FASEB bioAdvances最新文献

Alternative splicing (AS) is a highly conserved posttranscriptional mechanism, generating mRNA variants to diversify the proteome. Acute endurance exercise appears to transiently perturb AS in skeletal muscle, but transcriptome-wide responses are not well defined. We aimed to better understand differential AS (DAS) and differential isoform expression (DIE) in skeletal muscle by comparing short-read (SRS) and long-read RNA sequencing (LRS) data. Publicly accessible SRS of clinical exercise studies were extracted from the Gene Expression Omnibus. Oxford Nanopore LRS was performed on mouse gastrocnemius before and following treadmill exercise (30 m running, n = 5 mice/group, 20 total, 10 weeks old). Differential gene expression (DGE) and DIE were analyzed and validated using RT-PCR and immunoblots. Both SRS and LRS illustrated significant DGE in skeletal muscle postexercise, including 89 RNA-binding proteins (RBPs). rMATS analysis of SRS revealed that exon-skipping and intron-retaining events were the most common. Swan analysis of LRS revealed several common genes across postexercise cohorts with significant DAS but no DGE: 13 exercise-associated genes, including mSirt2 (24.5% shift at 24 h postexercise [24pe], p = 0.005); 61 RBPs, including mHnrnpa3 (28.5% at 24pe, p = 0.02), mHnrnpa1 (30.6% at 24pe, p = 0.004), and mTia1 (53.6% at 24pe, p = 0.004). We illustrated that acute endurance exercise can elicit changes in AS-related responses and RBP expression in skeletal muscle, especially at 24pe. SRS is a powerful tool for analyzing DGE but lacks isoform detection, posing a major gap in knowledge of “hidden” genes with no transcriptional but significant DIE and protein expression changes. Additionally, LRS can uncover previously unknown transcript diversity and mechanisms influencing endurance exercise adaptations and responses.

Copper metabolism MURR1 domain protein 10 (COMMD10) regulates numerous biological processes that are essential for cellular homeostasis. However, the role of COMMD10 in angiogenesis and bone formation remains unexplored. We constructed a COMMD10 knockdown model in endothelial cells and determined the influence of COMMD10 on angiogenesis and bone formation. Our results indicate that COMMD10 knockdown enhances vascular formation by influencing the expression of genes and proteins related to angiogenesis in endothelial cells. In addition, endothelial cells expressing low levels of COMMD10 facilitate bone formation by secreting pro-osteogenic factors. Further, the Rap1 signaling pathway is activated under low COMMD10 conditions. Double knockdown of RAP1B and COMMD10 attenuated the angiogenic ability of endothelial cells. In summary, our research demonstrates that low COMMD10 expression promotes angiogenesis and bone formation through the Rap1 signaling pathway.

Obesity is a global health crisis, with its prevalence particularly severe in the United States, where over 42% of adults live with obesity. Obesity is driven by complex molecular and tissue-level mechanisms that remain poorly understood. Among these, angiogenesis—primarily mediated by vascular endothelial growth factor-A (VEGF-A)—is critical for adipose tissue expansion but presents unique challenges for therapeutic targeting due to its intricate regulation. Systems biology approaches have advanced our understanding of VEGF-A signaling in vascular diseases, but their application to obesity is limited by scattered and sometimes contradictory data. To address this gap, we performed a comprehensive analysis of the existing literature to synthesize key findings, standardize data, and provide a holistic perspective on the adipose vascular microenvironment. The data mining revealed five key findings: (1) obesity increases adipocyte size by 78%; (2) vessel density in adipose tissue decreases by 51% in mice with obesity, with vessels being 47%–58% smaller and four to nine times denser in comparison with tumor vessels; (3) capillary basement membrane thickness remains similar regardless of obesity; (4) VEGF-A shows the strongest binding affinity for VEGFR1, with four times stronger affinity for VEGFR2 than for NRP1; and (5) binding affinities measured by radioligand binding assay and surface plasmon resonance are significantly different. These consolidated findings provide essential parameters for systems biology modeling, new insights into obesity-induced changes in adipose tissue, and a foundation for developing angiogenesis-targeting therapies for obesity.

Deuterium is a natural heavy isotope of hydrogen, having a neutron as well as a proton. Deuterium disrupts ATP synthesis in mitochondria, causing increased production of reactive oxygen species and reduced synthesis of ATP. Gut microbes likely play a significant role in providing deuterium depleted short chain fatty acids (SCFAs) to human colonocytes through hydrogen gas recycling. The production of deuterium depleted (deupleted) nutrients necessarily leaves behind deuterium enriched water, unless there is a process that can sequester deuterium in small molecules that are excreted through the feces. Here, we provide evidence that a small number of classes of uniquely structured carbon-nitrogen rings and bis-allylic carbon atoms in certain biologically active small molecules may play a crucial role in sequestering deuterium for export into feces or urine. Specifically, we have identified the imidazole ring present in histidine, histamine, and microbial derivatives of histidine, the tetraterpenoid lutein, bilirubin and the derivatives urobilinogen and stercobilinogen produced by gut microbes, and the bis-allylic carbons in polyunsaturated fatty acids as likely candidates for sequestering deuterium and thereby reducing the deuterium levels in the water-based medium. Normally, carbon atoms never exchange their bound protons with deuterons from the medium, but all the above classes of molecules are important exceptions to this rule, as has been shown experimentally.

Axon guidance proteins have been found to play a regenerative role in the peripheral nervous system and the cornea. Netrin-4 is a member of the Netrins family of axon guidance proteins implicated in diabetic retinopathy and corneal hemangiogenesis. However, its effects on corneal nerve and epithelium repair are not well understood. We performed in vitro and in vivo studies to assess the effects of Netrin-4 in corneal wound healing. We found that Netrin-4 induced extensive neurite growth and branching in trigeminal ganglia neurons and accelerated the scratch closure of corneal epithelial cells. In vivo, the dual action of Netrin-4 enhanced corneal epithelium healing and nerve regeneration in mice subjected to corneal epithelium debridement. Inhibition studies demonstrate that Netrin-4-induced neuronal growth may be mediated by interaction with Neogenin or α6β1 Integrin receptors. In conclusion, our data demonstrate that Netrin-4 has trophic and neuroregenerative effects in the cornea and could be a suitable therapeutic target to treat corneal injury.

Long-term steroid use, though essential for treating eye diseases, can cause increased intraocular pressure (IOP) in susceptible individuals and may lead to steroid-induced glaucoma in a subset of patients. This study investigated the effect of bone morphogenetic protein-7 (BMP-7) on steroid-induced extracellular matrix (ECM) synthesis in human trabecular meshwork (TM) cells. We sought to explore the potential of BMP-7 as a protective agent against steroid-induced ECM accumulation in the TM. Human TM cells (HTMCs) were treated with either steroids alone or a combination of steroids and BMP-7 to compare their effects on ECM production. BMP-7, known for its transforming growth factor beta (TGF-β) antagonistic properties, was administered using a micellized protein transduction domain (mPTD)-fused BMP-7 polypeptide to enhance activity. Gene expression analysis was conducted to identify specific genes involved in ECM regulation. BMP-7 effectively inhibited steroid-induced ECM accumulation in HTMCs. There was a significant reduction in ECM production in the steroid and BMP-7 co-treated group compared with that in the steroid-only group. Furthermore, several genes involved in ECM regulation were identified in the co-treatment, underscoring BMP-7's potential role in modulating ECM metabolism. These findings demonstrate that BMP-7 exerts protective, anti-fibrotic effects in HTMCs by inhibiting steroid-induced ECM synthesis. BMP-7 may serve as a promising therapeutic target for preventing or treating steroid-induced glaucoma by maintaining normal aqueous humor outflow and preventing IOP elevation.

This study investigated how NPC1L1, a cholesterol transporter, regulates osteogenic differentiation through cholesterol metabolism independently of its transport function. We also explored the role of NPC1L1 in osteoporosis (OP), focusing on the downstream C/EBPα/Cyp27a1/27-hydroxycholesterol (27-OHC) axis. High-throughput RNA sequencing and bioinformatics analysis identified NPC1L1 as a key regulator of osteogenesis. Osteogenic differentiation assays, Alizarin Red S and ALP staining, western blot analysis, and qRT-PCR were performed using osteoblast cell lines (C3H10 and C2C12). In addition, an ovariectomy (OVX)-induced mouse model of OP was established to validate the in vivo effects. ELISAs, chromatin immunoprecipitation (ChIP–qPCR), and rescue experiments were conducted to verify the functional interactions among NPC1L1, Cyp27a1, 27-OHC production, and the transcription factor C/EBPα. NPC1L1 expression was downregulated during osteogenesis, and its knockdown significantly enhanced osteogenic differentiation, proliferation, and migration. At the molecular level, NPC1L1 promoted cholesterol metabolism independently of its transport function, resulting in elevated 27-OHC levels through increased expression of Cyp27a1. Elevated 27-OHC suppressed osteogenesis through the induction of oxidative stress and the downregulation of osteogenic biomarkers (ALP, OPN, OSX, and OCN). In OVX mice, NPC1L1 knockdown significantly reversed osteoporosis-related bone loss, as evidenced by improved trabecular parameters (BV/TV%, Tb.Th, Tb.N). Furthermore, we identified C/EBPα as a transcriptional activator of Cyp27a1, which mediates the regulatory effects of NPC1L1 on 27-OHC production. NPC1L1 inhibits osteogenesis and contributes to OP by promoting the Cyp27a1-dependent synthesis of 27-OHC through the transcription factor C/EBPα. Targeted modulation of the NPC1L1-C/EBPα-Cyp27a1-27-OHC axis could provide novel therapeutic strategies for OP.

The importance of macrophage polarization through atherogenesis is established. However, most studies rely on immunohistological approaches, which have several limitations, such as precluding comprehensive phenotypic analysis. The aim of this study was to perform an alternative analysis of macrophage phenotypes in advanced human atherosclerotic plaques and compare them with their presence in non-atherosclerotic arteries. Atherosclerotic plaques from 70 individuals indicated for carotid endarterectomy, and samples of non-atherosclerotic arterial tissue (renal artery, control group) from 45 living kidney donors were processed to obtain immunocytes and incubated with antibodies (CD45, CD14, CD16, CD36, CD163, and CD206) to be analyzed by flow cytometry. Macrophages in the atherosclerotic plaques tend to express CD16 more intensively than in non-atherosclerotic arterial tissue (transient, CD16^low p < 0.001, pro-inflammatory, CD16^high p < 0.001), and the expression is more closely associated with CD36 expression. Both transient and pro-inflammatory macrophages are linked with the CD206⁻CD163⁺ or CD206⁺CD163⁺ phenotype in atherosclerotic plaques, while CD206⁻CD163⁻ dominates within the anti-inflammatory (CD16^neg) population in the control group. Interestingly, when evaluating all macrophages (regardless of CD16 expression), almost all are CD163⁺ in both groups, supporting the critical importance of using a combination of specific markers. Our results provide a deeper insight into macrophage subpopulations in advanced human atherosclerotic plaques compared with those in non-atherosclerotic vessels. Additionally, our data highlight the critical importance of using appropriate techniques, such as flow cytometry, allowing for simultaneous analysis of multiple markers to accurately and comprehensively characterize macrophages within the atherosclerotic plaque.

Age-related macular degeneration (AMD) is a major cause of vision loss in the elderly, with limited oral treatment options for the wet form characterized by choroidal neovascularization (CNV). This study evaluated GF103, a mutant superoxide dismutase (SOD) from Bacillus amyloliquefaciens, for its potential as an oral therapy in a laser-induced CNV rat model. GF103 was orally administered at varying doses, and outcomes included CNV area, retinal leakage, and VEGF/HIF-1α expression. GF103 was well tolerated and significantly reduced CNV area and retinal VEGF expression at higher doses (≥ 25 mg/kg for retinal VEGF expression; ≥ 50 mg/kg for CNV area). While reductions in fluorescein leakage and HIF-1α levels were not statistically significant, trends suggested modulation of oxidative and hypoxia-related pathways. These results support the potential of GF103 as a safe oral adjunct to existing therapies for wet AMD, meriting further investigation.

Skeletal muscle repair is primarily driven by muscle stem cells (MuSCs) that regenerate damaged myofibers. The differentiation process of MuSCs into differentiated myofibers, known as adult myogenesis, is tightly regulated by various transcription factors, which involve precise spatio-temporal gene expression patterns. Epigenetic factors play an important role in this regulation, as they modulate gene expression to maintain the balance between the different myogenic states. Histone lysine methyltransferases KMT sare key epigenetic regulators, with the SUV39 family being of particular interest for their role in gene repression via H3K9 methylation. This family comprises SUV39H1, SUV39H2, SETDB1, SETDB2, G9A, and GLP. While the functions of SUV39 family members have been well characterized during development in embryonic stem cells and in disease contexts such as cancer, their functions in adult stem cell populations, especially in MuSCs, are still not fully understood. Recent studies shed new light on how the SUV39 family influences muscle biology, particularly in regulating MuSCs fate and adult myogenesis. These enzymes are critical for maintaining the epigenetic landscape essential for effective muscle repair, as they regulate the transition between different myogenic states and ensure coordinated gene expression during regeneration. Here, we present a comprehensive overview of the functions of the SUV39 KMTs family in skeletal muscle biology, emphasizing their role in adult myogenesis and exploring the broader implications for muscle regeneration and related diseases.