Biology Direct最新文献

Background: Patients diagnosed with gallbladder carcinoma (GBC) accompanied by hepatic metastasis exhibit unfavorable prognoses generally. Mitochondrial dysfunction promotes cellular transformation and cancer cell survival implicating its importance in cancer development. Previous studies have indicated that dynamin 1 like (DNM1L) is a key mediator of mitochondrial fission. However, whether DNM1L regulates mitochondrial homeostasis in GBC remains unknown.

Methods: The morphological changes of mitochondria were investigated by transmission electron microscopy and mitoTracker red staining. Co-immunoprecipitation assay was performed to detect the interaction of ubiquitin-specific protease-3 (USP3) and DNM1L. The cell-derived xenograft and liver metastasis tumor models were established to validate the function of DNM1L in vivo. The metabolomics data from transcriptomics/metabolomics were analyzed to identify the differentially expressed genes/metabolites of DNM1L in GBC.

Results: DNM1L exhibited a marked upregulation in clinical GBC tissues compared to the adjacent tissues, and it promoted proliferation, invasiveness, and migration capability of GBC cells by inducing mitochondrial dysfunction. Mice subcutaneously injected with DNM1L overexpression cells exhibited elevated intrahepatic metastatic nodules within their livers. USP3, a deubiquitinating enzyme, was demonstrated to directly interact with DNM1L and it specifically cleaved the K48-linked polyubiquitin chains to deubiquitinate and stabilize DNM1L. By integrating two omics, we found several altered pathways and speculated that DNM1L disturbed DNA synthesis and glycine, serine, threonine, and pyrimidine metabolism pathways.

Conclusion: Our findings suggest that DNM1L is a promising clinical target for GBC treatment and that focusing on DNM1L may provide new insights into GBC strategy.

Endothelial senescence (ES) contributes to aging-related disorders and triggers a senescence-associated secretory-pattern (SASP), releasing Extracellular Vesicles (EVs), potentially impacting atherosclerosis. We used EVs from young (8 weeks) and aged (24 months) ApoE-knockout mice to detect ES in human aortic (HAEC) and coronary (CAEC) endothelial cells. Age-related atherosclerosis was confirmed by increased atheroma plaque formation in aged compared to young ApoE-knockout mice fed a high-fat diet, and the contribution of EVs from aged ApoE-knockout mice on ES was evidenced by a replicative senescence assay in cultured HAEC and CAEC, starting with the promotion of ES. A proteomic analysis depicted the recently PCSK9-associated CAP1 protein as a cargo component in EVs from aged animals and highly expressed in mouse and human endarterectomy plaques. Gene silencing of CAP1 inhibited HAEC and CAEC ES while overexpressing CAP1 in these cells restored the senescent-phenotype. The in vivo contribution of CAP1 was assessed by injecting CAP1-containing EVs isolated from aged ApoE-knockout mice into wild-type (WT) mice fed either a regular or high-fat diet. Compared to the EVs from young mice, the CAP1-containing EVs led to a pronounced ES along with the formation of intraluminal atheroma plaques. Similarly, young ApoE-knockout mice developed thickened and calcified atheroma plaques, along with increased ß-Gal-positive aortic staining when injected with EVs isolated from aged ApoE-knockout mice, like the atheroma plaques observed in aged ApoE-knockout animals. In conclusion, early molecular targets of ES may contribute to better management of atherosclerosis, in which here we unveiled CAP1 as a new molecular target.

Background: Neutrophils play a key role in the tumor microenvironment (TME); however, their functions in glioblastoma (GBM) are overlooked and insufficiently studied. A detailed analysis of GBM-associated neutrophil (GBMAN) subpopulations may offer new insights and opportunities for GBM immunotherapy.

Methods: We analyzed single-cell RNA sequencing (scRNA-seq) data from 127 isocitrate dehydrogenase (IDH) wild-type GBM samples to characterize the GBMAN subgroups, emphasizing developmental trajectories, cellular communication, and transcriptional networks. We implemented 117 machine learning combinations to develop a novel risk model and compared its performance to existing glioma models. Furthermore, we assessed the biological and molecular features of the GBMAN subgroups in patients.

Results: From integrated large-scale scRNA-seq data (498,747 cells), we identified 5,032 neutrophils and classified them into four distinct subtypes. VEGFA⁺GBMAN exhibited reduced inflammatory response characteristics and a tendency to interact with stromal cells. Furthermore, these subpopulations exhibited significant differences in transcriptional regulation. We also developed a risk model termed the "VEGFA⁺neutrophil-related signature" (VNRS) using machine learning methods. The VNRS model showed higher accuracy than previously published risk models and was an independent prognostic factor. Additionally, we observed significant differences in immunotherapy responses, TME interactions, and chemotherapy efficacy between high-risk and low-risk VNRS score groups.

Conclusion: Our study highlights the critical role of neutrophils in the TME of GBM, allowing for a better understanding of the composition and characteristics of GBMAN. The developed VNRS model serves as an effective tool for evaluating the risk and guiding clinical treatment strategies for GBM.

Clinical trial number: Not applicable.

Protein folding remains a fundamental challenge in molecular biology, particularly in understanding how polypeptide chains transition from denatured states to their functional conformations. Here we analyze the folding mechanisms of the engineered metamorphic proteins B4 and Sb3, which share highly similar sequences but adopt distinct topologies. Kinetic analyses revealed that B4 follows a two-state folding mechanism, whereas Sb3 involves the formation of an intermediate species. We further explore the role of topology in folding commitment using the metamorphic mutant Sb4, which can populate both conformations. By analyzing folding and unfolding behaviors under varying experimental conditions, our findings suggest that topology dictates folding mechanisms at an early stage. These results demonstrate that folding landscapes are primarily shaped by final native structures rather than sequence composition.

Background: Clear cell renal cell carcinoma (ccRCC) is the most common type of RCC. Even though the targeted drugs for the treatment of ccRCC have a certain therapeutic effect, due to the problem of drug resistance, the search for new targets for targeted therapy of ccRCC remains urgent. GAMT is an enzyme involved in creatine metabolism. However, the precise biological roles and molecular mechanisms of GAMT in ccRCC are not fully understood.

Results: Here, we found that GAMT was upregulated in ccRCC cells and tissues and associated with poor prognosis. Further, GAMT has pro-oncogenic abilities in promoting ccRCC development and progression. Intriguingly, GAMT exerted biological functions independent of its role in catalyzing creatine synthesis. Mechanistically, GAMT overexpression contributes to the development and progression of ccRCC by inhibiting tumor suppressor p53. Finally, we identified fisetin as a novel GAMT inhibitor and validated its role in suppressing ccRCC progression and sensitizing ccRCC cells to targeted drug axitinib via in vivo and in vitro assays.

Conclusions: This study reveals that GAMT has pro-oncogenic abilities in promoting ccRCC development and progression. GAMT exerted its non-enzymatic functions possibly by regulating the expression of p53. Fisetin, the novel GAMT inhibitor identified herein, may serve as a new antitumor drug for ccRCC treatment.

Background: Laryngotracheal stenosis (LTS), a pathological narrowing of the upper airway caused by excessive extracellular matrix (ECM) deposition, often leads to dyspnea and even respiratory failure. However, systematic studies addressing the specific subpopulations and their contribution to LTS development still remain underexplored.

Results: We collected laryngotracheal tissue at multiple time points of LTS rat model, established by injuring their laryngotracheal lining, and performed dynamic single-cell RNA sequencing (scRNA-seq) to elucidate the transcriptomic atlas of LTS development. The results showed, from the inflammatory state to the repair/fibrotic state, infiltration of immune cells such as monocyte macrophages decreased and fibroblast increased. We delineated the markers and functional status of different fibroblasts subsets and identified that fibrotic fibroblasts may originate from multiple fibroblast subpopulations, including a new subpopulation characterized by the expression of chondrogenic markers such as Ucma and Col2a1, we designated this subcluster as chondrocyte injury-related fibroblasts (CIRF). Furthermore, we categorized monocytes/macrophages into several subtypes and identified that SPP1 high macrophages represented the largest macrophage subpopulation in LTS, providing evidence to clarify the importance of SPP1 macrophages in fibrosis disease. Our findings also revealed the interactions among these cells to explore the molecular mechanism associated with LTS pathogenesis.

Conclusions: Our study, for the first time, conducted dynamic scRNA-seq on LTS, revealing the cellular heterogeneity and providing a valuable resource for exploring the intricate molecular landscape of LTS. We propose CIRF may represent a tissue-specific fibroblast lineage in LTS and potentially originate from cells in the perichondrium of the trachea and transform into fibrotic fibroblasts. Integration of our study with those of other respiratory fibrotic diseases will allow for a comprehensive understanding of airway remodeling in respiratory diseases and exploring potential new therapeutic targets for their treatment.

Background: Osteoarthritis (OA) is a degenerative joint disease marked by the breakdown of cartilage, where apoptosis plays a key role. Although apoptosis-related genes in OA have been studied, a detailed analysis of PANoptosis-related genes and the search for therapeutic drugs remains limited.

Methods: We performed a bioinformatics analysis combined with single-cell RNA sequencing to examine PANoptosis-related gene expression in OA cartilage. Key PANoptosis genes and critical cell populations involved in OA progression were identified. Drug prediction led to the selection of Andrographolide (AG), whose effects were validated through molecular docking, Western blotting, and qRT-PCR in chondrocyte models.

Results: Several PANoptosis-related genes, including CASP8, TLR3, CASP1, and IL18, were significantly differentially expressed in OA. These genes are linked to processes such as apoptosis, pyroptosis, and the inflammasome complex. Pathway analysis revealed necroptosis, Toll-like receptor, and apoptosis signaling pathways as important in OA pathology. Single-cell analysis identified HomC, EC, and preHTC as key cell populations. AG was predicted to regulate PANoptosis genes, which was confirmed experimentally, demonstrating AG's potential to modulate key genes involved in cartilage degeneration.

Conclusion: This study highlights PANoptosis-related genes in OA and identifies Andrographolide as a promising therapeutic drug, offering new insights into OA treatment strategies.

Background: Osteoporosis and kidney stones share several common pathophysiological risk factors, and their association is well-established. However, previous studies have primarily focused on environmental mediators, such as diet, and the precise mechanism linking these two conditions remains unclear.

Methods: The relationship between osteoporosis and kidney stones was analyzed using weighted multivariate logistic regression, employing data from five cycles of the National Health and Nutrition Examination Survey (NHANES) from 2007-2010, 2013-2014, and 2017-2020. Gene expression data from the Gene Expression Omnibus (GEO) microarray database were integrated with machine learning techniques to identify key genes involved in both osteoporosis and kidney stones. Common targets were then identified through the Comparative Toxicogenomics Database (CTD) and GeneCards. GMFA enrichment analysis was performed to identify shared biological pathways. Additionally, drug prediction and molecular docking were employed to further investigate the pharmacological relevance of these targets.

Results: Analysis of the NHANES database confirmed a strong association between osteoporosis and kidney stones. Weighted multivariate logistic regression showed that osteoporosis (OR: 1.41; 95% CI 1.11-1.79; P < 0.001) and bone loss (OR: 1.24; 95% CI 1.08-1.43; P < 0.001) were significantly correlated with an increased risk of kidney stones. Three hub genes-WNT1, AKT1, and TNF-were identified through various analytical methods. GMFA revealed that the mTOR signaling pathway is a key shared pathway. Molecular docking studies further confirmed the pharmacological relevance of these targets, demonstrating strong binding affinity between drugs and the proteins involved, consistent with previous findings.

Conclusion: Bone loss is associated with an increased risk of kidney stones. Targeting the mTOR signaling pathway may offer a potential therapeutic approach for treating both osteoporosis and kidney stones.

Background: Coeliac disease is an autoimmune disease that is primarily associated with chronic inflammation of the gut, but can also affect organs outside the gut, from the liver to the skin and CNS. The disease is triggered in predisposed individuals by a peptide mixture (PT) derived from the digestion of gliadin, a component of wheat, which is ingested with food. Although the induction of endoplasmic reticulum stress in intestinal epithelial cells (IECs) upon exposure to PT is known, the underlying molecular mechanisms remain unclear. Identifying the key players in this signaling pathway could therefore help to develop a new effective therapeutic strategy for the treatment of CD patients.

Methods: Two CD models were used to identify the molecular mechanism linking extracellular PT and endoplasmic reticulum (ER) stress in the IECs of predisposed individuals exposed to gliadin. These models were an in vitro model based on CaCo-2 cells and an ex vivo model based on our previously described gut ex vivo system (GEVS), both exposed to PT.

Results: Our results clearly show that the interaction of gliadin peptides with the transmembrane CXCR3 receptor on IECs leads to a rapid induction of PLC activity that generates IP3 molecules. This second messenger binds to the IP3R located in ER membranes, resulting in calcium efflux from the organelle.

Conclusion: The PT-dependent ER stress observed in the IECs of CD patients results from the excessive release of calcium from the ER. Importantly, inhibition of this signaling pathway abrogates ER stress, which in turn attenuates downstream signs of CD, such as TG2 expression and gut permeability dysregulation, as well as inhibits inflammation.

Background: Acute kidney injury (AKI) remains a critical condition with limited therapeutic options, predominantly managed by renal replacement therapy. The challenge of developing targeted treatments persists.

Methods: We integrated genetic data related to druggable proteins and gene expression with AKI genome-wide association study (GWAS) findings. Based on multi-omics Mendelian randomization (MR), we identified the potential causal influence of 5,883 unique proteins and genes on AKI. We also performed using reverse MR and external cohort-based analysis to verify the robustness of this causal relationship. Expression patterns of these targets were examined using bulk transcriptome and single-cell transcriptome data. In addition, drug repurposing analyses were conducted to explore the potential of existing medications. We also constructed a molecular interaction network to explore the interplay between identified targets and known drugs.

Results: Genetically predicted levels of seven proteins and twelve genes were associated with an increased risk of AKI. Of these, six targets (NCF1, TNFRSF1B, APEH, ACADSB, ADD1, and FAM3B) were prioritized based on robust evidence and validated in independent cohorts. Reverse MR showed a one-way causal relationship of targets. These targets are predominantly expressed in proximal tubular cells, endothelial cells, collecting duct-principal cells, and immune cells within both AKI-affected and normal tissues. Several promising drug repurposing opportunities were identified, such as telmisartan-NCF1, calcitriol-ACADSB, and ethinyl estradiol-ACADSB. The molecular interaction mapping and pathway integration analysis provided further insights, suggesting potential strategies for combinatorial therapies.

Conclusions: This extensive investigation identified several promising therapeutic targets for AKI and highlighted opportunities for drug repurposing. These findings offer valuable insights that could shape future research and the development of targeted treatments.