IUBMB Life最新文献

Ischemic preconditioning (IPC) is a phenomenon in which brief periods of ischemia trigger protective mechanisms that alleviate subsequent ischemia–reperfusion injury (IRI), although the precise protective mechanism remains unclear. This study investigated the mechanism by which IPC protects acute kidney injury (AKI) induced by renal IRI. We found that IPC for 10 min significantly ameliorated IRI-induced AKI, whereas IPC for 5 or 15 min did not have any protective effects. Renal ischemia increased the expression of caseinolytic protease P (CLPP) in tubular epithelial cells. The peak effect was reached after 10 min of renal ischemia, during which no mitochondrial deposition of misfolded/unfolded proteins or signs of AKI were evident. However, after 15 min of renal ischemia, there was no further increase in CLPP levels, which was accompanied by mitochondrial deposition of misfolded/unfolded proteins and signs of AKI. The increase in CLPP levels suggests potential activation of the mitochondrial unfolded protein response (UPR^mt), which is a cellular stress response pathway that regulates the expression of mitochondrial chaperones and proteases to maintain protein homeostasis within the mitochondria. Knockdown of Clpp led to the aggregation of mitochondrial unfolded/misfolded proteins and phosphorylation of eukaryotic translation initiation factor 2α (eIF2α), which indicated integrated stress response (ISR) activation. Clpp knockdown in mice antagonized the protective effects induced by IPC for 10 min during renal IRI. Furthermore, the inhibition of ISR activation by an ISR inhibitor (ISRIB) may also impede the protective effects of IPC for 10 min. This study indicates that IPC can ameliorate renal IRI injury and that its effect is dependent on CLPP.

Charcot-Marie-Tooth disease (CMT) is a genetically diverse hereditary disorder that affects the motor and sensory nerves, impacting about 1 in 2500 people. It can be inherited through autosomal dominant (AD), autosomal recessive (AR), or X-linked genetic patterns. CMT2, one of the primary subtypes, is characterized by axonal degeneration and commonly presents with muscle weakness, atrophy, foot deformities, and sensory loss. Aminoacyl-tRNA synthetases (aaRSs) play an important role in the genetic underpinnings of CMT2, with more than 60 disease-causing alleles identified across eight different aaRSs, including alanyl-, asparaginyl-, histidyl-, glycyl-, methionyl-, tryptophanyl-, seryl-, and tyrosyl-tRNA synthetases. Mutations in aaRS genes can lead to destabilization of the enzyme, reduced aminoacylation, and aberrant protein complex formation. Yeast as a simple organism provides a robust model system to study the pathogenic effects of aaRS CMT mutations. In this review, we discuss the advantages and limitations of the yeast model systems for CMT2-causative mutations in aaRS.

Tubulointerstitial fibrosis (TIF) is a significant determinant in the pathogenesis of chronic kidney disease (CKD) and is commonly concurrent with lipid infiltration in the renal tubules. Nonetheless, the precise regulatory mechanism of this phenomenon remains incompletely understood. This research sought to uncover the involvement and underlying mechanism of KLF9 in the accumulation of lipids linked to TIF. As renal fibrosis models, TGF-β1 treated HK-2 cells and a unilateral ureteral obstruction (UUO) mouse model were utilized. Histopathological analysis of kidney tissues were evaluated by hematoxylin eosin (HE), periodic acid schiff (PAS), and Masson's trichrome staining. The levels of KLF9 protein and mRNA were quantified through western blot and real-time quantitative PCR, respectively, while triglyceride (TG) levels and lipid accumulation were evaluated using a TG assay kit and Oil Red O staining, respectively. The Pearson correlation coefficient was employed to assess the relationship between KLF9 levels and lipid accumulation. To elucidate the mechanisms underlying KLF9's regulation of lipid accumulation in TIF, luciferase reporter assays, chromatin immunoprecipitation (ChIP), and rescue experiments were performed. This research identified a significant increase in KLF9 expression in TIF, correlating with lipid accumulation. The inhibition of KLF9 in HK-2 cells significantly mitigated TGF-β1 triggered fibrosis and lipid accumulation. Subsequent animal studies corroborated these findings, showing that downregulating KLF9 mitigated fibrosis and lipid accumulation. The expression level of FABP4 was considerably higher in TIF models both in vitro and in vivo. Mechanistically, KLF9 bound to the FABP4 promoter region and positively regulated the expression of FABP4. The KLF9-FABP4 pathway regulated lipid synthesis and promoted lipid accumulation, which in turn promotes the progression of TIF. Our study has unveiled the involvement of KLF9 in driving FABP4 expression at the transcriptional level, culminating in lipid accumulation and subsequent fibrosis in TIF. These findings propose that targeting lipid deposition as a therapeutic strategy may hold promise for addressing TIF.

The formation of foam cells triggered by excessive lipid accumulation within macrophages is a hallmark of atherosclerosis development. Scavenger receptor-A (SR-A) is a key regulator of lipid uptake by macrophages during oxidized low-density lipoprotein (oxLDL)-induced foam cell formation. Ubiquitination is a crucial post-translational modification that regulates the stability and function of targeted proteins, but whether SR-A is ubiquitinated and how ubiquitination affects SR-A function is unknown. We found that ovarian tumor domain protease 1 (OTUB1), a deubiquitinase (DUBs) that removes ubiquitination of targeted proteins, can stabilize SR-A in 293 T cells and THP-1 macrophages. Knockdown of OTUB1 in THP-1 macrophages reduced the SR-A protein level and impaired lipid accumulation in oxLDL-treated THP-1 macrophages, which can be rescued by excessive SR-A. These data suggested that OTUB1-mediated stabilization of SR-A may be critical for lipid accumulation in macrophages during foam cell formation.

Black Meristematic Fungi (BMF) are characterized by a thick melanized cell wall and an isodiametric cellular expansion. BMF represent one of the most damaging groups of microorganisms causing the deterioration of outdoor exposed stone monuments mainly due to the formation of dark spots and patches leading to the darkening of their surface, cracking, and bio-pitting. BMF are among the most stress-resistant organisms on Earth, known for their remarkable ability to withstand solar radiation, desiccation, and extreme temperature fluctuations, which has led to their widespread distribution across the globe. These features make BMF very difficult to remove and restrict, representing a challenge for restorers. Despite the number of scientific works about BMF isolation and ecology, little is known about their response to antimicrobial treatments. Conventional biocides remain the most used treatment for the control of biodeterioration on stone artworks. In recent years, interest in alternative and safer antimicrobial treatments has risen in conservation strategies. The number of scientific works in which their efficacy against BMF is evaluated is, however, still low. The aim of this review is to assess existing studies regarding the response of BMF to both conventional and innovative treatments. This will encompass an in-depth examination of methodologies for the application and evaluation of treatments. Furthermore, we aim to highlight future research directions that will contribute to a more informed selection of effective anti-BMF interventions for stone preservation. We underscore the significance of pioneering, environmentally low-impact solutions.

Laryngeal squamous cell carcinoma (LSCC) exhibits aggressive growth, frequent recurrence, and a notable resistance to existing treatments. Building upon prior discoveries that identified junctional adhesion molecule 3 (JAM3) as a critical tumor suppressor in LSCC, this study delves into the transcriptional regulation by upstream stimulatory factor 1 (USF1) and its implications for LSCC pathogenesis. Employing dual-luciferase assays and chromatin immunoprecipitation–quantitative polymerase chain reaction (ChIP-qPCR), we confirmed USF1's direct binding to the E-box within the JAM3 promoter, thereby enhancing JAM3 expression in AMC-HN-8 and FD-LSC-1 cells. Complementary in vitro assays and in vivo experiments corroborated that USF1 overexpression markedly reduces tumor aggressiveness, linked to heightened JAM3 activity. Further analysis, including Western blot and immunohistochemistry of xenograft tumor tissues, revealed that increased JAM3, stimulated by USF1, activates the Hippo signaling pathway, underscoring its role in tumor suppression. These findings position USF1 and JAM3 as pivotal elements in the molecular framework of LSCC, suggesting their potential as targets for therapeutic intervention.

The cGAS-STING signaling pathway has emerged as a critical player in the immune response against cancer, including colorectal adenocarcinoma (COAD). Understanding the impact of this pathway on COAD at multiple omics levels is crucial for advancing cancer immunotherapy and precision medicine. This study aimed to investigate the relationship between cGAS-STING-related genes and COAD, analyzing gene mutations, copy number variations, DNA methylation, and gene expression to uncover the pathway's influence on COAD prognosis. Utilizing multi-omics sequencing data from TCGA and GEO databases, key core genes in the cGAS-STING pathway were identified and further validated through PCR and Western blot analysis. Mutations and copy number variations in the CASP8 and RIPK1 genes, differential DNA methylation patterns, and mRNA expression levels of specific genes were assessed to determine their impact on COAD prognosis. Validation through tissue samples highlighted NLRC3, CASP1, AIM2, and CXCL10 as core genes in the cGAS-STING pathway. Our findings demonstrate that mutations and copy number variations in CASP8 and RIPK1, differential DNA methylation patterns, and altered gene expression levels significantly influence the prognosis of COAD. The identification of core genes in the cGAS-STING pathway, particularly NLRC3, CASP1, AIM2, and CXCL10, has led to the development of a prognostic model predicting poor tumor outcomes through immune cell infiltration. This study provides valuable insights into the mechanisms of the cGAS-STING pathway in COAD and offers potential directions for future research in cancer immunotherapy and precision medicine.

Lysine-specific demethylase 1 (LSD1), a histone demethylase crucial for embryonic development and tissue differentiation, has an undefined role in prostate cancer (PCa), especially castration-resistant PCa. The present study represents a pioneering endeavor to comprehensively dissect the function of LSD1 within the PCa landscape. Our investigations revealed that attenuation of LSD1 expression exerts multiple inhibitory effects on PCa cells. Specifically, it curtails the proliferation and colony-forming ability of PC-3 cells, concomitantly promotes apoptosis, and impedes cell invasion. Notably, knockdown of LSD1 triggers significant perturbations in the expression profiles of pivotal proteins, such as prostate-specific antigen (PSA), forkhead box A1 (FOXA1), and NKX3.1, thereby shedding new light on the underlying molecular mechanisms governing PCa progression. Leveraging bioinformatics analysis and transcriptome sequencing, we unearthed that LSD1 knockdown precipitates widespread gene expression dysregulation, with 3166 genes exhibiting differential expression patterns, which in turn impact a broad spectrum of cellular processes. Importantly, we identified that LSD1 modulates the methylation modification of histone H3 lysine 4 monomethylation (H3K4me1) in the promoter region of matrix metallopeptidase 13 (MMP13), thereby orchestrating its expression. In both orthotopic and metastatic tumor models, as well as in vitro cell cultures, the LSD1 inhibitor GSK2879552 demonstrated potent efficacy in suppressing PCa progression. To sum up, this study not only uncovers the oncogenic role of LSD1 in PCa but also validates the therapeutic promise of GSK2879552, furnishing novel perspectives and prospective targets for the clinical management of PCa.

Oligomerization can influence the stability and activity of a protein. The majority of enzymes, including aminoacyl-tRNA synthetases, become catalytically active upon forming homodimers. Residues located at the dimerization interface are highly conserved and mutations arising within can cause severe disease phenotypes. Beyond homozygous mutations, other disease-causing mutations, such as compound heterozygous and mono-allelic mutations, can lead to the formation of heterodimers between two distinct subunits. Purifying a recombinant heterodimer is required for its thorough characterization in vitro, yet there is a lack of established biochemical methods for the preparation. Here we describe a heterodimer purification and validation method with the example of a disease-causing mono-allelic, nonsense mutation R534* in cytoplasmic asparaginyl-tRNA synthetase (NARS1 or AsnRS). Our method involves co-expression of two separately tagged constructs to allow for purification of the wild-type and the R534* mutant heterodimers. While the two subunits can hardly be distinguished by size, their separate detection is achieved by western blotting against the tags. Quantification analysis confirmed that the subunits within the heterodimer are present in nearly equal proportions. This simple protocol can be adapted to study other size-indistinguishable heterodimers.

There is a limited understanding of specific DNA methylation patterns associated with HER2 overexpression in breast and gastric cancers. Here we aim to solve the problem using inferred DNA methylation markers. DNA methylation data from The Cancer Genome Atlas (TCGA) were analyzed for breast and gastric cancers regarding HER2 status. We further applied a targeted bisulfite sequencing approach to elaborate the DNA methylation profile of the HER2 region, covering 7635 CpG sites. Based on these two sets of data, we selected specific DNA methylation markers inferring HER2 status for both breast and gastric cancers and validated their performance in assisting HER2-status determination on a retrospective cohort with 496 breast cancer and 372 gastric cancer. HER2-Meth could well distinguish HER2 IHC0/1+ from HER2 IHC3+ cases in both breast cancer (AUC = 0.983, n = 130) and gastric cancer (AUC = 0.974, n = 63), also could effectively discriminate HER2 IHC2+/FISH+ from HER2 IHC2+/FISH- cases in equivocal situations for both breast cancer (test set AUC = 0.879, n = 74; validation set AUC = 0.875, n = 75) and gastric cancer (test set AUC = 0.910, n = 70; validation set AUC = 0.941, n = 71), outperforming regular HER2 copy number test (An AUC of 0.793 for breast cancer and an AUC of 0.759 for gastric cancer) on HER2 IHC2+ cases. Furthermore, HER2-Meth demonstrated its potential for stratifying HER2-positive patients, enabling predictions regarding overall survivals, and the potential benefits of HER2-targeted therapies in breast cancer. The strong agreement observed between the methylation qPCR test and the results of IHC and FISH indicates significant potential for this approach as a complementary tool in guiding HER2-targeted therapies for patients with breast and gastric cancers.