ABSTRACT
Despite the increasing number of 3D RNA structures in the Protein Data Bank, the majority of experimental RNA structures lack thorough functional annotations. As the significance of the functional roles played by noncoding RNAs becomes increasingly apparent, comprehensive annotation of RNA function is becoming a pressing concern. In response to this need, we have developed FURNA (Functions of RNAs), the first database for experimental RNA structures that aims to provide a comprehensive repository of high-quality functional annotations. These include Gene Ontology terms, Enzyme Commission numbers, ligand-binding sites, RNA families, protein-binding motifs, and cross-references to related databases. FURNA is available at https://seq2fun.dcmb.med.umich.edu/furna/ to enable quick discovery of RNA functions from their structures and sequences.
Subject(s)
Molecular Sequence Annotation , Nucleic Acid Conformation , RNA , RNA/metabolism , RNA/chemistry , RNA/genetics , Databases, Nucleic Acid , Binding Sites , HumansABSTRACT
Since the 60s of the 20th century, heart transplantation has been the best treatment for patients with end-stage heart failure. Due to the increasing number of patients, how to expand the number of donor organs and enhance immune compatibility has become an urgent problem to be solved at this stage. Although current immunosuppression is effective, its side effects are also quite obvious, such as opportunistic infections and malignant tumors. In this review, we focus on the important role in macrophages after heart transplantation and their potential targets for achieving allogeneic graft tolerance, in order to improve effective graft survival and reduce infection and the occurrence of malignant tumors.
ABSTRACT
Sequence database searches followed by homology-based function transfer form one of the oldest and most popular approaches for predicting protein functions, such as Gene Ontology (GO) terms. These searches are also a critical component in most state-of-the-art machine learning and deep learning-based protein function predictors. Although sequence search tools are the basis of homology-based protein function prediction, previous studies have scarcely explored how to select the optimal sequence search tools and configure their parameters to achieve the best function prediction. In this paper, we evaluate the effect of using different options from among popular search tools, as well as the impacts of search parameters, on protein function prediction. When predicting GO terms on a large benchmark dataset, we found that BLASTp and MMseqs2 consistently exceed the performance of other tools, including DIAMOND-one of the most popular tools for function prediction-under default search parameters. However, with the correct parameter settings, DIAMOND can perform comparably to BLASTp and MMseqs2 in function prediction. Additionally, we developed a new scoring function to derive GO prediction from homologous hits that consistently outperform previously proposed scoring functions. These findings enable the improvement of almost all protein function prediction algorithms with a few easily implementable changes in their sequence homolog-based component. This study emphasizes the critical role of search parameter settings in homology-based function transfer and should have an important contribution to the development of future protein function prediction algorithms.
Subject(s)
Databases, Protein , Proteins , Proteins/chemistry , Proteins/metabolism , Proteins/genetics , Computational Biology/methods , Gene Ontology , Algorithms , Sequence Analysis, Protein/methods , Software , Machine LearningABSTRACT
ETHNOPHARMACOLOGICAL RELEVANCE: Cervical cancer (CC) is a potentially lethal disorder that can have serious consequences for a woman's health. Because early symptoms are typically only present in the middle to late stages of the disease, clinical diagnosis and treatment can be challenging. Traditional Chinese medicine (TCM) has been shown to have unique benefits in terms of alleviating cancer clinical symptoms, lowering the risk of recurrence after surgery, and reducing toxic side effects and medication resistance after radiation therapy. It has also been shown to improve the quality of life for patients. Because of its improved anti-tumor effectiveness and biosafety, it could be considered an alternative therapy option. This study examines how TCM causes apoptosis in CC cells via signal transduction, including the active components and medicinal tonics. It also intends to provide a reliable clinical basis and protocol selection for the TCM therapy of CC. METHODS: The following search terms were employed in PubMed, Web of Science, Embase, CNKI, Wanfang, VIP, SinoMed, and other scientific databases to retrieve pertinent literature on "cervical cancer," "apoptosis," "signaling pathway," "traditional Chinese medicine," "herbal monomers," "herbal components," "herbal extracts," and "herbal formulas." RESULTS: It has been demonstrated that herbal medicines can induce apoptosis in cells of the cervix, a type of cancer, by influencing the signaling pathways involved. CONCLUSION: A comprehensive literature search was conducted, and 148 papers from the period between January 2017 and December 2023 were identified as eligible for inclusion. After a meticulous process of screening, elimination and summary, generalization, and analysis, it was found that TCM can regulate multiple intracellular signaling pathways and related molecular targets, such as STAT3, PI3K/AKT, Wnt/ß-catenin, MAPK, NF-κB, p53, HIF-1α, Fas/FasL and so forth. This regulatory capacity was observed to induce apoptosis in cervical cancer cells. The study of the mechanism of TCM against cervical cancer and the screening of new drug targets is of great significance for future research in this field. The results of this study will provide ideas and references for the future development of Chinese medicine in the diagnosis and treatment of cervical cancer.
Subject(s)
Apoptosis , Drugs, Chinese Herbal , Medicine, Chinese Traditional , Signal Transduction , Uterine Cervical Neoplasms , Humans , Uterine Cervical Neoplasms/drug therapy , Uterine Cervical Neoplasms/pathology , Uterine Cervical Neoplasms/metabolism , Female , Signal Transduction/drug effects , Apoptosis/drug effects , Medicine, Chinese Traditional/methods , Drugs, Chinese Herbal/pharmacology , Drugs, Chinese Herbal/therapeutic use , Animals , Antineoplastic Agents, Phytogenic/pharmacology , Antineoplastic Agents, Phytogenic/therapeutic useABSTRACT
The cyclic guanosine monophosphate (GMP)-adenosine monophosphate (AMP) synthase-stimulator of interferon genes (cGAS-STING) signaling pathway, an important component of the innate immune system, is involved in the development of several diseases. Ectopic DNA-induced inflammatory responses are involved in several pathological processes. Repeated damage to tissues and metabolic organelles releases a large number of damage-associated molecular patterns (mitochondrial DNA, nuclear DNA, and exogenous DNA). The DNA fragments released into the cytoplasm are sensed by the sensor cGAS to initiate immune responses through the bridging protein STING. Many recent studies have revealed a regulatory role of the cGAS-STING signaling pathway in cardiovascular diseases (CVDs) such as myocardial infarction, heart failure, atherosclerosis, and aortic dissection/aneurysm. Furthermore, increasing evidence suggests that inhibiting the cGAS-STING signaling pathway can significantly inhibit myocardial hypertrophy and inflammatory cell infiltration. Therefore, this review is intended to identify risk factors for activating the cGAS-STING pathway to reduce risks and to simultaneously further elucidate the biological function of this pathway in the cardiovascular field, as well as its potential as a therapeutic target.
ABSTRACT
Porcine circovirus type 2 (PCV2) is a globally prevalent infectious pathogen affecting swine, with its capsid protein (Cap) being the sole structural protein critical for vaccine development. Prior research has demonstrated that PCV2 Cap proteins produced in Escherichia coli (E. coli) can form virus-like particles (VLPs) in vitro, and nuclear localization signal peptides (NLS) play a pivotal role in stabilizing PCV2 VLPs. Recently, PCV2d has emerged as an important strain within the PCV2 epidemic. In this study, we systematically optimized the PCV2d Cap protein and successfully produced intact PCV2d VLPs containing NLS using E. coli. The recombinant PCV2d Cap protein was purified through affinity chromatography, yielding 7.5 mg of recombinant protein per 100 ml of bacterial culture. We augmented the conventional buffer system with various substances such as arginine, ß-mercaptoethanol, glycerol, polyethylene glycol, and glutathione to promote VLP assembly. The recombinant PCV2d Cap self-assembled into VLPs approximately 20 nm in diameter, featuring uniform distribution and exceptional stability in the optimized buffer. We developed the vaccine and immunized pigs and mice, evaluating the immunogenicity of the PCV2d VLPs vaccine by measuring PCV2-IgG, IL-4, TNF-α, and IFN-γ levels, comparing them to commercial vaccines utilizing truncated PCV2 Cap antigens. The HE staining and immunohistochemical tests confirmed that the PCV2 VLPs vaccine offered robust protection. The results revealed that animals vaccinated with the PCV2d VLPs vaccine exhibited high levels of PCV2 antibodies, with TNF-α and IFN-γ levels rapidly increasing at 14 days post-immunization, which were higher than those observed in commercially available vaccines, particularly in the mouse trial. This could be due to the fact that full-length Cap proteins can assemble into more stable PCV2d VLPs in the assembling buffer. In conclusion, our produced PCV2d VLPs vaccine elicited stronger immune responses in pigs and mice compared to commercial vaccines. The PCV2d VLPs from this study serve as an excellent candidate vaccine antigen, providing insights for PCV2d vaccine research.
Subject(s)
Antibodies, Viral , Capsid Proteins , Circovirus , Escherichia coli , Recombinant Proteins , Vaccines, Virus-Like Particle , Animals , Circovirus/immunology , Circovirus/genetics , Swine , Vaccines, Virus-Like Particle/immunology , Vaccines, Virus-Like Particle/genetics , Capsid Proteins/immunology , Capsid Proteins/genetics , Escherichia coli/genetics , Escherichia coli/metabolism , Mice , Antibodies, Viral/immunology , Antibodies, Viral/blood , Recombinant Proteins/immunology , Recombinant Proteins/genetics , Circoviridae Infections/prevention & control , Circoviridae Infections/immunology , Swine Diseases/prevention & control , Viral Vaccines/immunology , Viral Vaccines/genetics , Vaccine Development , Antigens, Viral/immunology , Antigens, Viral/genetics , Immunoglobulin G/blood , Cost-Benefit Analysis , Female , Interferon-gamma/metabolism , Immunogenicity, VaccineABSTRACT
BACKGROUND: Minimally invasive surgery has emerged as a favorable alternative to conventional surgery for various cardiac conditions. This study aimed to compare the perioperative outcomes and follow-up results of the robotic approach versus the sternotomy approach for left atrial myxoma (LAM) resection. METHOD: We retrospectively analyzed the perioperative outcomes and follow-up results of 94 patients who underwent left atrial myxoma resection using either the sternotomy approach (n = 64) or the robotic approach (n = 30) at our center between January 2017 and April 2023. Multiple linear regressions were employed to examine the actual impact of the surgical approach on perioperative outcomes while controlling for potential confounding factors. RESULTS: There were no in-hospital deaths or follow-up deaths in the robotic group. Univariate analyses revealed that robotic LAM resection had a longer cardiopulmonary bypass (CPB) time (99.93 ± 22.30 vs. 76.28 ± 24.92, P < 0.001), longer aortic clamping time (57.80 ± 20.27 vs. 47.89 ± 18.10, P = 0.019), reduced postoperative drainage (P < 0.001), shorter mechanical ventilation time (P = 0.005), shorter postoperative bed-stay time (P < 0.001), shorter postoperative hospitalization time (P = 0.040), and higher hospital costs (P = 0.001) compared to the sternotomy group. After adjusting for baseline characteristics in a multiple regression model, a longer CPB time (B = 28.328; CI, 18.609-38.047; P < 0.001), longer aortic clamping time (B = 11.856; CI, 4.069-19.644; P = 0.003), reduced postoperative drainage (B = -200.224; CI, -254.962- -145.486; P < 0.001), shorter mechanical ventilation time (B = -3.429; CI, -6.562- -0.295; P = 0.032), shorter postoperative bed-stay time (B = -2.230; CI, -3.267- -1.193; P < 0.001), shorter postoperative hospitalization time (B = -1.998; CI, -3.747- -0.250; P = 0.026), and higher hospital costs (B = 2096.866, P = 0.002) were found in the robotic group. Furthermore, the robotic group exhibited a faster return to exercise compared to the sternotomy group (Log-Rank χ2 = 34.527, P < 0.001). CONCLUSION: Both the robotic and sternotomy approaches are viable and safe options for LAM resection. However, despite the higher costs, longer CPB time, and longer aortic clamping time associated with robotic LAM resection, this technique was correlated with reduced postoperative drainage and faster postoperative recovery compared to the sternotomy technique.
ABSTRACT
AIMS: Long non-coding RNA (LncRNA) small nucleolar RNA host gene 18 (SNHG18) has been widely implicated in cancers. However, little is known about its functional involvement in vascular diseases. Herein, we attempted to explore a role for SNHG18 in modulating vascular smooth muscle cell (VSMC) contractile phenotype and injury-induced neointima formation. METHODS AND RESULTS: Analysis of single-cell RNA sequencing and transcriptomic datasets showed decreased levels of SNHG18 in injured and atherosclerotic murine and human arteries, which is positively associated with VSMC contractile genes. SNHG18 was upregulated in VSMCs by TGFß1 through transcription factors Sp1 and SMAD3. SNHG18 gene gain/loss-of-function studies revealed that VSMC contractile phenotype was positively regulated by SNHG18. Mechanistic studies showed that SNHG18 promotes a contractile VSMC phenotype by up-regulating miR-22-3p. SNHG18 up-regulates miR-22 biogenesis and miR-22-3p production by competitive binding with the A-to-I RNA editing enzyme, adenosine deaminase acting on RNA-2 (ADAR2). Surprisingly, we observed that ADAR2 inhibited miR-22 biogenesis not through increasing A-to-I editing within primary miR-22, but by interfering with the binding of microprocessor complex subunit DGCR8 to primary miR-22. Importantly, perivascular SNHG18 overexpression in the injured vessels dramatically up-regulated the expression levels of miR-22-3p and VSMC contractile genes, and prevented injury-induced neointimal hyperplasia. Such modulatory effects were reverted by miR-22-3p inhibition in the injured arteries. Finally, we observed a similar regulator role for SNHG18 in human VSMCs and a decreased expression level of both SNHG18 and miR-22-3p in diseased human arteries; and we found that the expression level of SNHG18 was positively associated with that of miR-22-3p in both healthy and diseased human arteries. CONCLUSION: We demonstrate that SNHG18 is a novel regulator in governing VSMC contractile phenotype and preventing injury-induced neointimal hyperplasia. Our findings have important implications for therapeutic targeting snhg18/miR-22-3p signalling in vascular diseases.
Subject(s)
Carotid Artery Injuries , Disease Models, Animal , Hyperplasia , Mice, Inbred C57BL , MicroRNAs , Muscle, Smooth, Vascular , Myocytes, Smooth Muscle , Neointima , Phenotype , RNA, Long Noncoding , Muscle, Smooth, Vascular/pathology , Muscle, Smooth, Vascular/metabolism , Myocytes, Smooth Muscle/metabolism , Myocytes, Smooth Muscle/pathology , Humans , RNA, Long Noncoding/genetics , RNA, Long Noncoding/metabolism , MicroRNAs/metabolism , MicroRNAs/genetics , Animals , Carotid Artery Injuries/pathology , Carotid Artery Injuries/genetics , Carotid Artery Injuries/metabolism , Cells, Cultured , Male , Signal Transduction , RNA-Binding Proteins/metabolism , RNA-Binding Proteins/genetics , Gene Expression Regulation , Mice , Mice, Knockout, ApoESubject(s)
Aortic Valve Stenosis , Transcatheter Aortic Valve Replacement , Humans , Transcatheter Aortic Valve Replacement/methods , Aortic Valve Stenosis/surgery , Aortic Valve Stenosis/diagnostic imaging , Aortic Valve/surgery , Aortic Valve/diagnostic imaging , Aged, 80 and over , Male , Female , Aged , Treatment OutcomeABSTRACT
OBJECTIVE: To investigate the independent risk factors for postoperative prolonged ICU stay in patients with Stanford type A aortic dissection (TAAD) and assess the clinical outcomes of prolonged ICU stay. METHOD: The clinical data of 100 patients with TAAD admitted to the Department of Cardiovascular Surgery, First Affiliated Hospital of Anhui Medical University from December 2018 to September 2022 were retrospectively collected and analyzed. Patients were divided into two groups, based on the postoperative ICU stay (7 days as the threshold), regular ICU stay group (< 7 days) and prolonged ICU stay group (≥ 7 days). First, preoperative and intraoperative materials were collected for univariate analysis. Then, the significant variables after univariate analysis were analyzed using logistic regression, and the final independent risk factors for prolonged ICU stay were determined. Meanwhile, the postoperative clinical outcomes were analyzed with the aim of assessing the clinical outcomes due to prolonged ICU stay. RESULTS: There were 65 and 35 patients in the regular ICU stay group and the prolonged ICU stay group, respectively. In accordance with the result of univariate analysis in the two groups, emergency surgery (χ2 = 13.598; P < 0.001), preoperative urea nitrogen (t = 3.006; P = 0.004), cardiopulmonary bypass (CPB) time (t = 2.671; P = 0.001) and surgery time (t = 2.630; P = 0.010) were significant. All significant variates were analyzed through logistic regression, and it was found that emergency surgery (OR = 0.192; 95% CI: 0.065-0.561), preoperative urea nitrogen (OR = 0.775; 95% CI: 0.634-0.947) and cardiopulmonary time (OR = 0.988; 95% CI: 0.979-0.998) were independent risk factors for prolonged postoperative ICU stay. The Receiver Operating Characteristic (ROC) curves of these three factors were also effective in predicting postoperative prolonged ICU stay (Emergency surgery, AUC = 0.308, 95% CI: 0.201-0.415; Preoperative urea nitrogen, AUC = 0.288, 95% CI: 0.185-0.392; cardiopulmonary time, AUC = 0.340, 95% CI: 0.223-0.457). Moreover, compared with a single factor, the predictive value of combined factors was more significant (AUC = 0.810, 95% CI: 0.722-0.897). For the comparison of postoperative data in the two groups,, compared with the regular ICU stay group, the incidence of adverse events in the prolonged ICU stay group increased significantly, including limb disability of limbs (χ2 = 22.182; P < 0.001), severe organ injury (χ2 = 23.077; P < 0.001), tracheotomy (χ2 = 17.582; P < 0.001), reintubation (χ2 = 28.020; P < 0.001), 72 h tracheal extubation after surgery (χ2 = 29.335; P < 0.001), 12 h consciousness recovery after surgery (χ2 = 18.445; P < 0.001), ICU re-entering (χ2 = 9.496; P = 0.002) and irregular discharging (χ2 = 24.969; P < 0.001). CONCLUSION: Emergency surgery, preoperative urea nitrogen, and CPB time are risk factors for postoperative prolonged ICU stay after TAAD surgery. Furthermore, prolonged ICU stay is associated with worse clinical outcomes. Hence, a reasonable strategy should be adopted proactively focusing on the risk factors to shorten ICU stays and improve clinical outcomes.
Subject(s)
Aortic Dissection , Azides , Deoxyglucose/analogs & derivatives , Humans , Retrospective Studies , Aortic Dissection/surgery , Risk Factors , Intensive Care Units , Nitrogen , Urea , Length of StayABSTRACT
Live streaming with goods is developing rapidly as an emerging platform economic model. Consumers can interact with the e-commerce platform in real-time and get a good shopping experience. This in turn generates value co-creation behaviors such as word-of-mouth communication. However, due to the lack of effective audit mechanisms on some platforms, the phenomenon of value co-destruction among them is becoming more and more common. This brings value loss to consumers, e-commerce platforms, and other multiple subjects. Based on the SOR model, this paper collects 212 sample data by using a questionnaire survey. The impact of live banding platform characteristics on consumers' value co-creation and value co-destruction behaviors is analyzed through multiple regression and other methods. The results show that platform information quality, functional quality, and interactive quality all positively affect consumers' value co-creation behavior and negatively affect value co-destruction behavior. Perceived value plays a mediating role, and promotional incentives enhance the positive relationship between platform features and perceived value. Therefore, if the live streaming bandwagon platform provides consumers with sufficiently rich, complete, and timely product information, responds quickly to consumer needs, and has high interaction quality. Consumers are more likely to exhibit value co-creation behavior. This study enriches the theoretical results of value co-creation and value co-destruction. It provides theoretical references for live streaming platforms to inhibit consumers' value co-destructive behaviors and promote value co-creation behaviors. In practice, it is pointed out that live streaming platforms should provide consumers with real information on all aspects of the products, update and improve the performance of the platform in a timely manner, and provide regular training to the staff.
Subject(s)
Commerce , Communication , Humans , Consumer Behavior , FaceABSTRACT
Leveraging iterative alignment search through genomic and metagenome sequence databases, we report the DeepMSA2 pipeline for uniform protein single- and multichain multiple-sequence alignment (MSA) construction. Large-scale benchmarks show that DeepMSA2 MSAs can remarkably increase the accuracy of protein tertiary and quaternary structure predictions compared with current state-of-the-art methods. An integrated pipeline with DeepMSA2 participated in the most recent CASP15 experiment and created complex structural models with considerably higher quality than the AlphaFold2-Multimer server (v.2.2.0). Detailed data analyses show that the major advantage of DeepMSA2 lies in its balanced alignment search and effective model selection, and in the power of integrating huge metagenomics databases. These results demonstrate a new avenue to improve deep learning protein structure prediction through advanced MSA construction and provide additional evidence that optimization of input information to deep learning-based structure prediction methods must be considered with as much care as the design of the predictor itself.
Subject(s)
Deep Learning , Computational Biology/methods , Proteins/genetics , Proteins/chemistry , Sequence Alignment , Genomics , AlgorithmsABSTRACT
Endoplasmic reticulum-associated degradation (ERAD) plays indispensable roles in many physiological processes; however, the nature of endogenous substrates remains largely elusive. Here we report a proteomics strategy based on the intrinsic property of the SEL1L-HRD1 ERAD complex to identify endogenous ERAD substrates both in vitro and in vivo. Following stringent filtering using a machine learning algorithm, over 100 high-confidence potential substrates are identified in human HEK293T and mouse brown adipose tissue, among which ~88% are cell type-specific. One of the top shared hits is the catalytic subunit of the glycosylphosphatidylinositol (GPI)-transamidase complex, PIGK. Indeed, SEL1L-HRD1 ERAD attenuates the biogenesis of GPI-anchored proteins by specifically targeting PIGK for proteasomal degradation. Lastly, several PIGK disease variants in inherited GPI deficiency disorders are also SEL1L-HRD1 ERAD substrates. This study provides a platform and resources for future effort to identify proteome-wide endogenous substrates in vivo, and implicates SEL1L-HRD1 ERAD in many cellular processes including the biogenesis of GPI-anchored proteins.
Subject(s)
Endoplasmic Reticulum-Associated Degradation , Glycosylphosphatidylinositols , Animals , Mice , Humans , HEK293 Cells , Proteomics , GPI-Linked Proteins , ProteinsABSTRACT
The quickly increasing size of the Protein Data Bank is challenging biologists to develop a more scalable protein structure alignment tool for fast structure database search. Although many protein structure search algorithms and programs have been designed and implemented for this purpose, most require a large amount of computational time. We propose a novel protein structure search approach, TM-search, which is based on the pairwise structure alignment program TM-align and a new iterative clustering algorithm. Benchmark tests demonstrate that TM-search is 27 times faster than a TM-align full database search while still being able to identify â¼90% of all high TM-score hits, which is 2-10 times more than other existing programs such as Foldseek, Dali, and PSI-BLAST.
Subject(s)
Algorithms , Proteins , Databases, Protein , Sequence Alignment , Proteins/chemistry , Benchmarking , SoftwareABSTRACT
With the progress of structural biology, the Protein Data Bank (PDB) has witnessed rapid accumulation of experimentally solved protein structures. Since many structures are determined with purification and crystallization additives that are unrelated to a protein's in vivo function, it is nontrivial to identify the subset of protein-ligand interactions that are biologically relevant. We developed the BioLiP2 database (https://zhanggroup.org/BioLiP) to extract biologically relevant protein-ligand interactions from the PDB database. BioLiP2 assesses the functional relevance of the ligands by geometric rules and experimental literature validations. The ligand binding information is further enriched with other function annotations, including Enzyme Commission numbers, Gene Ontology terms, catalytic sites, and binding affinities collected from other databases and a manual literature survey. Compared to its predecessor BioLiP, BioLiP2 offers significantly greater coverage of nucleic acid-protein interactions, and interactions involving large complexes that are unavailable in PDB format. BioLiP2 also integrates cutting-edge structural alignment algorithms with state-of-the-art structure prediction techniques, which for the first time enables composite protein structure and sequence-based searching and significantly enhances the usefulness of the database in structure-based function annotations. With these new developments, BioLiP2 will continue to be an important and comprehensive database for docking, virtual screening, and structure-based protein function analyses.
Subject(s)
Algorithms , Databases, Protein , Proteins , Binding Sites , Ligands , Proteins/chemistryABSTRACT
BACKGROUND: Lung adenocarcinoma (LUAD) is a common cancer with a poor prognosis. Pyroptosis is an important process in the development and progression of LUAD. We analyzed the risk factors affecting the prognosis of patients and constructed a nomogram to predict the overall survival of patients based on different pyroptosis-related genes (PRGs) subtypes. METHODS: The genomic data of LUAD were downloaded from the TCGA and GEO databases, and all data were filtered and divided into TCGA and GEO cohorts. The process of data analysis and visualization was performed via R software. The data were classified based on different PRGs subtypes using the K-means clustering method. Then, the differentially expressed genes were identified between two different subtypes, and risk factors analysis, survival analysis, functional enrichment analysis, and immune cells infiltration landscape analysis were conducted. The COX regression analysis was used to construct the prediction model. RESULTS: Based on the PRGs of LUAD, the patients were divided into two subtypes. We found the survival probability of patients in subtype 1 is higher than that in subtype 2. The results of the logistics analysis showed that gene risk score was closely associated with the prognosis of LUAD patients. The results of GO analysis and KEGG analysis revealed important biological processes and signaling pathways involved in the differentially expressed proteins between the two subtypes. Then we constructed a prediction model of patients' prognosis based on 13 genes, including IL-1A, P2RX1, GSTM2, ESYT3, ZNF682, KCNF1, STK32A, HHIPL2, GDF10, NDC80, GSTA1, BCL2L10, and CCR2. This model was strongly related to the overall survival (OS) and also reflects the immune status in patients with LUAD. CONCLUSION: In our study, we examined LUAD heterogeneity with reference to pyroptosis and found different prognoses between the two subtypes. And a novel prediction model was constructed to predict the OS of LUAD patients based on different PRGs signatures. The model has shown excellent predictive efficiency through validation.
Subject(s)
Adenocarcinoma of Lung , Lung Neoplasms , Humans , Pyroptosis/genetics , Adenocarcinoma of Lung/genetics , Risk Factors , Genetic Risk Score , Lung Neoplasms/genetics , Prognosis , SynaptotagminsABSTRACT
Sequence database searches followed by homology-based function transfer form one of the oldest and most popular approaches for predicting protein functions, such as Gene Ontology (GO) terms. Although sequence search tools are the basis of homology-based protein function prediction, previous studies have scarcely explored how to select the optimal sequence search tools and configure their parameters to achieve the best function prediction. In this paper, we evaluate the effect of using different options from among popular search tools, as well as the impacts of search parameters, on protein function prediction. When predicting GO terms on a large benchmark dataset, we found that BLASTp and MMseqs2 consistently exceed the performance of other tools, including DIAMOND - one of the most popular tools for function prediction - under default search parameters. However, with the correct parameter settings, DIAMOND can perform comparably to BLASTp and MMseqs2 in function prediction. This study emphasizes the critical role of search parameter settings in homology-based function transfer.
ABSTRACT
Background: Because the diameter of the suspicious lymph nodes is less than 1 cm and adjacent to important structures in the neck, the diagnosis of small LLNM is important but difficult without the help of fine needle aspiration (FNA). There are no relevant reports of risk factors that predict the risk of suspicious <1 cm LLNM. Methods: A total of 159 PTMC patients with suspicious <1 cm LLNM were included in the study. Multivariate logistic regression analysis was used to identify ultrasound independent predictors of LLNM. A predictive model was developed according to multivariate logistic regression and evaluated by Hosmer-Lemeshow fit test. Results: Age ≤ 38 years old, the largest PTMC was located in the upper part, and the presence of liquefaction or microcalcification in suspicious lymph nodes were independent risk factors for LLNM (univariate analysis P = 0.00, 0.00, 0.00; multivariate analysis P = 0.00, 0.02, 0.00. OR = 4.66 [CI: 1.78-12.21], 3.04 [CI: 1.24-7.46], 6.39 [CI: 1.85-22.00]). The predictive model for the diagnosis of suspicious <1 cm lymph nodes was established as: P = ex/(1 + ex). X = -1.29 + (1.11 × whether the largest tumor is located in the upper part) + (1.54 × whether the age is ≤ 38 years) + (1.85 × whether the suspicious lymph nodes have liquefaction/microcalcification). The Hosmer-Lemeshow fit test was used to test the predicted ability, and it found that the predictive model had a good fit and prediction accuracy (X2 = 6.214, P = 0.623 > 0.05). Chi squared trend analysis showed that the increase in the number of risk factors gradually increased the malignancy possibility of suspicious <1 cm lymph nodes (chi squared trend test, P = 0.00). Conclusions: Age ≤ 38 years old, the largest PTMC located in the upper part, and the presence of liquefaction or microcalcification in suspicious lymph nodes were independent risk factors for suspicious <1 cm LLNM in PTMC patients. Our result show that it is feasible to evaluate the malignant possibility of these lymph nodes using the number of risk factors.