Identification of PI3K-AKT Pathway-Related Genes and Construction of Prognostic Prediction Model for ccRCC.

BACKGROUND: Clear cell renal cell carcinoma (ccRCC), the predominate histological type of renal cell carcinoma (RCC), has been extensively studied, with poor prognosis as the stage increases. Research findings consistently indicated that the PI3K-Akt pathway is commonly dysregulated across various cancer types, including ccRCC. Targeting the PI3K-Akt pathway held promise as a potential therapeutic approach for treating ccRCC. Development and validation of PI3K-Akt pathway-related genes related biomarkers can enhance healthcare management of patients with ccRCC. PURPOSE: This study aimed to identify the key genes in the PI3K-Akt pathway associated with the diagnosis and prognosis of CCRCC using data mining from the Cancer Genome Atlas (TCGA) and Gene Expression Synthesis (GEO) datasets. METHODS: The purpose of this study is to use bioinformatics methods to screen data sets and clinicopathological characteristics associated with ccRCC patients. The exhibited significantly differential expressed genes (DEGs) associated with the PI3K-Akt pathway were examined by KEGG. In addition, Kaplan-Meier (KM) analysis used to estimate the survival function of the differential genes by using the UALCAN database and graphPad Prism 9.0. And exploring the association between the expression levels of the selected genes and the survival status and time of patients with ccRCC based on SPSS22.0. Finally, a multigene prognostic model was constructed to assess the prognostic risk of ccRCC patients. RESULTS: A total of 911 genes with common highly expressed were selected based on the GEO and TCGA databases. According to the KEGG pathway analysis, there were 42 genes enriched in PI3K-Akt signalling pathway. And seven of highly expressed genes were linked to a poor prognosis in ccRCC. And a multigene prognostic model was established based on IL2RG, EFNA3, and MTCP1 synergistic expression might be utilized to predict the survival of ccRCC patients. CONCLUSIONS: Three PI3K-Akt pathway-related genes may be helpful to identify the prognosis and molecular characteristics of ccRCC patients and to improve therapeutic regimens, and these risk characteristics might be further applied in the clinic.

The value of CT shape quantification in predicting pathological classification of lung adenocarcinoma.

OBJECTIVE: To evaluate whether quantification of lung GGN shape is useful in predicting pathological categorization of lung adenocarcinoma and guiding the clinic. METHODS: 98 patients with primary lung adenocarcinoma were pathologically confirmed and CT was performed preoperatively, and all lesions were pathologically ≤ 30 mm in size. On CT images, we measured the maximum area of the lesion's cross-section (MA). The longest diameter of the tumor (LD) was marked with points A and B, and the perpendicular diameter (PD) was marked with points C and D, which was the longest diameter perpendicular to AB. and D, which was the longest diameter perpendicular to AB. We took angles A and B as big angle A (BiA) and small angle A (SmA). We measured the MA, LD, and PD, and for analysis we derived the LD/PD ratio and the BiA/SmA ratio. The data were analysed using the chi-square test, t-test, ROC analysis, and binary logistic regression analysis. RESULTS: Precursor glandular lesions (PGL) and microinvasive adenocarcinoma (MIA) were distinguished from invasive adenocarcinoma (IAC) by the BiA/SmA ratio and LD, two independent factors (p = 0.007, p = 0.018). Lung adenocarcinoma pathological categorization was indicated by the BiA/SmA ratio of 1.35 and the LD of 11.56 mm with sensitivity of 81.36% and 71.79%, respectively; specificity of 71.79% and 74.36%, respectively; and AUC of 0.8357 (95% CI: 0.7558-0.9157, p < 0.001), 0.8666 (95% CI: 0.7866-0.9465, p < 0.001), respectively. In predicting the pathological categorization of lung adenocarcinoma, the area under the ROC curve of the BiA/SmA ratio combined with LD was 0.9231 (95% CI: 0.8700-0.9762, p < 0.001), with a sensitivity of 81.36% and a specificity of 89.74%. CONCLUSIONS: Quantification of lung GGN morphology by the BiA/SmA ratio combined with LD could be helpful in predicting pathological classification of lung adenocarcinoma.

Progress in TLE treatment from 2003 to 2023: scientific measurement and visual analysis based on CiteSpace.

Objective: Temporal lobe epilepsy (TLE) is the most common cause of drug-resistant epilepsy and can be treated surgically to control seizures. In this study, we analyzed the relevant research literature in the field of temporal lobe epilepsy (TLE) treatment to understand the background, hotspots, and trends in TLE treatment research. Methods: We discussed the trend, frontier, and hotspot of scientific output in TLE treatment research in the world in the last 20 years by searching the core collection of the Web of Science database. Excel and CiteSpace software were used to analyze the basic data of the literature. Result: We identified a total of 2,051 publications on TLE treatment from 75 countries between 2003 and 2023. We found that the publication rate was generally increasing. The United States was the most publishing country; among the research institutions on TLE treatment, the University of California system published the most relevant literature and collaborated the most with other institutions. The co-citation of literature, keyword co-occurrence, and its clustering analysis showed that the early studies focused on open surgical treatment, mainly by lobectomy. In recent years, the attention given to stereotactic, microsurgery, and other surgical techniques has gradually increased, and the burst analysis indicated that new research hotspots may appear in the future in the areas of improved surgical procedures and mechanism research.

IL-9 promotes methicillin-resistant Staphylococcus aureus pneumonia by regulating the polarization and phagocytosis of macrophages.

In this study, we examined the effect of Il9 deletion on macrophages in methicillin-resistant Staphylococcus aureus (MRSA) infection. MRSA-infected mice were employed for the in vivo experiments, and RAW264.7 cells were stimulated with MRSA for the in vitro experiments. Macrophage polarization was determined by flow cytometry and quantitative real-time PCR; macrophage phagocytosis was assessed by flow cytometry and laser scanning confocal microscopy; cell apoptosis was assessed by flow cytometry and western blotting. Il9 deletion markedly elevated macrophage phagocytosis and M2 macrophages in MRSA infection, which was accompanied by elevated expression of Il10 and Arg1 and reduced expression of Inos, tumor necrosis factor-α (Tnfα), and Il6. Il9 deletion also inhibited macrophage apoptosis in MRSA infection, which was manifested by elevated B-cell lymphoma 2 (BCL-2) protein level and reduced protein levels of cleaved cysteine protease 3 (CASPASE-3) and BCL2-Associated X (BAX). Both the in vivo and in vitro experiments further showed the activation of phosphoinositide 3-kinase (PI3K)/AKT (also known as protein kinase B, PKB) signaling pathway in MRSA infection and that the regulation of Il9 expression may be dependent on Toll-like receptor (TLR) 2/PI3K pathway. The above results showed that Il9 deletion exhibited a protective role against MRSA infection by promoting M2 polarization and phagocytosis of macrophages and the regulation of Il9 partly owing to the activation of TLR2/PI3K pathway, proposing a novel therapeutic strategy for MRSA-infected pneumonia.

Visual analysis of lung neuroendocrine tumors based on CiteSpace knowledge graph.

Objective: The relevant literatures in the field of pulmonary neuroendocrine tumor were analyzed to understand the lineage, hot spots and development trends of research in this tumor. Method: The Web of Science core collection was searched for English-language literature about neuroendocrine tumors of the lung published between 2000 and 2022. CiteSpace software was imported for visualization analysis of countries, institutions, co-cited authors and co-cited journals and sorting of high-frequency keywords, as well as co-cited references and keyword co-occurrence, clustering and bursting display. Results: A total of 594 publications on neuroendocrine tumours of the lung were available, from 2000 to 2022, with an overall upward trend of annual publications in the literature. Authors or institutions from the United States, Italy, Japan and China were more active in this field, but there was little cooperation among the major countries. Co-cited references and keyword co-occurrence and cluster analysis showed that research on diagnostic instruments, pathogenesis, ectopic ACTH signs, staging and prognosis and treatment was a current research hotspot. The keyword bursts suggested that therapeutic approaches might be a key focus of future research into the field for pulmonary neuroendocrine tumors. Conclusion: Over these 20 years, research related to neuroendocrine tumors of the lung has increased in fervour, with research on diagnostic instruments, pathogenesis, ectopic ACTH signs, staging and prognosis, and treatment being the main focus of research. Therapeutic treatments may be the future research trend in this field.

Systematic analysis of circRNA biomarkers for diagnosis, prognosis and therapy in colorectal cancer.

As the third most common cancer and the second leading cause of cancer death worldwide, colorectal cancer (CRC) poses a serious threat to people's health. In recent years, circRNA has been widely reported as a new biomarker in CRC, but a comprehensive summary and analysis is lacking. This study aims to evaluate the diagnostic, therapeutic and prognostic significance of circRNAs in CRC by systematically analysing their expression patterns, biological functions and clinical significance in CRC. The literature on circRNA in CRC was searched in the PubMed database and included for analysis after screening according to strict inclusion and exclusion criteria. The UALCAN online tool was used to obtain host gene expression data. The miRTargetLink 2.0 was used to predict target genes for miRNAs action in CRC patients. Cytoscape was used to construct circRNA-miRNA-mRNA interaction networks. From the 236 included papers, we identified 217 circRNAs and their associated 108 host genes and 145 miRNAs. Among the 145 miRNAs, 27 miRNAs had no corresponding target genes. After prediction of target genes and differential analysis, a total of 25 target genes were obtained and a circRNA-miRNA-mRNA interaction network was constructed. Among the 217 circRNAs, 74 were associated with diagnosis, 160 with treatment and 51 with prognosis. And 154 of them function as oncogenes while 58 as tumour suppressor genes. In addition, these circRNAs include 32 exosomal circRNAs, which have unique advantages as biomarkers. In total, we summarize and analyze the expression patterns, biological functions and clinical significance of circRNAs in CRC. In addition, we constructed some new circRNA-miRNA-mRNA regulatory axes based on the miRNAs sponged by circRNAs.

Global status of research on radiotherapy for rectal cancer: A bibliometric and visual analysis.

Radiotherapy for rectal cancer has received increasing research attention in recent years; however, no bibliometric assessment has been conducted on the progress of research in this field. This study aimed to visualize the research evolution and emerging research hotspots in the field of rectal cancer radiotherapy using bibliometric methods. Data were collected from the Web of Science Core Collection database, including countries, institutions, authors, keywords, and co-citations of references, and the CiteSpace software was used for bibliometric analysis. A total of 5,372 publications on radiotherapy for rectal cancer, published between January 2000 and January 2022, were included. An increasing trend in the number of published articles was observed. There is an overall upward trend in the number of publications published, with the US publishing the most in this field, followed by China and the Netherlands. Italian writer Vincenzo Valentini and German writer R. Sauer ranked first in terms of published articles and co-cited authors, respectively. Literature co-citation and keyword co-occurrence analyses showed that early studies focused on topics such as preoperative radiotherapy, combined radiotherapy and chemotherapy, and total mesorectal excision. In recent years, gradually increasing attention has been paid to short-course radiotherapy, x-ray brachytherapy, and stereotactic systemic radiotherapy. Burst analysis suggested that magnetic resonance (MR)-guided neoadjuvant radiotherapy studies, mechanistic studies, and clinical trials may emerge as new research hotspots. Rectal cancer radiotherapy has been widely studied and the research hotspots have considerably changed in recent years. Future research hotspots may include MR-guided neoadjuvant radiotherapy studies, mechanistic studies, and clinical trials.

Identification of ABCA5 among ATP-Binding Cassette Transporter Family as a New Biomarker for Colorectal Cancer.

Background: The increasing incidence and mortality of colorectal cancer (CRC) urgently requires updated biomarkers. The ABC transporter family is a widespread family of membrane-bound proteins involved in the transportation of substrates associated with ATP hydrolysis, including metabolites, amino acids, peptides and proteins, sterols and lipids, organic and inorganic ions, sugars, metals, and drugs. They play an important role in the maintenance of homeostasis in the body. Purpose: This study aims to search for new markers in the ABC transporter gene family for diagnostic and prognostic purposes through data mining of The Cancer Genome Atlas (TCGA) and GEO (Gene Expression Omnibus) datasets. Methods: A total of 980 samples, including 684 CRC patients and 296 controls from five different datasets, were included for analysis. The construction of the PPI (protein-protein interaction) network and pathway analysis were performed in STRING database and DAVID (database for annotation, visualization, and integrated discovery), respectively. In addition, GSEA (gene set enrichment analysis) and WGCNA (weighted gene co-expression network analysis) were also used for functional analysis. Results: After several rounds of screening and validation, only the ABCB5 gene was retained among the 49 genes. Conclusions: The results demonstrated that ABCA5 expression is reduced in CRC and patients with high ABCA5 expression have better OS, which can provide guidance for better management and treatment of CRC in the future.

The diterpenoid adenanthin upregulates the expression of natural killer group 2D receptor ligands in hepatocellular carcinoma cells.

OBJECTIVE: The natural killer (NK) group 2D (NKG2D) receptor plays a crucial role in NK cell-mediated anti-tumor immunity. NKG2D anti-proliferative effect is mediated by direct interactions of the receptor with its ligands that may be considered as a potential target for NK-based immunotherapeutic strategy in cancer cells. METHODS: Here we report that a natural product adenanthin significantly promotes NKG2D ligands expression in hepatoma cells. The effect was determined using flow cytometry analysis. The activity of NK cell was evaluated by measuring its degranulation activity and cytotoxicity. RESULTS: Our data indicates that the induction of NKG2D ligand binding to liver cancer cell surface receptors greatly improves the killing activity of NK cells against the cancer cells. CONCLUSIONS: This is the first report of a new mechanism anti-cancer effects of adenanthin mediated by an indirect activation of NK cells. Our data suggests that adenanthin may be used to sensitize NK cells in tumor immunotherapy.

Role of 5-HT1A in the nucleus of the solitary tract in the regulation of swallowing activities evoked by electroacupuncture in anesthetized rats.

Somatic stimulation therapy, such as electroacupuncture (EA), has been widely applied in the clinic to treat dysphagia. However, its underlying mechanism has remained unknown. In the present study, the effect of EA at acupoints Fengfu (DU16) and Lianquan (RN23) on swallowing activities and the involvement of 5-HT1A in the nucleus of the solitary tract (NTS) were examined in anesthetized rats. EA at DU16 and RN23 significantly evoked myoelectric activity of the mylohyoid muscle, which was attenuated by injection of 10 nmol 5-HT1A antagonist (WAY-100635) into the NTS. Meanwhile, 5-HT1A expression in the NTS increased following EA. The results suggested that EA at DU16 and RN23 promotes swallowing activity, and 5-HT1A in the NTS may play an important role in the excitatory effects.

Linking Doses with Clinical Scores of Hematopoietic Acute Radiation Syndrome.

In radiation accidents, determining the radiation dose the victim received is a key step for medical decision making and patient prognosis. To reconstruct and evaluate the absorbed dose, researchers have developed many physical devices and biological techniques during the last decades. However, using the physical parameter "absorbed dose" alone is not sufficient to predict the clinical development of the various organs injured in an individual patient. In operational situations for radiation accidents, medical responders need more urgently to classify the severity of the radiation injury based on the signs and symptoms of the patient. In this work, the author uses a unified hematopoietic model to describe dose-dependent dynamics of granulocytes, lymphocytes, and platelets, and the corresponding clinical grading of hematopoietic acute radiation syndrome. This approach not only visualizes the time course of the patient's probable outcome in the form of graphs but also indirectly gives information of the remaining stem and progenitor cells, which are responsible for the autologous recovery of the hematopoietic system. Because critical information on the patient's clinical evolution can be provided within a short time after exposure and only peripheral cell counts are required for the simulation, these modeling tools will be useful to assess radiation exposure and injury in human-involved radiation accident/incident scenarios.

Analysis of the lymphocytopoiesis dynamics in nonirradiated and irradiated humans: a modeling approach.

In this work, a recently developed mathematical model of the lymphocytopoietic system in acutely irradiated humans was extended to predict the dynamics of this system both in nonirradiated and acutely/chronically irradiated humans. The mathematical implementation of this model is a system of nonlinear ordinary differential equations, whose variables and parameters have clear biological meaning. We demonstrate that the model is capable of reproducing the dynamic regimes that are typical for lymphocytopoiesis in nonirradiated individuals with a hematological disorder (cyclic lymphocytopenia) and in patients receiving allogeneic stem cell transplantation. The model is also capable of predicting the dynamics of the lymphocytopoietic system in humans exposed to acute and chronic irradiation over a wide range of doses and dose rates. Additionally, the "lethal" dose rate of chronic irradiation, evaluated in the framework of the lymphocytopoiesis model, agrees with the actual minimum dose rate of lethal chronic irradiation observed for humans.

Epidermal homeostasis and radiation responses in a multiscale tissue modeling framework.

The surface of the skin is lined with several thin layers of epithelial cells that are maintained throughout a lifetime by a small population of stem cells. High dose radiation exposures could injure and deplete the underlying proliferative cells and induce cutaneous radiation syndrome. In this work we propose a multiscale computational model for skin epidermal dynamics that links phenomena occurring at the subcellular, cellular, and tissue levels of organization, to simulate the experimental data of the radiation response of swine epidermis, which is very similar to human epidermis. Incorporating experimentally measured histological and cell kinetic parameters, we obtain results of population kinetics and proliferation indices comparable to observations in unirradiated and acutely irradiated swine experiments. At the sub-cellular level, several recently published Wnt signaling controlled cell-cycle models are applied and the roles of key components and parameters are analyzed. This integrated model allows us to test the validity of several basic biological rules at the cellular level and sub-cellular mechanisms by qualitatively comparing simulation results with published research, and enhances our understanding of the pathophysiological effects of ionizing radiation on the skin.

A biomathematical model of lymphopoiesis following severe radiation accidents--potential use for dose assessment.

A biomathematical model of lymphopoiesis is described and used to analyze the lymphocyte changes observed in the blood of exposed victims in radiation accidents. The coarse-grained architecture of cellular replication and production and implicit cellular regulation mechanisms used in this model make it straightforward to incorporate various radiation conditions. Model simulations with reported absorbed doses as inputs are shown to qualitatively and quantitatively describe a wide range of accidental data in vastly different scenarios. In addition, the absolute lymphocyte counts and the depletion rate constants calculated by this model show good correlation with two widely recognized empirical methods for early dose assessment. This demonstrates the potential to use the biophysical model as an alternative method for the assessment of radiation injury in the case of large-scale radiation disaster. The physiological assumptions underlying the model are also discussed, which may provide a putative mechanism for some biodosimetric tools that use the peripheral blood cell counts as markers of radiation impairment.

Characterization of the radiation-damaged precursor cells in bone marrow based on modeling of the peripheral blood granulocytes response.

Bone marrow failure is the major cause of radiation lethality in mammals. Since bone marrow is distributed heterogeneously within trabecular spongiosa encased in a cortex of cortical bone, it is very difficult to measure the extent of the radiation damage directly. However, indirect consequences of damage to marrow, such as reductions in peripheral blood cell counts, are easily measured. In this paper, the authors investgate a mathematical model of the granulopoiesis system that provides quantitative relationships between reductions in peripheral blood cells and the bone marrow precursor cells following radiation exposure. A coarse-grained architecture of cellular replication and production as well as a mechanism for implicit regulation used in this model are discussed. The model is based on previous investigations of rodents. The authors test how well the model matches, in the principal dynamic regime of hematopoiesis, experimental data on large animals as well as empirical data on humans following radiation exposure. Due to its ability to infer, albeit indirectly, radiation damage to bone marrow, this model will provide a useful computational tool in radiation accident management, military operations involving nuclear warfare, radiation therapy, and space radiation risk assessment.

A cell kinetic model of granulopoiesis under radiation exposure: extension from rodents to canines and humans.

As significant ionising radiation exposure will occur during prolonged space travel in future, it is essential to understand their adverse effects on the radiosensitive organ systems that are important for immediate survival of humans, e.g. the haematopoietic system. In this paper, a biomathematical model of granulopoiesis is used to analyse the granulocyte changes seen in the blood of mammalians under acute and continuous radiation exposure. This is one of a set of haematopoietic models that have been successfully utilised to simulate and interpret the experimental data of acute and chronic radiation on rodents. Extension to canine and human systems indicates that the results of the model are consistent with the cumulative experimental and empirical data from various sources, implying the potential to integrate them into one united model system to monitor the haematopoietic response of various species under irradiation. The suppression of granulocytes' level of a space traveller under chronic stress of low-dose irradiation as well as the granulopoietic response when encountering a historically large solar particle event is also discussed.

Theoretical mechanism study of UF6 hydrolysis in the gas phase (II).

In our previous work (J. Phys. Chem. A 2008, 112, 8877.), we found theoretical evidence indicating UF5OH is an intermediate produced in the first step of UF6 hydrolysis. In this work, we explored the probable reaction channels starting from UF5OH + UF6 and UF5OH + UF5OH systems using relativistic density functional theory calculations. Initially, the two uranium containing species associate to form complex UF6.UF5OH or dimer (UF5OH)2 through hydrogen bonding. The energy released is 12-16 kcal/mol, which may promote further reactions. After H2O or HF are eliminated from the complex or dimer, compounds containing U-O-U bond are produced. These compounds are potentially feasible to associate into larger clusters or solidify. Relative to the isolated initial species, the energies of the final products are -6 to -13 kcal/mol lower, indicating that the reactions may spontaneously proceed. The calculated IR spectra features can be used to indicate the formation and interaction type of the intermediates and products.

Theoretical mechanism study of UF6 hydrolysis in the gas phase.

The mechanism of the gas-phase reaction UF 6 + H 2O --> UOF 4 + 2HF is explored using relativistic density functional theory calculations. Initially, H 2O coordinates with UF 6 to form a 1:1 complex UF 6.H 2O. Over an activation energy barrier of about 19 kcal/mol, H 2O transfers a H atom to a nearby ligand F, resulting in UF 5OH + HF. The eliminated HF or another H 2O molecule may form a hydrogen bond with UF 5OH. Starting from UF 5OH, the second HF elimination results in UOF 4. If UF 5OH is in the isolated form, UF 5OH --> UOF 4 + HF takes place over a barrier of 24 kcal/mol. If UF 5OH is hydrogen-bonded with H 2O or HF, the conversion barrier is less than 10 kcal/mol. Once formed, the unstable UOF 4 tends to associate with additional ligands and hydrogen-bonding donors. The calculated binding energies indicate the significance of such interactions, which may have profound impact on further HF eliminating reactions. The IR spectra features can be used to indicate the formation and interaction type of the intermediates and products.

Influence of H2 on the gas-phase decomposition of formic acid: a theoretical study.

Gas-phase decomposition of formic acid results in final products CO + H2O and CO2 + H2. Experimentally, the CO/CO2 ratio tends to be large, in contradiction with mechanism studies, which show almost equal activation energies for dehydration and decarboxylation. In this work, the influence of H2 on the decomposition mechanism of HCOOH was explored using ab initio calculations at the CCSD(T)/6-311++G**//MP2/6-311++G** level. It was found that, in the presence of H2, the reaction channels leading to CO + H2O are more than those leading to CO2 + H2. With competitive energy, H2 addition to HCOOH can reduce the latter into HCHO, which then dissociates into CO + H2 catalyzed by H2O. Compared to trans-HCOOH, cis-HCOOH and cis-C(OH)2, conformers required for decarboxylation, are less populated due to interactions with H2.

Preparation and biodistribution of technetium-99m-labeled 1-(2-nitroimidazole-1-yl)-propanhydroxyiminoamide (N2IPA) as a tumor hypoxia marker.

A new hydroxyiminoamide ligand, 1-(2-nitroimidazole-1-yl)-propanhydroxyiminoamide (N2IPA) was synthesized. The biodistribution of (99m)Tc-N2IPA in mice bearing S180 tumor demonstrated that the complex showed a selective accumulation in tumor and slow clearance from it. The tumor-to-tissue uptake ratios increased with time. At 4 hours after injection, the uptake ratios of tumor to muscle, blood, liver, heart, and lung reached 8.4, 1.5, 0.6, 2.9, and 2.3, respectively. Moreover, the tumor-to-liver uptake ratio steadily increased to 0.9 at 8 hours and 2.3 at 24 hours. The complex showed little uptake and quick clearance in blood, lung and other organs. Compared with other proposed hypoxia-imaging agents, this novel agent has advantages of higher tumor-to-muscle and tumor-to-blood uptake ratios and easier synthesis.