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Rationale: Tumor cells remodel transcriptome to construct an ecosystem with stemness features, which maintains tumor growth and highly malignant characteristics. However, the core regulatory factors involved in this process still need to be further discovered. Methods: Single cell RNA-sequncing (scRNA-seq) and bulk RNA-sequencing profiles derived from fetal liver, normal liver, liver tumors, and their adjacent samples were collected to analyze the ecosystem of liver cancer. Mouse models were established to identify molecular functions of oncofetal-related oncogenes using hydrodynamic tail vein injection. Results: We found that liver cancer rebuilt oncofetal ecosystem to maintain malignant features. Interestingly, we identified a group of RNA-binding proteins (RBPs) that were highly overexpressed with oncofetal features. Among them, TRIM71 was specifically expressed in liver cancers and was associated with poor outcomes. TRIM71 drove the carcinogenesis of hepatocellular carcinoma (HCC), and knockdown of TRIM71 significantly abolished liver cancer cell proliferation. Mechanistically, TRIM71 formed a protein complex with IGF2BP1, bound to and stabilized the mRNA of CEBPA in an m6A-dependent manner, enhance the serine/glycine metabolic pathway, and ultimately promoted liver cancer progression. Furthermore, we identified that all-trans-retinoic acid (ATRA) combined with e1A binding protein p300 (EP300) inhibitor A-485 repressed TRIM71, attenuated glycine/serine metabolism, and inhibited liver cancer cell proliferation with high TRIM71 levels. Conclusions: We demonstrated the oncofetal status in liver cancer and highlighted the crucial role of TRIM71 and provided potential therapeutic strategies and liver cancer-specific biomarker for liver cancer patients.

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Astroblastoma is an extremely rare central nervous system tumor characterized by astroblastic pseudorosettes and vascular hyalinization. Despite these histologic hallmarks, its morphology can vary, occasionally resembling other central nervous system tumors such as ependymoma. A novel tumor entity, astroblastoma, meningioma 1 (MN1)-altered, has been identified, featuring MN1 gene rearrangements typically involving BEN-domain containing 2 (BEND2) as a fusion partner. Most astroblastomas arise in the cerebral hemisphere. Here, we report 4 cases of spinal cord astroblastoma in female patients, all showing Ewing sarcoma RNA-binding protein 1 fusion with BEND2, rather than MN1. These tumors displayed growth patterns akin to traditional intracranial astroblastomas, with three cases demonstrating high-grade histology, including elevated mitotic activity and necrosis. Interestingly, some cases exhibited positive staining for pan-cytokeratin and hormone receptors. DNA methylation profiling clustered three of the four cases with the reference "AB_EWSR," whereas one case exhibited an independent methylation signature near the reference methylation group "AB_EWSR" and "pleomorphic xanthoastrocytoma." Together with the existing literature, we summarized a total of eleven cases, which predominantly affected children and young adults with female predilection. Eight of 10 patients experienced recurrence, underscoring the aggressive nature of this disease. We suggest recognizing a new molecular subgroup of spinal astroblastoma and recommend testing newly diagnosed infratentorial astroblastomas for Ewing sarcoma RNA-binding protein 1-BEND2 fusion.

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Protein-protein interactions (PPIs) stabilization with molecular glues plays a crucial role in drug discovery, albeit with significant challenges. In this study, we propose a dual-site approach, targeting the PPI region and its dynamic surroundings. We conduct molecular dynamics simulations to identify critical sites on the PPI that stabilize the cyclin-dependent kinase 12 - DNA damage-binding protein 1 (CDK12-DDB1) complex, resulting in further cyclin K degradation. This exploration leads to the creation of LL-K12-18, a dual-site molecular glue, which enhances the glue properties to augment degradation kinetics and efficiency. Notably, LL-K12-18 demonstrates strong inhibition of gene transcription and anti-proliferative effects in tumor cells, showing significant potency improvements in MDA-MB-231 (88-fold) and MDA-MB-468 cells (307-fold) when compared to its precursor compound SR-4835. These findings underscore the potential of dual-site approaches in disrupting CDK12 function and offer a structural insight-based framework for the design of cyclin K molecular glues.

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It has been believed that immunosenescence plays a crucial role in tumorigenesis and cancer therapy. Nevertheless, there is still a lack of understanding regarding its role in determining clinical outcomes and therapy selection for gastric cancer patients, due to the lack of a feasible immunosenescence signature. Therefore, this research aims to develop a gene signature based on immunosenescence, which is used for stratification of gastric cancer. By integrative analysis of bulk transcriptome and single-cell data, we uncovered immunosenescence features in gastric cancer. Random forest algorithm was used to select hub genes and multivariate Cox algorithm was applied to construct a scoring system to evaluate the prognosis and the response to immunotherapy and chemotherapy. The Cancer Genome Atlas of Stomach Adenocarcinoma (TCGA-STAD) cohort was implemented as the training cohort and two independent cohorts from the Gene Expression Omnibus (GEO) database were used for validation. The model was further tested by our Fudan cohort. In this study, immunosenescence was identified as a hallmark of gastric cancer that is linked with transcriptomic features, genomic variations, and distinctive tumor microenvironment (TME). Four immunosenescence genes, including APOD, ADIPOR2, BRAF, and C3, were screened out to construct a gene signature for risk stratification. Higher risk scores indicated strong predictive power for poorer overall survival. Notably, the risk score signature could reliably predict response to chemotherapy and immunotherapy, with patients with high scores benefiting from immunotherapy and patients with low scores responding to chemotherapy. We report immunosenescence as a hitherto unheralded hallmark of gastric cancer that affects prognosis and treatment efficiency.

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Neoantigen-based therapy is a promising approach that selectively activates the immune system of the host to recognize and eradicate cancer cells. Preliminary clinical trials have validated the feasibility, safety, and immunogenicity of personalized neoantigen-directed vaccines, enhancing their effectiveness and broad applicability in immunotherapy. While many ongoing oncological trials concentrate on neoantigens derived from mutations, these targets do not consistently provoke an immune response in all patients harboring the mutations. Additionally, tumors like ovarian cancer, which have a low tumor mutational burden (TMB), may be less amenable to mutation-based neoantigen therapies. Recent advancements in next-generation sequencing and bioinformatics have uncovered a rich source of neoantigens from non-canonical RNAs associated with transposable elements (TEs). Considering the substantial presence of TEs in the human genome and the proven immunogenicity of TE-derived neoantigens in various tumor types, this review investigates the latest findings on TE-derived neoantigens, examining their clinical implications, challenges, and unique advantages in enhancing tumor immunotherapy.

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To investigate the changes in the intestinal flora in the Chinese elderly with cardiovascular disease (CVD) and its correlation with the metabolism of trimethylamine (TMA), the intestinal flora composition of elderly individuals with CVD and healthy elderly individuals was analyzed using 16S rRNA sequencing, the TMA levels in the feces of elderly were detected using headspace-gas chromatography (HS-GC), and four kinds of characterized TMA-producing intestinal bacteria in the elderly were quantified using real-time fluorescence quantitative polymerase chain reaction (qPCR). The results showed that Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, and Verrucomicrobia are the dominant microorganisms of the intestinal flora in the Chinese elderly. And there were significant differences in the intestinal bacteria composition between healthy elderly individuals and those with CVD, accompanied by a notable difference in the TMA content. The richness and diversity of the intestinal flora in the elderly with CVD were higher than those in the healthy elderly. Correlation analysis indicated that certain significantly different intestinal flora were associated with the TMA levels. Our findings showed a significant difference in TMA-producing intestinal flora between healthy elderly individuals and those with CVD. The TMA levels were found to be positively and significantly correlated with Klebsiella pneumoniae, suggesting that this bacterium is closely linked to the production of TMA in the elderly gut. This may have implications for the development and progression of CVD in the elderly population.

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Introduction: Gut microbiota are closely related to the nutrition, immunity, and metabolism of the host and play important roles in maintaining the normal physiological activities of animals. Cranes are important protected avian species in China, and they are sensitive to changes in the ecological environment and are thus good environmental indicators. There have been no reports examining gut fungi or the correlation between bacteria and fungi in wild Demoiselle cranes (Grus virgo) and Common cranes (Grus grus). Related research can provide a foundation for the protection of rare wild animals. Methods: 16S rRNA and ITS high-throughput sequencing techniques were used to analyze the gut bacterial and fungal diversity of Common and Demoiselle cranes migrating to the Yellow River wetland in Inner Mongolia. Results: The results revealed that for gut bacteria α diversity, Chao1 index in Demoiselle cranes was remarkably higher than that in Common cranes (411.07 ± 79.54 vs. 294.92 ± 22.38), while other index had no remarkably differences. There was no remarkable difference in fungal diversity. There were marked differences in the gut microbial composition between the two crane species. At the phylum level, the highest abundance of bacteria in the Common crane and Demoiselle crane samples was Firmicutes, accounting for 87.84% and 74.29%, respectively. The highest abundance of fungi in the guts of the Common and Demoiselle cranes was Ascomycota, accounting for 69.42% and 57.63%, respectively. At the genus level, the most abundant bacterial genus in the Common crane sample was Turicibacter (38.60%), and the most abundant bacterial genus in the Demoiselle crane sample was Catelicoccus (39.18%). The most abundant fungi in the Common crane sample was Penicillium (6.97%), and the most abundant fungi in the Demoiselle crane sample was Saccharomyces (8.59%). Correlation analysis indicated that there was a significant correlation between gut bacteria and fungi. Discussion: This study provided a research basis for the protection of cranes. Indeed, a better understanding of the gut microbiota is very important for the conservation and management of wild birds, as it not only helps us to understand their life history and related mechanisms, but also can hinder the spread of pathogenic microorganisms.

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BACKGROUND: The tumor microenvironment (TME) significantly influences prognosis and drug resistance in various tumors, yet its heterogeneity and the mechanisms affecting therapeutic response remain unclear in gastric cancer (GC). METHODS: The heterogenous TME were explored with single-cell RNA-sequencing (scRNA-seq) data of 50 primary GC samples. We then identified four GC TME subtypes with nonnegative matrix factorization (NMF) and constructed a pearson nearest-centroid classifier based on subtype-specific upregulated genes. Genomic features and clinical significance of four subtypes were comprehensively evaluated. We reclustered fibroblasts to identify cancer-associated fibroblast (CAF) subtype associated with poor clinical outcomes. RT-qPCR and double immunofluorescence staining were applied to validate the findings. Cellchat analysis elucidated potential molecular mechanisms of the CAF subtype in GC disease progression and chemotherapy resistance. FINDINGS: The GC TME exhibited high heterogeneity, influencing chemo-sensitivity. Four TME-based subtypes predicting response to immunotherapy and chemotherapy were identified and validated in 1406 GC patients. Among which, ISG1 subtype displayed higher fibroblasts infiltration and heightened oncogenic pathways, and inferior response to chemotherapy with unfavorable prognosis. Microsatellite instability-high (MSI-H) GCs within four TME subtypes showed immunological heterogeneity. We then reported an IGF1-overexpressing CAF was associated with chemo-resistance and GC recurrence. Cell communication analysis revealed IGF1+ CAF may induce drug-resistant phenotypes in tumor cells through IGF1-α6ß4 integrin ligand-receptor binding and activation of EMT biological process. INTERPRETATION: We identified four TME-based subtypes with different clinical outcomes and IGF1+ CAFs contributing to poor clinical outcomes in GC, which might provide guidance for individualized treatment and facilitate the development of novel therapeutic targets.

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BACKGROUND: Cyclin-dependent Kinase Subunit 2 is a protein closely related to the regulation of the cell cycle. In recent years, there has been an increasing number of research articles on this topic. However, there is a lack of comprehensive synthesis and evaluation in the field of CKS2 research. This study aims to summarize and visualize the literature distribution, research hotspots, and development trends of CKS2 based on bibliometric methods. METHODS: Publications from 1999 to 2022 were extracted from the Web of Science. Citespace was used to analyze the relevant information of each article. RESULTS: A total of 138 publications focused on CKS2 showed a positive growth trend from 1999 to 2022 and were published by 27 countries. The most prolific countries are China and the USA. The most prolific institution is Scripps Research Institute. The most prolific author is Steven I. Reed from Scripps Research Institute. The most cited article is published by Todd R Golub. The most cited author is Hanna-Stina Martinsson-Ahlzen. The journal with the most published articles is International Journal of Oncology. The high frequency keywords suggest that expression and function of CKS2 in cancer are dominated topics. The clusters and burst words suggest that expression and function of CKS2 still active in the future. CONCLUSION SUBSECTIONS: The results of this bibliometric analysis provide information on the state and trends in CKS2 from 1999 to 2022. It is helpful for scholars to pinpoint hot issues and discover new areas of study.

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Knee osteoarthritis (KOA) is the most common joint disease worldwide and, with the progression of an aging population, is one of the most important causes of disability worldwide. Its main symptoms include articular cartilage damage, periarticular pain, swelling, and stiffness. Intra-articular (IA) injections offer many advantages over systemic administration and surgical treatment, including direct action on the target joint to improve local bioavailability, reduce systemic toxicity, and lower costs. This study analyzed KOA intra-articular injection treatment and its hot literature and research horizons using bibliometric methodologies and graphical tools to aid future research. We performed a bibliometric analysis of 2360 publications in the Web of Science core collection using CiteSpace software. The United States (28.26% of publications) and China (18%) had the biggest publications. Rush University was the most active institution, but Boston University had the greatest citation/publication rate (65.77), suggesting a high literature standard. The majority of publications were in Osteoarthritis and cartilage. Bannuru RR was the most referenced author, while Filardo, Giuseppe was the most productive author. Studies in platelet-rich plasma (PRP), mesenchymal stem cells (MSCs), and microsphere formulation are likely to be future research hotspots. The current scientometric study provides an overview of KOA intra-articular injection therapy studies from 2012 to 2022. This study outlines the current research hotspots and potential future research hotspots in the field of intra-articular injection treatment for KOA and may serve as a resource for researchers interested in this topic.

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BACKGROUND: Cervical spondylotic radiculopathy is a common form of cervical spondylosis caused by degeneration of the cervical spine. Currently, non-surgical treatment is the preferred treatment method, and Chinese medicine is widely used. OBJECTIVE: To investigate the effect of radiculopathy spondylosis by tuina spinning and lifting technique. EXPERIMENTAL DESIGN: We conducted a 12-week, open-label, analyst-blinded, randomized clinical trial ( 2 weeks of intervention plus 10 weeks of observational follow-up ). A total of 25 patients with radiculopathy were collected, and data was analyzed during the treatment and recovery period. INTERVENTIONS: Neck pain granules group: a package of oral neck pain granules after meals, three times a day, treatment for 2 weeks; neck pain granules combined with massage lifting technique, treatment group: use, massage lifting technique treatment, once every two days, normal take neck pain granules, treatment for 2 weeks. All cases were followed up for 2.5 months. Main monitoring indicators: Visual Analog Scale, Neck Dysfunction Index score, and Tanaka jiu ( Tanaka Yasuhisa Cervical Spondylosis Symptom Scale ) were recorded on time, and statistical statistics were made. RESULT: The scores of VAS and NDI were significantly more effective in the neck pain granules combined with the tuina group than in the neck pain granules group, while the Tanaka Yasuhisa Cervical Spondylosis Symptom Scale was not significantly different between the two groups. CONCLUSION: The treatment effect of neck pain granules combined with tuina was significantly better than that of traditional Chinese medicine alone.

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Detecting toxic gases, such as CH4, CO, and H2S, in everyday life holds great significance. This research article focuses on investigating the adsorption characteristics of CH4, CO, and H2S on MoTe2 and MoTe2 doped with Au and Ru using the density functional theory. The study examines various aspects, including adsorption energy, charge transfer, density of states, and charge density difference of the adsorption configuration. The findings demonstrate that the adsorption properties of Ru-doped MoTe2 exhibit a significant enhancement for all three gases, with CO displaying the highest adsorption performance. Through comparative analysis, it is evident that the adsorption affinity between MoTe2-Ru and the three gases is robust, thus indicating improved gas detection capabilities.

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Introduction: The collection and process of human brain activity signals play an essential role in developing brain-computer interface (BCI) systems. A portable electroencephalogram (EEG) device has become an important tool for monitoring brain activity and diagnosing mental diseases. However, the miniaturization, portability, and scalability of EEG recorder are the current bottleneck in the research and application of BCI. Methods: For scalp EEG and other applications, the current study designs a 32-channel EEG recorder with a sampling rate up to 30 kHz and 16-bit accuracy, which can meet both the demands of scalp and intracranial EEG signal recording. A fully integrated electrophysiology microchip RHS2116 controlled by FPGA is employed to build the EEG recorder, and the design meets the requirements of high sampling rate, high transmission rate and channel extensive. Results: The experimental results show that the developed EEG recorder provides a maximum 30 kHz sampling rate and 58 Mbps wireless transmission rate. The electrophysiological experiments were performed on scalp and intracranial EEG collection. An inflatable helmet with adjustable contact impedance was designed, and the pressurization can improve the SNR by approximately 4 times, the average accuracy of steady-state visual evoked potential (SSVEP) was 93.12%. Animal experiments were also performed on rats, and spike activity was captured successfully. Conclusion: The designed multichannel wireless EEG collection system is simple and comfort, the helmet-EEG recorder can capture the bioelectric signals without noticeable interference, and it has high measurement performance and great potential for practical application in BCI systems.

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In recent years, substantial advancements have been made in the development of enzyme-free glucose sensors utilizing pristine metal-organic frameworks (MOFs) and their combinations. This paper provides a comprehensive exploration of various MOF-based glucose sensors, encompassing monometallic MOF sensors as well as multi-metal MOF combinations. These approaches demonstrate improved glucose detection capabilities, facilitated by the augmented surface area and availability of active sites within the MOF structures. Furthermore, the paper delves into the application of MOF complexes and derivatives in enzyme-free glucose sensing. Derivatives incorporating carbon or metal components, such as carbon cloth synthesis, rGO-MOF composites, and core-shell structures incorporating noble metals, exhibit enhanced electrochemical performance. Additionally, the integration of MOFs with foams or biomolecules, such as porphyrins, enhances the electrocatalytic properties for glucose detection. Finally, this paper concludes with an outlook on the future development prospects of enzyme-free glucose MOF sensors.

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Metal oxide gas sensors have long faced the challenge of low response and poor selectivity, especially at room temperature (RT). Herein, a synergistic effect of electron scattering and space charge transfer is proposed to comprehensively improve gas sensing performance of n-type metal oxides toward oxidizing NO2 (electron acceptor) at RT. To this end, the porous SnO2 nanoparticles (NPs) assembled from grains of about 4 nm with rich oxygen vacancies are developed through an acetylacetone-assisted solvent evaporation approach combined with precise N2 and air calcinations. The results show that the as-fabricated porous SnO2 NPs sensor exhibits an unprecedented NO2 -sensing performance, including outstanding response (Rg /Ra  = 772.33 @ 5 ppm), fast recovery (<2 s), an extremely low detection limit (10 ppb), and exceptional selectivity (response ratio >30) at RT. Theoretical calculation and experimental tests confirm that the excellent NO2 sensing performance is mainly attributed to the unique synergistic effect of electron scattering and space charge transfer. This work proposes a useful strategy for developing high-performance RT NO2 sensors using metal oxides, and provides an in-depth understanding for the basic characteristics of the synergistic effect on gas sensing, paving the way for efficient and low power consumption gas detection at RT.

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The gut microbiota promotes host health by maintaining homeostasis and enhancing digestive efficiency. The gut microflora in wild birds affects host physiological characteristics, nutritional status, and stress response. The relict gull (Larus Relictus, a Chinese national first-class protected species) and the black-necked grebe (Podiceps Nigricollis, a secondary protected species) bred in the Ordos Relic Gull National Nature Reserve share similar feeding habits and living environments but are distantly related genetically. To explore the composition and differences in the gut microbiota of these two key protected avian species in Erdos Relic Gull National Nature Reserve and provide a basis for their protection, 16S rRNA gene high-throughput sequencing was performed and the gut microbial diversity and composition of the relict gull (L. Relictus) and black-necked grebe (P. Nigricollis) was characterized. In total, 445 OTUs (operational taxonomic units) were identified and classified into 15 phyla, 22 classes, 64 orders, 126 families, and 249 genera. Alpha diversity analysis indicates that the gut microbial richness of the relict gull is significantly lower than that of the black-necked grebe. Gut microbe composition differs significantly between the two species. The most abundant bacterial phyla in these samples were Proteobacteria, Firmicutes, Fusobacteria, and Bacteroidetes. The prominent phylum in the relict gull was Proteobacteria, whereas the prominent phylum in the black-necked grebe was Firmicutes. The average relative abundance of the 17 genera identified was greater than 1%. The dominant genus in the relict gull was Escherichia-Shigella, whereas Halomonas was dominant in the black-necked grebe. Microbial functional analyses indicate that environmental factors exert a greater impact on relict gulls than on black-necked grebes. Compared with the relict gull, the black-necked grebe was able to use food more efficiently to accumulate its nutrient requirements, and the gut of the relict gull harbored more pathogenic bacteria, which may be one reason for the decline in the relict gull population, rendering it an endangered species. This analysis of the gut microbial composition of these two wild avian species in the same breeding grounds is of great significance, offers important guidance for the protection of these two birds, especially relict gulls, and provides a basis for understanding the propagation of related diseases.

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Chronic liver diseases usually developed through stepwise pathological transitions under the persistent risk factors. The molecular changes during liver transitions are pivotal to improve liver diagnostics and therapeutics yet still remain elusive. Cumulative large-scale liver transcriptomic studies have been revealing molecular landscape of various liver conditions at bulk and single-cell resolution, however, neither single experiment nor databases enabled thorough investigations of transcriptomic dynamics along the progression of liver diseases. Here we establish GepLiver, a longitudinal and multidimensional liver expression atlas integrating expression profiles of 2469 human bulk tissues, 492 mouse samples, 409,775 single cells from 347 human samples and 27 liver cell lines spanning 16 liver phenotypes with uniformed processing and annotating methods. Using GepLiver, we have demonstrated dynamic changes of gene expression, cell abundance and crosstalk harboring meaningful biological associations. GepLiver can be applied to explore the evolving expression patterns and transcriptomic features for genes and cell types respectively among liver phenotypes, assisting the investigation of liver transcriptomic dynamics and informing biomarkers and targets for liver diseases.

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Recent reports indicate that immune cells in solid cancers have significant predictive and therapeutic value. IgG4 is a subclass of IgG and we recently found that it exerted an inhibitory effect in tumor immunity. We aimed to assess the significance of IgG4 and T cell subtypes in tumor prognosis. We investigated the density, distribution and relationship of five immune markers CD4, CD8, Foxp3, IL-10 and IgG4 with multiple immunostaining method in 118 esophageal squamous cell carcinoma (ESCC) together with clinical data. The relationship among different immune cell types and with clinical data were analyzed with Kaplan-Meier survival analysis and Cox proportional hazards model to identify independent risk factors among immune and clinicopathological parameters. Five-year survival rate of these patients treated with surgery reached 61%. Higher number of CD4+ plus CD8+ T cells predicted better prognosis (p=0.01) in tertiary lymphoid structure (TLS) and could add to the value of TNM staging. Density of the newly identified immune inhibitor IgG4+ B lymphocytes was found positively correlated to that of CD4+ cells (p=0.02) and IL-10+ cells (p=0.0005), but number of infiltrating IgG4+ cells by itself was not an independent factor for prognosis. However, increased serum concentration of IgG4 indicated a poor prognosis of ESCC (p=0.03). 5-year survival rate of esophageal cancer after surgery has been significantly improved. Increased T cells in TLS predicted better survival, suggesting that T cells in TLS may actively participate in anti-tumor immunity. Serum IgG4 could be a useful predictor of prognosis.

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Objective: Neutrophil gelatinase-associated lipoprotein (NGAL), a protein encoded by the lipocalcin-2 (LCN2) gene, has been reported to be involved in multiple processes of innate immunity, but its relationship with spinal cord injury (SCI) remains unclear. This study set out to determine whether NGAL played a role in the development of cognitive impairment following SCI. Methods: At the Neck-Shoulder and Lumbocrural Pain Hospital, a total of 100 SCI patients and 72 controls were enrolled in the study through recruitment. Through questionnaires, baseline data on the participants' age, gender, education level, lifestyle choices (drinking and smoking) and underlying illnesses (hypertension, diabetes, coronary heart disease, and hyperlipidemia) were gathered. The individuals' cognitive performance was evaluated using the Montreal Cognitive Scale (MoCA), and their serum NGAL levels were discovered using ELISA. Results: The investigation included 72 controls and 100 SCI patients. The baseline data did not differ substantially between the two groups, however the SCI group's serum NGAL level was higher than the control group's (p < 0.05), and this elevated level was adversely connected with the MoCA score (p < 0.05). According to the results of the ROC analysis, NGAL had a sensitivity of 58.24% and a specificity of 86.72% for predicting cognitive impairment following SCI. Conclusions: The changes in serum NGAL level could serve as a biomarker for cognitive impairment in SCI patients, and this holds true even after taking in account several confounding variables.

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Structural flexibility is an intrinsic characteristics of a protein upon interacting with other molecules, which mainly comes from the movement of a residue's side chain, backbone and even an entire domain. Considering this property can be very helpful in protein binding analysis, such as epitope identification during antibody-antigen interaction. Unfortunately, to our knowledge, no approach is available at studying the dynamicity of protein binding from the computational perspective. We are pioneering a new perspective of exploring protein binding sites with considering the structural flexibility, particularly from the epitopes identification angle in antibody-antigen binding. To this end, we first obtained protein antigen structures with epitopes available, and built residue-level graphs of antigens. These graphs were highly densified subsequently by incorporating the structural flexibility. Later, the edge enriched graphs were clustered into overlapping subgraphs and were classified as epitope or non-epitope by a graph convolutional network. Experiments on epitope identification shown that the proposed flexibility-aware model markedly outperformed existing approaches by lifting the F1-score to 0.656, making a remarkable increment of 16.3% compared to the state-of-the-art. A quick study on generic protein binding site prediction also made a noteworthy improvement with increasing the F1-score by 8%. The superior performance obtained from both the specific and generic protein interaction analysis demonstrate that incorporating flexibility in computational models is helpful to strength the capability of identifying epitopes as well as general protein binding sites. This seminal study can be inspiring and promising to the wide range of protein interaction analysis.

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