Biology Direct最新文献

Background: Hepatocellular carcinoma (HCC) is among the deadliest cancers globally. Yes-Associated Protein (YAP), a Hippo pathway effector, crucially regulates cell proliferation and apoptosis. Recent research has implicated YAP's role in HCC progression, but the mechanisms are unclear. This study aims to clarify YAP's function in HCC, emphasizing its regulation of key pathways and targets.

Results: Gene knockout and overexpression models were established in nude mice and cell lines of HCC cells to investigate YAP's impact on tumorigenesis. Additionally, functional assays and molecular biology techniques were employed to identify YAP's regulatory networks. The study demonstrates that LDHA-regulated lactate production promotes YAP activation and malignant phenotypes in HCC. Overexpression of LDHA in HepG2 and Huh7 cells increased lactate levels and activated the YAP pathway, enhancing cell proliferation, migration, and invasion. Lactate treatment also promoted these malignant phenotypes by inhibiting YAP phosphorylation at Ser127. In a xenograft model, lactate accelerated tumor growth through YAP activation. YAP lactylation at K102 antagonized its Ser127 phosphorylation, further promoting malignant progression.

Conclusions: This study highlights the significance of YAP in HCC pathogenesis, providing insights into potential therapeutic targets for HCC management.

Adaptor proteins play a crucial role in signal transduction by facilitating the assembly of protein complexes at specific subcellular domains. These multifunctional molecules contain multiple binding modules that enhance the efficiency and flexibility of cellular signaling pathways, thereby orchestrating complex responses. Among these proteins, Grb2 (growth factor receptor-bound protein 2) emerges as a key regulator owing to its unique "sandwich" structure. Despite lacking intrinsic enzymatic activity, recent investigations have revealed that Grb2 acts not merely as a passive bridge but also utilizes intramolecular allosteric communication to modulate binding specificity. In this study, we compared the kinetic binding properties of SH2-SH3 belonging to Grb2 with Gab2 and the same experiment with bound states of the SH2 domain using two different peptides that mimics the physiological ligands of SH2. Our results demonstrate that the SH2 domain plays a critical regulatory role, exhibiting remarkably distinct behaviors in free and bound states, and depending on the ligand it binds to. This suggests how selectivity can be modulated by intradomain allostery. In vitro functional assays measuring the activation levels of the target protein further supported our hypothesis.

Background: This study employs Caenorhabditis elegans (C. elegans) as a model organism to explore the anti-aging effects of hydroxytyrosol (HT) and its underlying mechanisms.

Results: The findings reveal that HT significantly extends the lifespan of C. elegans while improving their functional performance (motility and pharyngeal function), and antioxidant capacity when administered on the first day of adulthood (D1). However, its efficacy diminishes when treatment begins on or after the third day of adulthood (D3). HT prolongs lifespan through a mechanism akin to that of skn-1 modulating the oxidative stress pathway.

Conclusions: This study suggests that the administration timing is an important factor for of anti-oxidation compounds to be effective in counteracting aging.

Background: Glioma is a malignant tumor associated with poorer prognosis. This study aims to elucidate the mechanism of LINC01018/miR-182-5p/Rab27B axis in PD-L1-mediated CD8⁺ T cell suppression in the progression of gliomas.

Methods: LINC01018, miR-182-5p, and Rab27B expression levels in glioblastoma tissues were measured. The proportion of infiltrating macrophages and monocytes and CD8⁺ T cell function were assessed. The relationship between miR-182-5p and Rab27B was analyzed. Glioma cell activity, invasion, and migration were measured. The expression of E-cadherin, N-cadherin, Vimentin, PD-L1, iNOS, and CD206 was determined. Glioma cell-derived EVs were isolated, and the co-localization of Rab27B and PD-L1 and the binding of Rab27B to PD-L1 were analyzed. The endocytosis of EVs by microglia was assayed. The impact of LINC01018/miR-182-5p/Rab27B on glioma growth was observed. The function of macrophages and CD8⁺ T cells in tumors was analyzed.

Results: Rab27B was downregulated, and infiltrating macrophages and monocytes were increased in glioblastoma. miR-182-5p inhibited Rab27B expression. Rab27B knockdown reverses the inhibitory effect of LINC01018 overexpression on glioma cell growth. Glioma cells-derived EVs with low Rab27B expression carried more PD-L1 to increase PD-L1 expression and M2 polarization in microglia. LINC01018 overexpression reduced macrophages in orthotopic tumors. CD8⁺ T cell numbers showed no significant difference, but TIM-3 increased and IFN-γ decreased. miR-182-5p inhibition enhanced the therapeutic effect of anti-PD-L1, which was reversed after glioma cell-derived EVs.

Conclusion: LINC01018 promotes PD-L1-mediated CD8⁺ T cell suppression via the miR-182-5p/Rab27B axis in glioma cell-derived EVs, thereby contributing to immune escape in gliomas.

Background: Protein arginine methyltransferases (Prmts) are essential regulators of various biological processes and have been implicated in the pathogenesis of numerous diseases. However, their role in osteomyelitis remains poorly understood.

Methods: A mouse model of chronic hematogenous osteomyelitis (CHOM) was established by intravenous inoculation with Staphylococcus aureus (S. aureus). Gene and protein expression levels were quantified using RT-qPCR and immunoblot analysis, respectively. Protein interactions were determined via immunoprecipitation and co-immunoprecipitation assays. In vitro and in vivo assays were employed to evaluate protein methylation and ubiquitination. Bone destruction was assessed through histological staining.

Results: Among 9 Prmt members, Prmt1 was the only one significantly upregulated in osteomyelitis-affected mice. Our findings revealed that the inflammatory microenvironment specifically upregulated Prmt1 expression in osteoblasts and osteocytes, which facilitated its interaction with the transcriptional activator Ncoa4 (nuclear receptor coactivator 4) and mediated Ncoa4 arginine methylation, thereby enhancing Ncoa4 protein stability. Methylated Ncoa4 formed a transcriptional complex with the histone acetyltransferase Cbp (CREB-binding protein) and transcription factor Ap1 (Activator protein 1), driving the expression of four Adamts genes (Adamts3/8/12/14) that promoted extracellular matrix (ECM) degradation in osteoblasts and osteocytes. In contrast, depletion or pharmacological inhibition of Prmt1 prevented Ncoa4 methylation upon stimulation with pro-inflammatory cytokines, leading to Ncoa4 ubiquitination by Rnf8 (Ring finger protein 8) E3 ligase and subsequent proteasomal degradation, eventually leading to downregulation of Adamts expression. Importantly, treatment with Prmt1 inhibitors TCE-5003 and MS023 significantly mitigated bone ECM degradation and prevented osteomyelitis progression in S. aureus-infected mice.

Conclusion: These findings identify Prmt1 as a pivotal regulator of bone ECM degradation in osteomyelitis through stabilization of Ncoa4 and highlight Prmt1 as a promising therapeutic target for osteomyelitis treatment.

Ubiquitin-specific protease 8 (USP8) is a deubiquitinating enzyme with essential functions in protein trafficking and stability. It is a multidomain protein, with an N-terminal MIT (microtubule interacting and trafficking) domain, followed by a non-catalytic rhodanese (Rhod) domain, a long intrinsically disordered region, and a C-terminal catalytic domain. The N-terminal MIT domain of USP8 is known to mediate protein-protein interactions through binding to short linear motifs. The non-catalytic Rhod domain is also involved in protein-protein interactions, however detailed insights into these interactions remain limited. In this study we explore the short linear motif-based interactions of the MIT and Rhod domains of USP8 using a combination of proteomic peptide-phage display, peptide arrays and deep mutational scanning. We show that the MIT domain can bind ligands with a general [DE][LIF]x{2,3}R[FYIL]xxL[LV] consensus motif. We uncover that the rhodanese domain of USP8 is a peptide-binding domain, and define two distinct binding motifs (Rx[LI]xGxxxPxxL and G[LV][DE][IM]WExKxxxLxE) for this domain by deep mutational scanning of two different peptide ligands. Using the motif information, we predict binding sites within known USP8 interactors and substrates and validate interactions through peptide array analysis. Our findings demonstrate that both the USP8 MIT and rhodanese domains are peptide-binding domains that can be bound by degenerate and distinct binding motifs. The detailed information on the peptide binding preference of the two N-terminal domains of USP8 provide novel insights into the molecular recognition events that underlie the function of this essential deubiquitinating enzyme.

M2 macrophages play a crucial role in the initiation and progression of various tumors, including diffuse large B-cell lymphoma (DLBCL). However, the characterization of M2 macrophage-related genes in DLBCL remains incomplete. In this study, we downloaded DLBCL-related datasets from the Gene Expression Omnibus (GEO) database and identified 77 differentially expressed genes (DEGs) between the control group and the treat group. We assessed the immune cell infiltration using CIBERSORT analysis and identified modules associated with M2 macrophages through weighted gene co-expression network analysis (WGCNA). Using the Least Absolute Shrinkage and Selection Operator (LASSO), Support Vector Machine Recursive Feature Elimination (SVM-RFE), and Random Forest (RF) algorithms, we screened for seven potential diagnostic biomarkers with strong diagnostic capabilities: SMAD3, IL7R, IL18, FAS, CD5, CCR7, and CSF1R. Subsequently, the constructed logistic regression model and nomogram demonstrated robust predictive performance. We further investigated the expression levels, prognostic values, and biological functions of these biomarkers. The results showed that SMAD3, IL7R, IL18, FAS and CD5 were associated with the survival of DLBCL patients and could be used as markers to predict the prognosis of DLBCL. Our study introduces a novel diagnostic strategy and provides new insights into the potential mechanisms underlying DLBCL. However, further validation of the practical value of these genes in DLBCL diagnosis is warranted before clinical application.

Background: Dry age-related macular degeneration (AMD) is a common chronic degenerative eye disease for which there is currently no effective treatment. Insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) is a recently identified m6A reader that binds RNA and maintains its stability, thereby participating in various biological processes. However, its role in dry AMD remains unclear.

Methods: In this study, we investigated the role of IGF2BP2 in macrophage NLRP3 inflammasomes using a sodium iodate-induced dry AMD model.

Results: Our results demonstrated that IGF2BP2 is highly expressed in the retinal-choroidal tissue induced by sodium iodate, with its effects primarily occurring in macrophages. The loss of IGF2BP2 ameliorating dry AMD. Mechanistically, methylated NLRP3 transcripts were subsequently directly recognized by the specific m 6 A "reader", IGF2BP2, to prevent NLRP3 mRNA degradation. Furthermore, in in vivo experiments, to maintain the eye's "immune privilege", we employed mesoporous silica-based cell therapy to target and regulate macrophage IGF2BP2, providing a foundation for the evaluation and translation of therapies targeting this gene.

Conclusion: our study reveals that the molecular mechanism of dry AMD pathogenesis involves IGF2BP2-mediated NLRP3 inflammasome activation in macrophages, highlighting IGF2BP2 as a promising biomarker and therapeutic target for dry AMD treatment.

Background: Mitotic catastrophe is well-known as a major pathway of endogenous tumor death, but the prognostic significance of its heterogeneity regarding bladder cancer (BLCA) remains unclear.

Methods: Our study focused on digging deeper into the TCGA and GEO databases. Through differential expression analysis as well as Weighted Gene Co-expression Network Analysis (WGCNA), we identified dysregulated mitotic catastrophe-associated genes, followed by univariate cox regression as well as ten machine learning algorithms to construct robust prognostic models. Based on prognostic stratification, we revealed intergroup differences by enrichment analysis, immune infiltration assessment, and genomic variant analysis. Subsequently by multivariate cox regression as well as survshap(t) model we screened core prognostic gene and identified it by Mendelian randomization. Integration of qRT-PCR, immunohistochemistry, and single-cell analysis explored the core gene expression landscape. In addition, we explored the ceRNA axis containing upstream non-coding RNAs after detailed analysis of pathway activation, immunoregulation, and methylation functions of the core genes. Finally, we performed drug screening and molecular docking experiments based on the core gene in the DSigDB database.

Results: Our efforts culminated in the establishment of an accurate prognostic model containing 16 genes based on Coxboost as well as the Random Survival Forest (RSF) algorithm. Detailed analysis from multiple perspectives revealed a strong link between model scores and many key indicators: pathway activation, immune infiltration landscape, genomic variant landscape, and personalized treatment. Subsequently ANLN was identified as the core of the model, and prognostic analysis revealed that it portends a poor prognosis, further corroborated by Mendelian randomization analysis. Interestingly, ANLN expression was significantly upregulated in cancer cells and specifically clustered in epithelial cells and provided multiple pathways to mediate cell division. In addition, ANLN regulated immune infiltration patterns and was also inseparable from overall methylation levels. Further analysis revealed potential regulation of the MIR4435-2HG, hsa-miR-15a-5p, ANLN axis and highlighted a range of potential therapeutic agents including Phytoestrogens.

Conclusion: The model we developed was a powerful predictive tool for BLCA prognosis and revealed the impact of mitotic catastrophe heterogeneity on BLCA in multiple dimensions, which then guided clinical decision-making. Furthermore, we highlighted the potential of ANLN as a BLCA target.

Background: Celiac disease (CD) is an autoimmune disorder that primarily affects the gut of genetically predisposed individuals and is triggered by gliadin peptides (PT) produced by the digestion of gluten. Although inappropriate activation of the immune system is thought to be the main trigger of CD, the interaction between PT and intestinal epithelial cells (IECs) remains a key step. Recently, the possible involvement of ER stress in the pathogenesis of CD has been pointed out, although its role is still largely unclear. Therefore, discovering the molecular mechanism(s) activated in IECs exposed to PT represents a unique opportunity to better understand the disease and define new potential therapeutic targets.

Methods: In this study we used three different experimental set-ups: intestinal biopsies from CD patients and non-CD control subjects, an in vitro model, based on human CaCo-2 cells, and an ex vivo model, based on our recently described mouse gut-ex-vivo system (GEVS), with the latter two systems were studied after stimulation with gliadin peptides (PT). To understand the signaling pathways involved we monitor the expression of a number of proteins by qPCR, Western blotting, IF, ELISA or a combination of tests. Specifically, we have analyzed the level of CD, ER stress, tissue permeability, and inflammation markers.

Results: Indeed, our study demonstrated a prompt induction of the transcription factors ATF4, ATF6 and XBP1 in IECs upon PT exposure. Thus, the upregulation of TG2 and downregulation of CFTR were prevented by ER stress inhibition/buffering by a pharmacological chaperone, also leading to restored physiological expression of OCL, CLD-2 and CLD-15, while preventing the expression of IFNγ, IL-15 and IL-17 A.

Conclusion: Overall, our analysis has highlighted the key role of ER stress in the pathogenesis of CD and identified the chemical chaperones as a new potential valuable therapeutic treatment for CD patients.