RNA binding proteins (RBPs) are found to be vital. RBPs regulate gene expression through various post-transcriptional mechanisms, including alternative splicing, RNA export, messenger RNA translation, RNA degradation, and RNA stabilization.

Major Conclusions

Here, we summarized recent studies on the roles and mechanisms of RBPs in mediating abnormal gene expression in diabetes and its complications. Moreover, we discussed the potential and theoretical basis of RBPs to treat diabetes and its complications.

• Mechanisms of action of RBPs involved in diabetic complications are summarized and elucidated.

• We discuss the theoretical basis and potential of RBPs for the treatment of diabetes and its complications.

• We summarize the possible effective drugs for diabetes based on RBPs promoting the development of future therapeutic drugs.

Targeting Splicing Factor SRSF6 for Cancer Therapy

Aberrant alternative splicing of pre-mRNA is an emerging cancer hallmark. Many cancer-associated genes undergo alternative splicing to produce multiple isoforms with diverse or even antagonistic functions. Oncogenic isoforms are often up-regulated, whereas tumor suppressive isoforms are down-regulated during tumorigenesis. Serine/arginine-rich splicing factor 6 (SRSF6) is an important splicing factor that regulates the alternative splicing of hundreds of target genes, including many cancer-associated genes. The potential roles of SRSF6 in cancers have attracted increasing attentions in the past decade. Accumulated pieces of evidence have shown that SRSF6 is a potential oncogenic gene that promotes oncogenic splicing when overexpressed. Targeting SRSF6 may suppress tumorigenesis. In this review, we describe the gene, mRNA, and protein structure of SRSF6; summarize the current understanding of the expression, functions, and regulatory mechanisms of SRSF6 during tumorigenesis; and discuss the potential application of targeting SRSF6 in cancer treatment.

miRNA-Based Regulation of Alternative RNA Splicing in Metazoans

Alternative RNA splicing is an important regulatory process used by genes to increase their diversity. This process is mainly executed by specific classes of RNA binding proteins that act in a dosage-dependent manner to include or exclude selected exons in the final transcripts. While these processes are tightly regulated in cells and tissues, little is known on how the dosage of these factors is achieved and maintained. Several recent studies have suggested that alternative RNA splicing may be in part modulated by microRNAs (miRNAs), which are short, non-coding RNAs (~22 nt in length) that inhibit translation of specific mRNA transcripts. As evidenced in tissues and in diseases, such as cancer and neurological disorders, the dysregulation of miRNA pathways disrupts downstream alternative RNA splicing events by altering the dosage of splicing factors involved in RNA splicing. This attractive model suggests that miRNAs can not only influence the dosage of gene expression at the post-transcriptional level but also indirectly interfere in pre-mRNA splicing at the co-transcriptional level. The purpose of this review is to compile and analyze recent studies on miRNAs modulating alternative RNA splicing factors, and how these events contribute to transcript rearrangements in tissue development and disease.