We extracted 33 pyroptosis-related genes from prior reviews17 (link)–20 (link), and they are presented in Table S1 . Due to the lack of normal ovarian tissue data in the TCGA cohort, we also considered GTEx data from 88 normal ovarian samples to identify the DEGs between normal and tumour tissues. The expression data in both datasets were normalized to fragment per kilobase million (FPKM) values before comparison. The “limma” package was used to identify DEGs with a P value <0.05. The DEGs are notated as follows: * if P < 0.05, ** if P < 0.01, and *** if P < 0.001. A PPI network for the DEGs was constructed with Search Tool for the Retrieval of Interacting Genes (STRING), version 11.0 (https://string-db.org/ ).
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Physiology
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Cell Function
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Pyroptosis
Pyroptosis
Pyroptosis is a form of programmed cell death characterized by the rapid lysis of the cell and the release of inflammatory cellular contents.
This process is triggered by the activation of inflammatory caspases, such as caspase-1, which cleave the pore-forming protein gasdermin D.
Pyroptosis is important in host defense against pathogens and can also contribute to the pathogenesis of certain diseases.
Understading the mechanisms and regulatoin of pyroptosis is a key area of research, and utilziing AI-driven platforms like PubCompare.ai can help optimize this research by efficiently locating relevant protocols from the literature, preprints, and patents.
This process is triggered by the activation of inflammatory caspases, such as caspase-1, which cleave the pore-forming protein gasdermin D.
Pyroptosis is important in host defense against pathogens and can also contribute to the pathogenesis of certain diseases.
Understading the mechanisms and regulatoin of pyroptosis is a key area of research, and utilziing AI-driven platforms like PubCompare.ai can help optimize this research by efficiently locating relevant protocols from the literature, preprints, and patents.
Most cited protocols related to «Pyroptosis»
To assess the prognostic value of the pyroptosis-related genes, we further employed Cox regression analysis to evaluate the correlations between each gene and survival status in the TCGA cohort. To prevent omissions, we set 0.2 as the cut-off P-value, and 7 survival-related genes were identified for further analysis. The LASSO Cox regression model (R package “glmnet”) was then utilized to narrow down the candidate genes and to develop the prognostic model. Ultimately, the seven genes and their coefficients were retained, and the penalty parameter (λ) was decided by the minimum criteria. The risk score was calculated after centralization and standardization (applying the “scale” function in R) of the TCGA expression data, and the risk score formula was as follows: Risk Score= (X: coefficients, Y: gene expression level). The TCGA OC patients were divided into low- and high-risk subgroups according to the median risk score, and the OS time was compared between the two subgroups via Kaplan–Meier analysis. PCA based on the 7-gene signature was performed by the “prcomp” function in the “stats” R package. The “survival”, “survminer” and “timeROC” R packages were employed to perform a 3-year ROC curve analysis. For the validation studies, an OC cohort from the GEO database (GSE140082) was employed. The expression of each pyroptosis-related gene was also normalized by the “scale” function, and the risk score was then calculated by the same formula used for the TCGA cohort. By applying the median risk score from the TCGA cohort, the patients in the GSE140082 cohort were also divided into low- or high-risk subgroups, and these groups were then compared to validate the gene model.
Gene Expression
Genes
Patients
Pyroptosis
We retrieved all literature data regarding the inflammasome/pyroptosis in brain indexed in the Web of Science (WOS) Core Collection (Clarivate Analysis, Boston, United States; http://apps.webofknowledge.com/WOS_GeneralSearch_input.do?product=WOS&SID=7DLaapxWMwSkqZf4LRr&search_mode=GeneralSearch ). The term pyroptosis was detected with MeSH (https://www.ncbi.nlm.nih.gov/mesh ), whereas the “pyroptosis”, “inflammasome”, and “brain” show other expressions, such as “pyroptotic” and “pyroptosome”. The articles from 2000 to 2020 (October 16, 2020) were searched, the language type was set to English, and the document type was set to article and review.
The search terms and strategies used for the WOS database are as follows: # 1, “pyroptosis”; # 2, “pyroptotic”; # 3, “inflammasome”; # 4, “pyroptosome”; # 5 “brain”; # 6, “# 1” OR “# 2” OR “# 3” OR “# 4”; # 7, “# 5” AND “# 6”.
A total of 14,343 documents of “inflammasome OR pyroptosis” and 1,222 documents of “inflammasome OR pyroptosis AND brain” were retrieved from WOS Core Collection, and then the documents were used to make visual analysis ultimately. The deadline for researched publications was October 16, 2020.
The search terms and strategies used for the WOS database are as follows: # 1, “pyroptosis”; # 2, “pyroptotic”; # 3, “inflammasome”; # 4, “pyroptosome”; # 5 “brain”; # 6, “# 1” OR “# 2” OR “# 3” OR “# 4”; # 7, “# 5” AND “# 6”.
A total of 14,343 documents of “inflammasome OR pyroptosis” and 1,222 documents of “inflammasome OR pyroptosis AND brain” were retrieved from WOS Core Collection, and then the documents were used to make visual analysis ultimately. The deadline for researched publications was October 16, 2020.
Brain
CTSB protein, human
Inflammasomes
Pyroptosis
Cells
Mass Spectrometry
Plasma
Protoplasm
Pyroptosis
Spectrometry
Tissue, Membrane
Vision
Yttrium
To measure membrane lysis, culture medium was collected and LDH release was measured using CytoTox 96 cytotoxicity assay (Promega) according to the manufacturer’s instructions. For GSDME-NT induced pyroptosis in HEK293T cells, HEK293T transfection was performed by the calcium-phosphate method and LDH release was measured 20 hours after transfection. Pyroptotic cells were also imaged using an Olympus IX70 inverted microscope and protein expression was analyzed by immunoblot. For raptinal-induced pyroptosis in B16 GSDME cells, 10 μM raptinal was used to treat B16 cells for 2 h and LDH release was measured at indicated timepoints. For TRAIL-induced pyroptosis in HeLa GSDME cells, LDH release was measured 16 h after cells were treated with 100 ng/ml TRAIL. For YT-induced pyroptosis in HeLa GSDME, LDH release was measured 4 h after treatment (E:T ratio = 2:1). For PFN/GzmB-induced pyroptosis in SH-SY5Y cells, LDH was measured 1 h after treatment in GSDME KO cells or 2 h post treatment in the presence of caspase inhibitors.
Overall cell death due to pyroptosis or apoptosis was measured at the same time as LDH release. To measure overall cell death in raptinal-treated B16 cells, samples were stained with APC-conjugated Annexin V (Invitrogen) and PI (Sigma) according to the manufacturer’s instructions and analyzed by BD FACSCanto II (BD Biosciences) using FlowJo V.10 (TreeStar) software. Cell death was determined by counting annexin V and/or PI positive cells. To measure overall cell death in HeLa or SH-SY5Y, cell viability was assessed by measuring ATP levels using CellTiter-Glo kit (Promega). The untreated cells were considered as an 100% viability control and cell death was inferred as the reduction in viable cells.
Overall cell death due to pyroptosis or apoptosis was measured at the same time as LDH release. To measure overall cell death in raptinal-treated B16 cells, samples were stained with APC-conjugated Annexin V (Invitrogen) and PI (Sigma) according to the manufacturer’s instructions and analyzed by BD FACSCanto II (BD Biosciences) using FlowJo V.10 (TreeStar) software. Cell death was determined by counting annexin V and/or PI positive cells. To measure overall cell death in HeLa or SH-SY5Y, cell viability was assessed by measuring ATP levels using CellTiter-Glo kit (Promega). The untreated cells were considered as an 100% viability control and cell death was inferred as the reduction in viable cells.
Aftercare
Annexin A5
Apoptosis
Biological Assay
Calcium Phosphates
Caspase Inhibitors
Cell Death
Cells
Cell Survival
Culture Media
Cytotoxin
GZMB protein, human
HeLa Cells
Immunoblotting
Microscopy
Promega
Proteins
Pyroptosis
raptinal
Tissue, Membrane
TNFSF10 protein, human
Transfection
Most recents protocols related to «Pyroptosis»
Subsequently, we used the Tumor Immune Estimation Resource (TIMER, https://cistrome.shinyapps.io/timer/ ), a web portal for comprehensive analysis of tumor-infiltrating immune cells, to analyze the association between prognostic PRGs and immune infiltration. The correlation between pyroptosis-related prognostic genes and the level of immune infiltration in ACC can be visually shown by the “Gene” module of TIMER. Spearman’s correlation analysis was performed for TMB and MSI analysis to calculate the correlation between gene expression and TMB and MSI scores. Results with a p-value less than 0.05 was considered statistically significant.
Cells
Gene Expression
Gene Modules
Genes
Hepatocyte
Neoplasms
Neoplasms, Liver
Pyroptosis
To assess GSDMD-driven pyroptotic cell death, cells were lipotransfected with a plasmid expressing mNeoGreen-GSDMD, a gift from Dr. Derek W. Abbott (Case Western Reserve University School of Medicine, Cleveland, OH). Cells were seeded in m-Slide 8-well chambered coverslips treated with ibiTreat (Ibidi, 80826) to 60%–70% of confluence. Transfections were conducted using Lipofectamine 3000 (Thermo Fisher Sci., L3000) in opti-MEM medium. Forty hours after transfection, cells were exposed to the corresponding treatment and imaged. In each experiment, 2–3 fields/condition were selected for time-lapse imaging using an Andor Dragonfly spinning disk confocal microscope (Andor Technology, Oxford Instruments) equipped with a Zyla 4.2 PLUS sCMOS camera. Cells were incubated in a chamber with a 5% CO2 atmosphere at 37 °C throughout the experiment. Fluorescence images were acquired at regular intervals of 20 min, with the use of a 60 × /0.17 MI-oil plan fluor objective. Image acquisition started at the moment of stimulation. Cells were imaged for 8 h. Mock-treated cells were followed in parallel to ensure that imaging and staining procedures were not cytotoxic. Representative images and movies were extracted and edited using ImageJ software [34 (link)].
Anisoptera
Atmosphere
Cells
Fluorescence
Lipofectamine
Microscopy, Confocal
Plasmids
Pyroptosis
Transfection
To assess GSDMD-driven pyroptotic cell death, cells were lipotransfected with a plasmid expressing mNeoGreen-GSDMD, a gift from Dr. Derek W. Abbott (Case Western Reserve University School of Medicine, Cleveland, OH). Cells were seeded in m-Slide 8-well chambered coverslips treated with ibiTreat (Ibidi, 80826) to 60%–70% of confluence. Transfections were conducted using Lipofectamine 3000 (Thermo Fisher Sci., L3000) in opti-MEM medium. Forty hours after transfection, cells were exposed to the corresponding treatment and imaged. In each experiment, 2–3 fields/condition were selected for time-lapse imaging using an Andor Dragonfly spinning disk confocal microscope (Andor Technology, Oxford Instruments) equipped with a Zyla 4.2 PLUS sCMOS camera. Cells were incubated in a chamber with a 5% CO2 atmosphere at 37 °C throughout the experiment. Fluorescence images were acquired at regular intervals of 20 min, with the use of a 60 × /0.17 MI-oil plan fluor objective. Image acquisition started at the moment of stimulation. Cells were imaged for 8 h. Mock-treated cells were followed in parallel to ensure that imaging and staining procedures were not cytotoxic. Representative images and movies were extracted and edited using ImageJ software [34 (link)].
Anisoptera
Atmosphere
Cells
Fluorescence
Lipofectamine
Microscopy, Confocal
Plasmids
Pyroptosis
Transfection
By using the expression profiles and survival data of ATF/CREB genes, the full TCGA set was employed as the training dataset and the full ICGC set as the test dataset. The ATF/CREB family genes model was developed using the training dataset and validated using the full and test datasets. The Lasso and Cox regression (“glmnet” and “survival” packages) were employed to examine the link between pyroptosis-related genes and overall survival rate. The Lasso model was developed using cross-validation to ensure reliability. By applying the penalty parameter (λ), we identified six genes that were associated with survival and used them to construct a multivariate Cox regression model. Using a forward-backward Cox regression technique, the optimal set of genes was chosen and used to predict survival. Kaplan-Meier (KM) analysis was conducted to generate survival curves for both the training and testing sets. The risk score was computed using the following equation.
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$${\rm{Risks}}\ {\rm{core}}\,{\rm{=}}\,\mathop \sum \limits_{{\rm{i=1}}}^{\rm{n}} {\rm{coefi\times{Xi}}}$$
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$${\rm{Risks}}\ {\rm{core}}\,{\rm{=}}\,\mathop \sum \limits_{{\rm{i=1}}}^{\rm{n}} {\rm{coefi\times{Xi}}}$$
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Genes
Pyroptosis
Following the manufacturer’s instructions, alveolar macrophage pyroptosis was detected by the FAM-FLICA Caspase-1 Detection Kit (Immunochemistry Technologies, Minnesota, USA). The cells were gently collected and cocultured with the caspase-1 fluorescent probe in the dark at 37 ℃ for 1 h. Washing with 1X apoptosis wash buffer for removing from unbound FLICA in cells. Then, the nucleus was counterstained with Hoechst 33,342 and PI sequentially. The morphology of pyroptotic AM was identified by microscopy and analyzed with ZEN 3.1 software (Carl Zeiss).
Apoptosis
Buffers
Caspase 1
Cell Nucleus
Cells
Fluorescent Probes
Macrophages, Alveolar
Microscopy
Pyroptosis
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The CytoTox 96 Non-Radioactive Cytotoxicity Assay kit is a colorimetric assay designed to quantify cytotoxicity by measuring the release of lactate dehydrogenase (LDH) from damaged cells. The assay provides a simple, reproducible method for determining cytotoxicity in a variety of cell types.
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More about "Pyroptosis"
Pyroptosis is a form of programmed cell death characterized by rapid cell lysis and the release of inflammatory cellular contents.
This process is triggered by the activation of inflammatory caspases, such as caspase-1, which cleave the pore-forming protein gasdermin D.
Pyroptosis is a key mechanism in host defense against pathogens and can also contribute to the pathogenesis of certain diseases.
Understading the mechanisms and regulatoin of pyroptosis is a critical area of research.
Researchers can leverage AI-driven platforms like PubCompare.ai to optimize their work by efficiently locating relevant protocols from the literature, preprints, and patents.
PubCompare.ai's advanced AI comparisons help identify the best protocols and products to enhance reproducibility and accuracy in pyroptosis research.
Pyroptosis is closely linked to other cellular processes, such as those involving lipopolysaccharide (LPS), fetal bovine serum (FBS), and ATP.
Techniques like flow cytometry using FACSCalibur or FACSCanto II instruments, as well as assays like the CytoTox 96 Non-Radioactive Cytotoxicity Assay, can be used to study pyroptosis.
The FAM-FLICA Caspase-1 Assay Kit and propidium iodide staining are also common tools in this field of research.
By understanding the complex mechanisms and regulation of pyroptosis, researchers can develop new therapies and interventions to address diseases where this process plays a role, such as infectious diseases, autoimmune disorders, and neurodegenerative conditions.
Leveraging AI-powered platforms and advanced experimental techniques can help drive progress in this important area of biomedical research.
This process is triggered by the activation of inflammatory caspases, such as caspase-1, which cleave the pore-forming protein gasdermin D.
Pyroptosis is a key mechanism in host defense against pathogens and can also contribute to the pathogenesis of certain diseases.
Understading the mechanisms and regulatoin of pyroptosis is a critical area of research.
Researchers can leverage AI-driven platforms like PubCompare.ai to optimize their work by efficiently locating relevant protocols from the literature, preprints, and patents.
PubCompare.ai's advanced AI comparisons help identify the best protocols and products to enhance reproducibility and accuracy in pyroptosis research.
Pyroptosis is closely linked to other cellular processes, such as those involving lipopolysaccharide (LPS), fetal bovine serum (FBS), and ATP.
Techniques like flow cytometry using FACSCalibur or FACSCanto II instruments, as well as assays like the CytoTox 96 Non-Radioactive Cytotoxicity Assay, can be used to study pyroptosis.
The FAM-FLICA Caspase-1 Assay Kit and propidium iodide staining are also common tools in this field of research.
By understanding the complex mechanisms and regulation of pyroptosis, researchers can develop new therapies and interventions to address diseases where this process plays a role, such as infectious diseases, autoimmune disorders, and neurodegenerative conditions.
Leveraging AI-powered platforms and advanced experimental techniques can help drive progress in this important area of biomedical research.