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SIAM Journal on Applied Mathematics 2024The transport of particles in cells is influenced by the properties of intracellular networks they traverse while searching for localized target regions or reaction...
The transport of particles in cells is influenced by the properties of intracellular networks they traverse while searching for localized target regions or reaction partners. Moreover, given the rapid turnover in many intracellular structures, it is crucial to understand how temporal changes in the network structure affect diffusive transport. In this work, we use network theory to characterize complex intracellular biological environments across scales. We develop an efficient computational method to compute the mean first passage times for simulating a particle diffusing along two-dimensional planar networks extracted from fluorescence microscopy imaging. We first benchmark this methodology in the context of synthetic networks, and subsequently apply it to live-cell data from endoplasmic reticulum tubular networks.
PubMed: 38912397
DOI: 10.1137/22m1509308 -
Molecular Therapy. Methods & Clinical... Jun 2024Excessive cytosolic calcium accumulation contributes to muscle degeneration in Duchenne muscular dystrophy (DMD). Sarco/endoplasmic reticulum calcium ATPase (SERCA) is a...
Excessive cytosolic calcium accumulation contributes to muscle degeneration in Duchenne muscular dystrophy (DMD). Sarco/endoplasmic reticulum calcium ATPase (SERCA) is a sarcoplasmic reticulum (SR) calcium pump that actively transports calcium from the cytosol into the SR. We previously showed that adeno-associated virus (AAV)-mediated SERCA2a therapy reduced cytosolic calcium overload and improved muscle and heart function in the murine DMD model. Here, we tested whether AAV SERCA2a therapy could ameliorate muscle disease in the canine DMD model. 7.83 × 10 vector genome particles of the AAV vector were injected into the extensor carpi ulnaris (ECU) muscles of four juvenile affected dogs. Contralateral ECU muscles received excipient. Three months later, we observed widespread transgene expression and significantly increased SERCA2a levels in the AAV-injected muscles. Treatment improved SR calcium uptake, significantly reduced calpain activity, significantly improved contractile kinetics, and significantly enhanced resistance to eccentric contraction-induced force loss. Nonetheless, muscle histology was not improved. To evaluate the safety of AAV SERCA2a therapy, we delivered the vector to the ECU muscle of adult normal dogs. We achieved strong transgene expression without altering muscle histology and function. Our results suggest that AAV SERCA2a therapy has the potential to improve muscle performance in a dystrophic large mammal.
PubMed: 38911286
DOI: 10.1016/j.omtm.2024.101268 -
Iranian Journal of Basic Medical... 2024The present study aimed to explore the mechanisms underlying the potency of the renoprotective effect of the EtOAc fraction of (EALD) (Plumbaginaceae) against...
OBJECTIVES
The present study aimed to explore the mechanisms underlying the potency of the renoprotective effect of the EtOAc fraction of (EALD) (Plumbaginaceae) against cyclosporine A (CsA), in comparison to vitamin E (Vit. E).
MATERIALS AND METHODS
In the experiment, a model of CsA-induced nephrotoxicity was established by dosing male Wistar rats with 25 mg/kg, for 14 days. The protective effect of EALD was investigated through pretreatment of rats with a dose of 200 mg/kg for 14 days, compared to the oral administration of Vit. E at 100 mg/kg. Renal function and markers of oxidative stress were then assessed. Furthermore, a complementary study was carried out to evaluate CsA-induced endoplasmic reticulum stress (ERS) and inflammation on cell culture (3T3 cells and MCT cells) using western blot and quantitative RT-PCR..
RESULTS
Pretreatment of rats with EALD significantly attenuated the elevated levels of renal dysfunction markers (BUN, creatinine) and suppressed malondialdehyde (MDA) levels; It also significantly regulated the changes in superoxide dismutase (SOD), reduced glutathione (GSH), glutathione peroxydase (GPx), and glutathione S-transferase (GST) levels as compared to Vit. E, demonstrating a more effective recovery in renal tissues. Treatment of cells with CsA was linked to the expression of ERS and inflammatory markers activating transcription factor (ATF4), inositol-requiring enzyme 1α (IRE1α), binding immunoglobulin protein (BiP), and monocyte chemoattractant protein-1 (MCP1). In contrast, pretreatment of cells with EALD resulted in a significant decrease in both ERS and inflammatory markers.
CONCLUSION
These findings indicate the renoprotective potential of , as it demonstrated the ability to ameliorate CsA-induced renal dysfunction through its distinctive antioxidant properties.
PubMed: 38911250
DOI: 10.22038/IJBMS.2024.77052.16661 -
Cureus May 2024Recurrent pregnancy loss (RPL) is characterized by consecutive pregnancy losses before 20 weeks of gestation, with evolving definitions necessitating adjustments to...
INTRODUCTION
Recurrent pregnancy loss (RPL) is characterized by consecutive pregnancy losses before 20 weeks of gestation, with evolving definitions necessitating adjustments to prevent delays in couples' evaluation. Limited etiological data on RPL prompts comprehensive evaluations, often yielding no pathological findings. Emerging research implicates endoplasmic reticulum (ER) stress in various reproductive processes, yet its association with RPL remains understudied.
AIM
To evaluate ER stress in patients with RPL with unknown etiology by determining the plasma concentration of X-box binding protein-1 (XBP-1).
MATERIALS AND METHODS
A total of 45 patients aged 18 to 35 years with at least two pregnancy losses with unknown etiology before the completion of 20 weeks of gestation between March 2020 and September 2020 were included in the study group. The control group consisted of 45 healthy women with at least two previous live births, no pregnancy-associated complications, and no history of pregnancy loss or infertility. The XBP-1 levels were determined from serum samples. Statistical analyses assessed differences between groups, and receiver operating characteristic (ROC) curve analysis determined XBP-1's predictive value for RPL.
RESULTS
The mean XBP-1 concentration in the RPL group was significantly higher than in the control group (p < 0.001). The mean values were 2243.65 ± 9425.27 pg/mL and 1196.32 ± 4378.81 pg/mL, respectively. The use of XBP-1 levels for the prediction of RPL was evaluated. In an ROC curve analysis, the area under the curve was found to be 87% (95% CI: 80% to 94.8%). The specificity was 78%, the sensitivity was 88%, the positive likelihood ratio (LR) was 4, the negative LR was 0.15, the positive predictive value was 80%, and the negative predictive value was 87% for the cut-off XBP-1 level at 1364.68 pg/mL.
CONCLUSION
This study highlights the potential role of ER stress in RPL and proposes XBP-1 as a predictive biomarker for pregnancy loss. Understanding ER stress mechanisms in RPL could inform diagnostic and therapeutic strategies. Further research is essential to validate these findings and explore their clinical implications.
PubMed: 38910737
DOI: 10.7759/cureus.60899 -
Yonsei Medical Journal Jul 2024Orbital fibroblasts play key roles in the pathogenesis of Graves' orbitopathy (GO), and previous findings have shown that endoplasmic reticulum (ER) stress and autophagy...
PURPOSE
Orbital fibroblasts play key roles in the pathogenesis of Graves' orbitopathy (GO), and previous findings have shown that endoplasmic reticulum (ER) stress and autophagy also contribute to GO. In this study, we investigated the presently unclear roles of inositol-requiring enzyme 1 (IRE1) and related autophagy processes in the pro-fibrotic mechanism of GO.
MATERIALS AND METHODS
Orbital adipose/connective tissues were obtained from eight GO patients and six normal individuals during surgery. GO fibroblasts were transfected with IRE1 small-interfering RNA and treated with bafilomycin A1 (Baf-A1) to evaluate the inhibitory effects of ER stress and autophagy, and protein-expression levels were analyzed through western blotting after stimulation with transforming growth factor (TGF)-β.
RESULTS
TGF-β stimulation upregulated IRE1 in GO orbital fibroblasts, whereas silencing IRE1 suppressed fibrosis and autophagy responses. Similarly, Baf-A1, an inhibitor of late-phase autophagy, decreased the expression of pro-fibrotic proteins.
CONCLUSION
IRE1 mediates autophagy and the pro-fibrotic mechanism of GO, which provides a more comprehensive interpretation of GO pathogenesis and suggests potential therapeutic targets.
Topics: Humans; Autophagy; Graves Ophthalmopathy; Fibroblasts; Endoribonucleases; Protein Serine-Threonine Kinases; Endoplasmic Reticulum Stress; Transforming Growth Factor beta; Fibrosis; Male; RNA, Small Interfering; Macrolides; Female; Cells, Cultured; Adult; Middle Aged
PubMed: 38910302
DOI: 10.3349/ymj.2023.0294 -
Mechanisms of Ageing and Development Jun 2024Cellular senescence contributes to ageing and age-related diseases, and multiple therapeutic strategies are being developed to counteract it. Senolytic drugs are being...
Cellular senescence contributes to ageing and age-related diseases, and multiple therapeutic strategies are being developed to counteract it. Senolytic drugs are being tested in clinical trials to eliminate senescent cells selectively, but their effects and mechanisms are still unclear. Several studies reveal that the upregulation of senescence-associated secretory phenotype (SASP) factors in senescent cells is accompanied by increased autophagic activity to counteract the endoplasmic reticulum (ER) stress. Our study shows that Doxo-induced senescent fibroblasts yield several SASP factors and exhibit increased autophagy. Interestingly, Quercetin, a bioactive flavonoid, reduces autophagy, increases ER stress, and partially triggers senescent fibroblast death. Given the role of senescent cells in cancer progression, we tested the effect of conditioned media from untreated and quercetin-treated senescent fibroblasts on osteosarcoma cells to determine whether senolytic treatment affected tumour cell behaviour. We report that the partial senescent fibroblast clearance, achieved by quercetin, reduced osteosarcoma cell invasiveness, curbing the pro-tumour effects of senescent cells. The reduction of cell autophagic activity and increased ER stress, an undescribed effect of quercetin, emerges as a new vulnerability of Doxo-induced senescent fibroblasts and may provide a potential therapeutic target for cancer treatment and suggest novel drug combinations as a promising strategy against the tumour.
PubMed: 38909661
DOI: 10.1016/j.mad.2024.111957 -
Scientific Reports Jun 2024Alternative splicing plays a crucial role in increasing the diversity of mRNAs expressed in the genome. Serine/arginine-rich splicing factor 3 (SRSF3) is responsible for...
Alternative splicing plays a crucial role in increasing the diversity of mRNAs expressed in the genome. Serine/arginine-rich splicing factor 3 (SRSF3) is responsible for regulating the alternative splicing of its own mRNA and ensuring that its expression is balanced to maintain homeostasis. Moreover, the exon skipping of SRSF3 leads to the production of a truncated protein instead of a frameshift mutation that generates a premature termination codon (PTC). However, the precise regulatory mechanism involved in the splicing of SRSF3 remains unclear. In this study, we first established a platform for coexpressing full-length SRSF3 (SRSF3-FL) and SRSF3-PTC and further identified a specific antibody against the SRSF3-FL and truncated SRSF3 (SRSF3-TR) proteins. Next, we found that exogenously overexpressing SRSF3-FL or SRSF3-PTC failed to reverse the effects of digoxin, caffeine, or both in combination on this molecule and its targets. Endoplasmic reticulum-related pathways, transcription factors, and chemicals such as palmitic acid and phosphate were found to be involved in the regulation of SRSF3 expression. The downregulation of SRSF3-FL by palmitic acid and phosphate was mediated via different regulatory mechanisms in HeLa cells. In summary, we provide new insights into the altered expression of the SRSF3-FL and SRSF3-TR proteins for the identification of the functions of SRSF3 in cells.
Topics: Serine-Arginine Splicing Factors; Humans; HeLa Cells; Alternative Splicing; Protein Stability; Gene Expression Regulation, Neoplastic; Neoplasms; RNA, Messenger
PubMed: 38909100
DOI: 10.1038/s41598-024-64640-1 -
Nature Communications Jun 2024Cytoplasmic polyadenylation plays a vital role in gametogenesis; however, the participating enzymes and substrates in mammals remain unclear. Using knockout and knock-in...
Cytoplasmic polyadenylation plays a vital role in gametogenesis; however, the participating enzymes and substrates in mammals remain unclear. Using knockout and knock-in mouse models, we describe the essential role of four TENT5 poly(A) polymerases in mouse fertility and gametogenesis. TENT5B and TENT5C play crucial yet redundant roles in oogenesis, with the double knockout of both genes leading to oocyte degeneration. Additionally, TENT5B-GFP knock-in females display a gain-of-function infertility effect, with multiple chromosomal aberrations in ovulated oocytes. TENT5C and TENT5D both regulate different stages of spermatogenesis, as shown by the sterility in males following the knockout of either gene. Finally, Tent5a knockout substantially lowers fertility, although the underlying mechanism is not directly related to gametogenesis. Through direct RNA sequencing, we discovered that TENT5s polyadenylate mRNAs encoding endoplasmic reticulum-targeted proteins essential for gametogenesis. Sequence motif analysis and reporter mRNA assays reveal that the presence of an endoplasmic reticulum-leader sequence represents the primary determinant of TENT5-mediated regulation.
Topics: Animals; Female; Male; Polyadenylation; RNA, Messenger; Mice; Mice, Knockout; Spermatogenesis; Gametogenesis; Oogenesis; Polynucleotide Adenylyltransferase; Oocytes; Fertility; Mice, Inbred C57BL
PubMed: 38909026
DOI: 10.1038/s41467-024-49479-4 -
Cell Stress & Chaperones Jun 2024Heat shock protein 70 (HSP70), the most prominent and well-characterized stress protein in animals, plays an important role in assisting animals in responding to various...
Heat shock protein 70 (HSP70), the most prominent and well-characterized stress protein in animals, plays an important role in assisting animals in responding to various adverse conditions. In the present study, a total of 113 HSP70 gene family members were identified in the updated genome of Magallana gigas (designated MgHSP70) (previously known as Crassostrea gigas). There were 75, 12, 11 and 8 HSP70s located in the cytoplasm, nucleus, mitochondria and endoplasmic reticulum, respectively, and 7 HSP70s were located in both the nucleus and cytoplasm. Among 113 MgHSP70 genes, 107 were unevenly distributed in 8 chromosomes of M. gigas with the greatest number in chromosome 07 (61 genes, 57.01%). The MgHSP70 gene family members were mainly assigned into five clusters, among which the HSPa12 subfamily underwent lineage-specific expansion, consisting of 89 members. A total of 68 MgHSP70 genes (60.18%) were tandemly duplicated and formed 30 gene pairs, among which 14 gene pairs were under strong positive selection. In general, the expression of MgHSP70s was tissue-specific, with the highest expression in labial palp and gill, and the lowest expression in adductor muscle and haemocytes. There were 35, 31 and 47 significantly upregulated genes at 6, 12 and 24h after heat shock treatment (28 °C), respectively. The expression patterns of different tandemly duplicated genes exhibited distinct characteristics after heat stress indicating that these genes may have different functions. Nevertheless, genes within the same tandemly duplicated group exhibit similar expression patterns. Most of the tandemly duplicated HSP70 gene pairs showed the highest expression levels at 24h. This study provides a comprehensive description of the MgHSP70 gene family in M. gigas and offers valuable insights into the functions of HSP70 in the mollusc adaptation of oysters to environmental stress.
PubMed: 38908469
DOI: 10.1016/j.cstres.2024.06.002 -
Science Advances Jun 2024Ufmylation is implicated in multiple cellular processes, but little is known about its functions and regulation in protein trafficking. Here, we demonstrate that the...
Ufmylation is implicated in multiple cellular processes, but little is known about its functions and regulation in protein trafficking. Here, we demonstrate that the genetic depletion of core components of the ufmylation cascade, including ubiquitin-fold modifier 1 (UFM1), UFM1 activation enzyme 5, UFM1-specific ligase 1 (UFL1), UFM1-specific protease 2, and UFM1-binding protein 1 (UFBP1) each markedly inhibits the endoplasmic reticulum (ER)-Golgi transport, surface delivery, and recruitment to COPII vesicles of a subset of G protein-coupled receptors (GPCRs) and UFBP1's function partially relies on UFM1 conjugation. We also show that UFBP1 and UFL1 interact with GPCRs and UFBP1 localizes at COPII vesicles coated with specific Sec24 isoforms. Furthermore, the UFBP1/UFL1-binding domain identified in the receptors effectively converts non-GPCR protein transport into the ufmylation-dependent pathway. Collectively, these data reveal important functions for the ufmylation system in GPCR recruitment to COPII vesicles, biosynthetic transport, and sorting at ER via UFBP1 ufmylation and interaction directly.
Topics: COP-Coated Vesicles; Endoplasmic Reticulum; Receptors, G-Protein-Coupled; Humans; Protein Transport; Golgi Apparatus; Protein Binding; Vesicular Transport Proteins; HEK293 Cells; HeLa Cells; Proteins
PubMed: 38905340
DOI: 10.1126/sciadv.adm9216