This review article discusses mTOR inhibitors and their use in cancer and transplantation. It outlines the mTOR signaling pathway and how mTOR inhibitors like sirolimus, everolimus and temsirolimus work. It describes how mTOR inhibitors are used to prevent organ rejection after transplantation. It also discusses how dysregulation of the PI3K/Akt/mTOR pathway promotes cancer and how mTOR inhibitors have shown efficacy in renal cell carcinoma and mantle cell lymphoma. The article concludes that biomarkers are needed to identify cancers sensitive to mTOR inhibition and that combination targeted therapies may help overcome resistance.
1. Receptor tyrosine kinases (RTKs) drive key cancer pathways and can be exploited as therapeutic targets, as shown by drugs like imatinib that inhibit mutated kinases in cancers.
2. RTK inhibitors have shown efficacy against cancers dependent on single kinases, but resistance often emerges through secondary mutations or bypass pathways.
3. Effective combination therapies are needed to overcome resistance, such as combining RTK inhibitors with other drugs that block downstream or bypass pathways.
The PTEN and PI3-Kinase Pathway in Cancer pptBernard Bahaah
The document presents information on PTEN and the PI3-kinase pathway in cancer. It discusses how PTEN acts as a tumor suppressor by negatively regulating the PI3-kinase pathway, which promotes cell growth and survival. Mutations or deletions of the PTEN gene are common in many cancer types as they lead to overactivation of the PI3-kinase pathway. The document outlines the signaling events in the PI3-kinase pathway, how PTEN regulates it, additional functions of PTEN, and potential cancer therapeutics that target this pathway.
The PI3K-Akt-mTOR pathway is an intracellular signal transduction pathway that promotes metabolism, proliferation, cell survival, growth and angiogenesis. Key components include receptor tyrosine kinases, PI3K, PIP2, PIP3, and Akt. Akt is activated by phosphorylation and regulates various proteins involved in functions like cell growth. Dysregulation of this pathway can lead to cancer due to abnormal cell proliferation and is associated with neurodevelopmental disorders.
study of EGFR protein expression and mutation premvarma064
This document discusses oral squamous cell carcinoma (OSCC), which represents 90% of oral cancers and is characterized by a poor prognosis and lower survival rate. It notes that 0.7 million new cases and 0.3 million deaths occur annually from OSCC globally. In India, approximately 30-40% of all cancer cases are oral cancers, which is much higher than in Western countries. Risk factors for oral cancer include smoking, tobacco use, HPV infection, oral submucous fibrosis, and certain other conditions. The document discusses using immunohistochemistry to examine EGFR expression levels in oral cancer tissue samples and using PCR and restriction enzyme digestion to analyze for EGFR mutations, which can indicate prognosis and treatment options.
This document discusses tyrosine kinases, which are enzymes that transfer phosphate groups and act as on-off switches in cellular functions. Tyrosine kinases are implicated in cancer development and progression. The document describes the structural classification, general characteristics, and mechanism of action of tyrosine kinases. It also discusses kinetic studies of tyrosine kinases like Bruton's tyrosine kinase and applications of tyrosine kinase inhibitors in cancer therapy and other diseases.
This review article discusses mTOR inhibitors and their use in cancer and transplantation. It outlines the mTOR signaling pathway and how mTOR inhibitors like sirolimus, everolimus and temsirolimus work. It describes how mTOR inhibitors are used to prevent organ rejection after transplantation. It also discusses how dysregulation of the PI3K/Akt/mTOR pathway promotes cancer and how mTOR inhibitors have shown efficacy in renal cell carcinoma and mantle cell lymphoma. The article concludes that biomarkers are needed to identify cancers sensitive to mTOR inhibition and that combination targeted therapies may help overcome resistance.
1. Receptor tyrosine kinases (RTKs) drive key cancer pathways and can be exploited as therapeutic targets, as shown by drugs like imatinib that inhibit mutated kinases in cancers.
2. RTK inhibitors have shown efficacy against cancers dependent on single kinases, but resistance often emerges through secondary mutations or bypass pathways.
3. Effective combination therapies are needed to overcome resistance, such as combining RTK inhibitors with other drugs that block downstream or bypass pathways.
The PTEN and PI3-Kinase Pathway in Cancer pptBernard Bahaah
The document presents information on PTEN and the PI3-kinase pathway in cancer. It discusses how PTEN acts as a tumor suppressor by negatively regulating the PI3-kinase pathway, which promotes cell growth and survival. Mutations or deletions of the PTEN gene are common in many cancer types as they lead to overactivation of the PI3-kinase pathway. The document outlines the signaling events in the PI3-kinase pathway, how PTEN regulates it, additional functions of PTEN, and potential cancer therapeutics that target this pathway.
The PI3K-Akt-mTOR pathway is an intracellular signal transduction pathway that promotes metabolism, proliferation, cell survival, growth and angiogenesis. Key components include receptor tyrosine kinases, PI3K, PIP2, PIP3, and Akt. Akt is activated by phosphorylation and regulates various proteins involved in functions like cell growth. Dysregulation of this pathway can lead to cancer due to abnormal cell proliferation and is associated with neurodevelopmental disorders.
study of EGFR protein expression and mutation premvarma064
This document discusses oral squamous cell carcinoma (OSCC), which represents 90% of oral cancers and is characterized by a poor prognosis and lower survival rate. It notes that 0.7 million new cases and 0.3 million deaths occur annually from OSCC globally. In India, approximately 30-40% of all cancer cases are oral cancers, which is much higher than in Western countries. Risk factors for oral cancer include smoking, tobacco use, HPV infection, oral submucous fibrosis, and certain other conditions. The document discusses using immunohistochemistry to examine EGFR expression levels in oral cancer tissue samples and using PCR and restriction enzyme digestion to analyze for EGFR mutations, which can indicate prognosis and treatment options.
This document discusses tyrosine kinases, which are enzymes that transfer phosphate groups and act as on-off switches in cellular functions. Tyrosine kinases are implicated in cancer development and progression. The document describes the structural classification, general characteristics, and mechanism of action of tyrosine kinases. It also discusses kinetic studies of tyrosine kinases like Bruton's tyrosine kinase and applications of tyrosine kinase inhibitors in cancer therapy and other diseases.
Strong reversal of the lung fibrosis disease signature by autotaxin inhibitor...Maté Ongenaert
Strong reversal of the lung fibrosis disease signature by autotaxin inhibitor GLPG1690 in a mouse model for IPF
Maté Ongenaert (Mechelen, Belgium), Maté Ongenaert, Sonia Dupont, Roland Blanqué, Reginald Brys, Ellen van der Aar, Bertrand Heckmann
ERS - European Respiratory Society International Congress 2016. Session: Therapeutic horizons: novel targets and pharmacological models
Background and objectives
GLPG1690 is a novel potent autotaxin (ATX) inhibitor shown to be efficacious in the mouse bleomycin (BLM) lung fibrosis model. Here, we analyze the impact of GLPG1690 on the gene expression signature in mouse fibrotic lung tissue.
Methods
Lung fibrosis was induced by intranasal administration of BLM. Animals were treated with GLPG1690 or vehicle.Whole superior right lung was used for RNA extraction. Full transcriptome analysis was performed using the Agilent SurePrint G3 mouse chip. Analysis was performed using empirical Bayes methods and linear models. Public human IPF expression data were re-analyzed.
Results
GLPG1690 strongly reduced lung fibrosis as shown by reduction of Ashcroft scores and collagen content. Microarray analysis of the lungs revealed that GLPG1690 strongly reversed the impact of gene expression caused by BLM (367 out of the 2375 probes). As GLPG1690 treatment affects 395 probes, this treatment effect is highly relevant in the model. Gene clusters affected by BLM treatment and reverted by GLPG1690 are related to extracellular matrix (such as Tnc and Spp1), collagen (Col3a1) and cytokines/chemokines (Cxcl12). Several of the affected genes are known to be involved in the development or progression of lung fibrosis in IPF patients.
Conclusions
These data provide further mechanistic understanding of the efficacy of ATX inhibition in a pre-clinical lung fibrosis model, highlighting a role for extracellular matrix and inflammation biology. These data strongly suggest that GLPG1690 may be beneficial in treating IPF patients and support its evaluation in a clinical study
Epidermal growth factor and its receptor tyrosine kinaseGedion Yilma
The document discusses epidermal growth factor (EGF) signaling and the EGF receptor. It notes that EGF is involved in normal cell processes like development, differentiation, and wound healing. The EGF receptor belongs to the ErbB family of receptor tyrosine kinases and plays a key role in signaling pathways regulating cell proliferation, survival, and apoptosis. Overexpression or abnormal activation of the EGF receptor and other ErbB family members is implicated in many epithelial cancers.
Inhibition of the mtorc pathway in the antiphospholipidSaris Arango
The document discusses the mTOR pathway and its relationship to the antiphospholipid syndrome. It provides background on mTOR and its role in regulating cell growth. Studies have shown that in patients with the antiphospholipid syndrome, IgG antibodies activate the mTOR pathway through PI3K-AKT signaling in endothelial cells. Inhibition of the mTOR pathway may help prevent complications in these patients such as thrombosis and graft loss after kidney transplantation. The document reviews several studies that demonstrate activation of mTOR and how it contributes to conditions common in antiphospholipid syndrome.
Tyrosine kinases are enzymes that transfer phosphate groups from ATP to tyrosine residues on proteins. There are two main families of tyrosine kinases: receptor tyrosine kinases and non-receptor tyrosine kinases. Receptor tyrosine kinases are transmembrane receptors that transmit extracellular signals to intracellular pathways. Examples include receptors for epidermal growth factor, insulin, fibroblast growth factors, platelet-derived growth factor, nerve growth factor, ephrins, and vascular endothelial growth factor.
- The document discusses the role of miRNAs in diabetes, focusing on miRNA-375. It states that miRNA-375 negatively regulates glucose stimulated insulin secretion and that inhibiting it leads to increased insulin secretion while overexpression leads to decreased secretion.
- It also mentions several other miRNAs - miR-9, miR-96, miR-124a - that regulate insulin secretion and discusses how their functions relate to diabetes. Additionally, it discusses how hyperglycemia and inflammatory cytokines influence miRNA expression and how specific miRNAs like miR-30d, miR-15a, and miR-335 impact insulin production and secretion.
- The role of miRNAs in insulin target tissues like the liver and heart is also covered, focusing on miR-122,
Metabolic investigation of segmental overgrowth: new insights in pathogenic m...BiologInc
This document summarizes a study investigating the metabolic mechanisms underlying segmental overgrowth disorders and potential treatments. The study found that mutations in the PI3K-AKT pathway, such as in PIK3CA and AKT1, lead to increased cell proliferation and metabolism. Functional studies showed that cell lines with PIK3CA mutations had increased AKT phosphorylation and responded strongly to growth factors, while AKT1 mutant cell lines responded less. Treatment with PI3K or mTOR inhibitors normalized the metabolic profile in both AKT1 and PIK3CA mutant cell lines, suggesting these may be effective treatments. The study provides new insights into the molecular mechanisms and potential targeted therapies for segmental overgrowth disorders.
Epidermal growth factor (EGF) is a protein that binds to EGF receptors on epithelial and epidermal cells and initiates the EGF signaling pathway. When EGF binds to EGF receptors, it causes them to dimerize and activate their tyrosine kinase activity, leading to phosphorylation and activation of downstream proteins in the MAPK pathway. Mutations that cause constitutive activation of this pathway can lead to uncontrolled cell growth and cancer. Potential cancer treatments discussed include RGD-based peptides that target the αvβ3 integrin receptor involved in angiogenesis, and a conjugate of low molecular weight heparin and suramin that may inhibit tumor growth by blocking vascular endothelial growth factor (VEGF).
This document discusses signal transduction and how it relates to cancer. It describes how growth factors and receptors contribute to normal signal transduction and how this process is deregulated in cancer. It explains that growth factors regulate growth, proliferation and survival, which are all altered in cancer. Several growth factors and receptors that can contribute to oncogenesis are identified. It also summarizes several key intracellular signaling pathways, like MAPK pathways, that are activated by growth factors and can result in the cancer phenotype if altered.
Primary Human Cell Systems Analysis of Drug MechanismsBioMAP® Systems
The document summarizes a presentation about using BioMAP human cell systems to analyze the mechanisms of drug compounds, including PPAR agonists. It describes how BioMAP uses primary human cells in disease-like conditions to generate quantitative readouts that can discriminate between clinical compounds. Profiling of PPAR agonists using BioMAP revealed both shared and unique anti-inflammatory, tissue remodeling, and prostaglandin pathway effects. Differential activities suggested priorities for therapeutic areas and potential side effects.
URECA poster - Sara Supriyatno & Regina ZambranoRegina Zambrano
TRAF4 is a member of the TRAF protein family that regulates signaling pathways involved in development. This study investigated the role of TRAF4 in BMP signaling and ectodermal differentiation during Xenopus laevis embryonic development. The results showed that knockdown of TRAF4 decreased epidermal marker expression and BMP signaling, while increasing expression of the early neural marker SOX2. However, late neural markers were unaffected, suggesting TRAF4 promotes early neural differentiation but not terminal neural differentiation. These findings indicate TRAF4 positively regulates BMP signaling to promote epidermal fate specification in the ectoderm.
The experiment aimed to isolate the focal adhesion kinase (FAK) promoter from human genomic DNA and ligate it upstream of the thiaminase gene in the pTRE3G-Thiaminase vector. The FAK promoter was amplified using PCR and ligated into the pGEM T Easy Vector. Both the FAK promoter and pTRE3G-Thiaminase vector were then digested with restriction enzymes before ligating the FAK promoter into the linearized vector. However, self-ligation of the empty vector occurred instead of successful ligation and insertion of the FAK promoter.
TRISTETRAPROLIN - its role in inflammation and cancerHimadri Nath
1. Tristetraprolin (TTP) is a protein that binds to AU-rich elements in the 3' untranslated regions of mRNAs involved in inflammation. This binding recruits deadenylase complexes that shorten the mRNA poly-A tails and trigger degradation.
2. During inflammation, TTP expression is induced to degrade inflammatory mRNAs like TNF-α and IL-8, terminating the inflammatory response. TTP expression is regulated by phosphorylation and dephosphorylation mediated by p38 MAPK and PP2A phosphatase respectively.
3. Loss of TTP expression contributes to cancer by stabilizing mRNAs of pro-inflammatory and pro-angiogenic factors like VEGF. Inducing TTP
Cellular Signaling Pathways have direct implications on our understanding of tumor cell behavior. A general overview is presented here followed by a brief discussion of some of the major pathways currently implicated in cancer progression : Ras/RAF/MAP kinase pathway and PI3K/AKT/mTOR pathway s
The document discusses the role of the target of rapamycin (TOR) pathway in aging and disease. Specifically:
1. The TOR pathway senses nutrients and growth factors and regulates processes involved in growth and homeostasis. In mammals, TOR forms two complexes, mTORC1 and mTORC2, that regulate cellular processes implicated in age-related diseases.
2. Inhibition of mTORC1 by rapamycin extends lifespan in model organisms and may mitigate aging-related diseases in humans by reducing inflammation and restoring stem cell function.
3. mTORC1 acts as a sensor of nutrient availability and growth factors early in life to promote growth, but its activity later in life may contribute to disease; rap
This is the Powerpoint presentation from my recent presentation at the TTP LabTech US Acumen Users Group Meeting (UGM) held at the British Consulate-General in Cambridge, MA on May 18, 2010
PRESENTATION ON JANUS KINASE INHIBITORS IN TREATMENT OF MPN'SSamaira Mujeeb
The document discusses Janus kinase 2 (JAK2) inhibitors as a potential treatment for myeloproliferative diseases. It describes how the discovery of activating JAK2 mutations in patients with myeloproliferative neoplasms led pharmaceutical companies to develop JAK2 selective inhibitors. JAK2 inhibitors effectively reduce JAK2 phosphorylation of STAT5 and cell survival in JAK2 activated cells. Patients treated with JAK2 inhibitors experience reductions in spleen size and improvements in symptoms. The document examines different scaffolds that have been used to develop JAK2 inhibitors and some inhibitors currently in clinical trials, such as CEP-701 and AZD1480.
EGCG, a component of green tea, was investigated for its effects on epigenetic regulation of the RNA polymerase III subunit Brf2 in lung cancer cells. Treatment of lung cancer cells with EGCG or green tea for 24 hours showed no change in methylation of the Brf2 promoter region or significant change in cell proliferation, respectively. Restriction digestion and PCR analysis indicated EGCG did not alter methylation of the Brf2 promoter. Preliminary data also showed green tea treatment did not significantly affect cancer cell growth over 24 hours.
This document discusses tyrosine kinase inhibitors (TKIs), a class of targeted cancer drugs. It begins by introducing protein kinases and their role in cell signaling. There are two main categories of protein kinases - those that phosphorylate tyrosine residues and those that phosphorylate serine and threonine residues. Tyrosine kinases function as on/off switches in many cellular functions by adding phosphate groups to tyrosine residues on proteins. The document then discusses the different types of tyrosine kinases and how they can become mutated and cause unregulated cell growth leading to cancer. It describes targeted therapy and TKIs as targeted drugs that block specific molecules needed for tumor growth. The final sections provide examples of approved TKIs
This document discusses the role of the Wnt signaling pathway in cancer. It begins by describing how the Wnt pathway is normally regulated and how dysregulation can lead to cancer. It then summarizes key points about how the Wnt pathway is altered in cancer at the membrane, cytoplasmic, and nuclear levels. Mutations in genes that encode proteins in the Wnt pathway, such as APC, Axin, and β-catenin, have been implicated in various cancers like colorectal cancer. Understanding how the Wnt pathway is involved in cancer is important for developing new cancer therapeutics.
This report analyzes differential RNA methylation between wild type and FTO knockout mouse midbrain cell lines using MeRIP-Seq data. The study found that FTO targets m6A sites mainly around stop codons and in coding sequences. Differential expression analysis found no significant changes, indicating FTO may not regulate gene expression levels. Gene ontology analysis revealed FTO could regulate mRNAs related to neuronal signal transduction. The study developed an interactive web application using Shiny to allow custom analysis of the data.
Strong reversal of the lung fibrosis disease signature by autotaxin inhibitor...Maté Ongenaert
Strong reversal of the lung fibrosis disease signature by autotaxin inhibitor GLPG1690 in a mouse model for IPF
Maté Ongenaert (Mechelen, Belgium), Maté Ongenaert, Sonia Dupont, Roland Blanqué, Reginald Brys, Ellen van der Aar, Bertrand Heckmann
ERS - European Respiratory Society International Congress 2016. Session: Therapeutic horizons: novel targets and pharmacological models
Background and objectives
GLPG1690 is a novel potent autotaxin (ATX) inhibitor shown to be efficacious in the mouse bleomycin (BLM) lung fibrosis model. Here, we analyze the impact of GLPG1690 on the gene expression signature in mouse fibrotic lung tissue.
Methods
Lung fibrosis was induced by intranasal administration of BLM. Animals were treated with GLPG1690 or vehicle.Whole superior right lung was used for RNA extraction. Full transcriptome analysis was performed using the Agilent SurePrint G3 mouse chip. Analysis was performed using empirical Bayes methods and linear models. Public human IPF expression data were re-analyzed.
Results
GLPG1690 strongly reduced lung fibrosis as shown by reduction of Ashcroft scores and collagen content. Microarray analysis of the lungs revealed that GLPG1690 strongly reversed the impact of gene expression caused by BLM (367 out of the 2375 probes). As GLPG1690 treatment affects 395 probes, this treatment effect is highly relevant in the model. Gene clusters affected by BLM treatment and reverted by GLPG1690 are related to extracellular matrix (such as Tnc and Spp1), collagen (Col3a1) and cytokines/chemokines (Cxcl12). Several of the affected genes are known to be involved in the development or progression of lung fibrosis in IPF patients.
Conclusions
These data provide further mechanistic understanding of the efficacy of ATX inhibition in a pre-clinical lung fibrosis model, highlighting a role for extracellular matrix and inflammation biology. These data strongly suggest that GLPG1690 may be beneficial in treating IPF patients and support its evaluation in a clinical study
Epidermal growth factor and its receptor tyrosine kinaseGedion Yilma
The document discusses epidermal growth factor (EGF) signaling and the EGF receptor. It notes that EGF is involved in normal cell processes like development, differentiation, and wound healing. The EGF receptor belongs to the ErbB family of receptor tyrosine kinases and plays a key role in signaling pathways regulating cell proliferation, survival, and apoptosis. Overexpression or abnormal activation of the EGF receptor and other ErbB family members is implicated in many epithelial cancers.
Inhibition of the mtorc pathway in the antiphospholipidSaris Arango
The document discusses the mTOR pathway and its relationship to the antiphospholipid syndrome. It provides background on mTOR and its role in regulating cell growth. Studies have shown that in patients with the antiphospholipid syndrome, IgG antibodies activate the mTOR pathway through PI3K-AKT signaling in endothelial cells. Inhibition of the mTOR pathway may help prevent complications in these patients such as thrombosis and graft loss after kidney transplantation. The document reviews several studies that demonstrate activation of mTOR and how it contributes to conditions common in antiphospholipid syndrome.
Tyrosine kinases are enzymes that transfer phosphate groups from ATP to tyrosine residues on proteins. There are two main families of tyrosine kinases: receptor tyrosine kinases and non-receptor tyrosine kinases. Receptor tyrosine kinases are transmembrane receptors that transmit extracellular signals to intracellular pathways. Examples include receptors for epidermal growth factor, insulin, fibroblast growth factors, platelet-derived growth factor, nerve growth factor, ephrins, and vascular endothelial growth factor.
- The document discusses the role of miRNAs in diabetes, focusing on miRNA-375. It states that miRNA-375 negatively regulates glucose stimulated insulin secretion and that inhibiting it leads to increased insulin secretion while overexpression leads to decreased secretion.
- It also mentions several other miRNAs - miR-9, miR-96, miR-124a - that regulate insulin secretion and discusses how their functions relate to diabetes. Additionally, it discusses how hyperglycemia and inflammatory cytokines influence miRNA expression and how specific miRNAs like miR-30d, miR-15a, and miR-335 impact insulin production and secretion.
- The role of miRNAs in insulin target tissues like the liver and heart is also covered, focusing on miR-122,
Metabolic investigation of segmental overgrowth: new insights in pathogenic m...BiologInc
This document summarizes a study investigating the metabolic mechanisms underlying segmental overgrowth disorders and potential treatments. The study found that mutations in the PI3K-AKT pathway, such as in PIK3CA and AKT1, lead to increased cell proliferation and metabolism. Functional studies showed that cell lines with PIK3CA mutations had increased AKT phosphorylation and responded strongly to growth factors, while AKT1 mutant cell lines responded less. Treatment with PI3K or mTOR inhibitors normalized the metabolic profile in both AKT1 and PIK3CA mutant cell lines, suggesting these may be effective treatments. The study provides new insights into the molecular mechanisms and potential targeted therapies for segmental overgrowth disorders.
Epidermal growth factor (EGF) is a protein that binds to EGF receptors on epithelial and epidermal cells and initiates the EGF signaling pathway. When EGF binds to EGF receptors, it causes them to dimerize and activate their tyrosine kinase activity, leading to phosphorylation and activation of downstream proteins in the MAPK pathway. Mutations that cause constitutive activation of this pathway can lead to uncontrolled cell growth and cancer. Potential cancer treatments discussed include RGD-based peptides that target the αvβ3 integrin receptor involved in angiogenesis, and a conjugate of low molecular weight heparin and suramin that may inhibit tumor growth by blocking vascular endothelial growth factor (VEGF).
This document discusses signal transduction and how it relates to cancer. It describes how growth factors and receptors contribute to normal signal transduction and how this process is deregulated in cancer. It explains that growth factors regulate growth, proliferation and survival, which are all altered in cancer. Several growth factors and receptors that can contribute to oncogenesis are identified. It also summarizes several key intracellular signaling pathways, like MAPK pathways, that are activated by growth factors and can result in the cancer phenotype if altered.
Primary Human Cell Systems Analysis of Drug MechanismsBioMAP® Systems
The document summarizes a presentation about using BioMAP human cell systems to analyze the mechanisms of drug compounds, including PPAR agonists. It describes how BioMAP uses primary human cells in disease-like conditions to generate quantitative readouts that can discriminate between clinical compounds. Profiling of PPAR agonists using BioMAP revealed both shared and unique anti-inflammatory, tissue remodeling, and prostaglandin pathway effects. Differential activities suggested priorities for therapeutic areas and potential side effects.
URECA poster - Sara Supriyatno & Regina ZambranoRegina Zambrano
TRAF4 is a member of the TRAF protein family that regulates signaling pathways involved in development. This study investigated the role of TRAF4 in BMP signaling and ectodermal differentiation during Xenopus laevis embryonic development. The results showed that knockdown of TRAF4 decreased epidermal marker expression and BMP signaling, while increasing expression of the early neural marker SOX2. However, late neural markers were unaffected, suggesting TRAF4 promotes early neural differentiation but not terminal neural differentiation. These findings indicate TRAF4 positively regulates BMP signaling to promote epidermal fate specification in the ectoderm.
The experiment aimed to isolate the focal adhesion kinase (FAK) promoter from human genomic DNA and ligate it upstream of the thiaminase gene in the pTRE3G-Thiaminase vector. The FAK promoter was amplified using PCR and ligated into the pGEM T Easy Vector. Both the FAK promoter and pTRE3G-Thiaminase vector were then digested with restriction enzymes before ligating the FAK promoter into the linearized vector. However, self-ligation of the empty vector occurred instead of successful ligation and insertion of the FAK promoter.
TRISTETRAPROLIN - its role in inflammation and cancerHimadri Nath
1. Tristetraprolin (TTP) is a protein that binds to AU-rich elements in the 3' untranslated regions of mRNAs involved in inflammation. This binding recruits deadenylase complexes that shorten the mRNA poly-A tails and trigger degradation.
2. During inflammation, TTP expression is induced to degrade inflammatory mRNAs like TNF-α and IL-8, terminating the inflammatory response. TTP expression is regulated by phosphorylation and dephosphorylation mediated by p38 MAPK and PP2A phosphatase respectively.
3. Loss of TTP expression contributes to cancer by stabilizing mRNAs of pro-inflammatory and pro-angiogenic factors like VEGF. Inducing TTP
Cellular Signaling Pathways have direct implications on our understanding of tumor cell behavior. A general overview is presented here followed by a brief discussion of some of the major pathways currently implicated in cancer progression : Ras/RAF/MAP kinase pathway and PI3K/AKT/mTOR pathway s
The document discusses the role of the target of rapamycin (TOR) pathway in aging and disease. Specifically:
1. The TOR pathway senses nutrients and growth factors and regulates processes involved in growth and homeostasis. In mammals, TOR forms two complexes, mTORC1 and mTORC2, that regulate cellular processes implicated in age-related diseases.
2. Inhibition of mTORC1 by rapamycin extends lifespan in model organisms and may mitigate aging-related diseases in humans by reducing inflammation and restoring stem cell function.
3. mTORC1 acts as a sensor of nutrient availability and growth factors early in life to promote growth, but its activity later in life may contribute to disease; rap
This is the Powerpoint presentation from my recent presentation at the TTP LabTech US Acumen Users Group Meeting (UGM) held at the British Consulate-General in Cambridge, MA on May 18, 2010
PRESENTATION ON JANUS KINASE INHIBITORS IN TREATMENT OF MPN'SSamaira Mujeeb
The document discusses Janus kinase 2 (JAK2) inhibitors as a potential treatment for myeloproliferative diseases. It describes how the discovery of activating JAK2 mutations in patients with myeloproliferative neoplasms led pharmaceutical companies to develop JAK2 selective inhibitors. JAK2 inhibitors effectively reduce JAK2 phosphorylation of STAT5 and cell survival in JAK2 activated cells. Patients treated with JAK2 inhibitors experience reductions in spleen size and improvements in symptoms. The document examines different scaffolds that have been used to develop JAK2 inhibitors and some inhibitors currently in clinical trials, such as CEP-701 and AZD1480.
EGCG, a component of green tea, was investigated for its effects on epigenetic regulation of the RNA polymerase III subunit Brf2 in lung cancer cells. Treatment of lung cancer cells with EGCG or green tea for 24 hours showed no change in methylation of the Brf2 promoter region or significant change in cell proliferation, respectively. Restriction digestion and PCR analysis indicated EGCG did not alter methylation of the Brf2 promoter. Preliminary data also showed green tea treatment did not significantly affect cancer cell growth over 24 hours.
This document discusses tyrosine kinase inhibitors (TKIs), a class of targeted cancer drugs. It begins by introducing protein kinases and their role in cell signaling. There are two main categories of protein kinases - those that phosphorylate tyrosine residues and those that phosphorylate serine and threonine residues. Tyrosine kinases function as on/off switches in many cellular functions by adding phosphate groups to tyrosine residues on proteins. The document then discusses the different types of tyrosine kinases and how they can become mutated and cause unregulated cell growth leading to cancer. It describes targeted therapy and TKIs as targeted drugs that block specific molecules needed for tumor growth. The final sections provide examples of approved TKIs
This document discusses the role of the Wnt signaling pathway in cancer. It begins by describing how the Wnt pathway is normally regulated and how dysregulation can lead to cancer. It then summarizes key points about how the Wnt pathway is altered in cancer at the membrane, cytoplasmic, and nuclear levels. Mutations in genes that encode proteins in the Wnt pathway, such as APC, Axin, and β-catenin, have been implicated in various cancers like colorectal cancer. Understanding how the Wnt pathway is involved in cancer is important for developing new cancer therapeutics.
This report analyzes differential RNA methylation between wild type and FTO knockout mouse midbrain cell lines using MeRIP-Seq data. The study found that FTO targets m6A sites mainly around stop codons and in coding sequences. Differential expression analysis found no significant changes, indicating FTO may not regulate gene expression levels. Gene ontology analysis revealed FTO could regulate mRNAs related to neuronal signal transduction. The study developed an interactive web application using Shiny to allow custom analysis of the data.
RNA-Seq transcriptome analysis of Gonium pectorale cell cycle.Jennifer Shelton
This document summarizes Dr. Tara N. Marriage's RNA-Seq analysis of the cell cycle transcriptome in the multicellular alga Gonium pectorale. RNA was extracted from G. pectorale cells collected hourly across a 24 hour period and pooled into time points corresponding to different cell cycle phases. RNA-Seq libraries were constructed and sequenced, and the reads were mapped and analyzed for differential gene expression. Preliminary results identified over 2400 differentially expressed genes across the cell cycle and hierarchical clustering of expression profiles. Several key cell cycle genes were found to be differentially expressed during mitosis. The analysis is ongoing to further investigate cell cycle regulation and changes contributing to multicellularity in Gonium compared
Dr. William Herring - Genetic Influences on Robustness of Weaned PigsJohn Blue
Genetic Influences on Robustness of Weaned Pigs - Dr. William Herring, PIC, from the 2016 Allen D. Leman Swine Conference, September 17-20, 2016, St. Paul, Minnesota, USA.
More presentations at http://www.swinecast.com/2016-leman-swine-conference-material
Dr. Leah Dorman - Antibiotic Free (ABF), No Antibiotics Ever (NAE) - What’s I...John Blue
Antibiotic Free (ABF), No Antibiotics Ever (NAE) - What’s It to Me? - Dr. Leah Dorman, Director, Food Integrity & Consumer Engagement, Phibro Animal Health, from the 2016 NIAA Annual Conference: From Farm to Table - Food System Biosecurity for Animal Agriculture, April 4-7, 2016, Kansas City, MO, USA.
More presentations at http://www.trufflemedia.com/agmedia/conference/2016_niaa_farm_table_food_system_biosecurity
Dr. Albert Rovira - Diagnostic View of Porcine Epidemic Diarrhea VirusJohn Blue
Diagnostic View of Porcine Epidemic Diarrhea Virus - Dr. Albert Rovira, Assistant Clinical Professor, Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, from the 2013 Allen D. Leman Swine Conference, September 14-17, 2013, St. Paul, Minnesota, USA.
More presentations at http://www.swinecast.com/2013-leman-swine-conference-material
Dr. Tom Fangman - Comparison Of Nursery Pig Behavior Assessed Using Human Obs...John Blue
Comparison Of Nursery Pig Behavior Assessed Using Human Observation And Digital-Image Evaluation Methodologies - Dr. Tom Fangman, Boehringer Ingelheim Vetmedica, Inc., from the 2015 Allen D. Leman Swine Conference, September 19-22, 2015, St. Paul, Minnesota, USA.
More presentations at http://www.swinecast.com/2015-leman-swine-conference-material
Dr. Kent Schwartz - Understanding RotavirusJohn Blue
Understanding Rotavirus - Dr. Kent Schwartz, Iowa State University, from the 2016 Power Of The Past, Force Of The Future Customer Appreciation event, August 16, 2016, hosted by Rensselaer Swine Services and Bethany Swine Health Services, Jasper Country Fairgrounds, IN, USA.
More presentations at http://www.swinecast.com/2016-power-of-past-force-of-future-customer-appreciation
Pigs are raised commercially through various production methods including pasture and confinement units, with sows averaging 2 litters per year of around 10 piglets each. Proper nutrition, housing, disease prevention including vaccinations, and management from birth through market weight around 250 pounds are required for optimal health and productivity of the swine herd. Common diseases include respiratory illnesses, diarrhea in young pigs, reproductive issues, and infections requiring vaccination and sanitation to control spread.
Dr. Bradley Wolter, Dr. Aaron Gaines, Ms. Julie Berling - Growth Of A Pig Pro...John Blue
Growth Of A Pig Production Business: Consumer Challenges, Strategy, and Opportunities - Dr. Bradley Wolter, President, Dr. Aaron Gaines, VP, of Technology & Support Operation, and Julie Berling, Senior Director, Strategic Insights and Communications, The Maschhoffs, from the 2016 Allen D. Leman Swine Conference, September 17-20, 2016, St. Paul, Minnesota, USA.
More presentations at http://www.swinecast.com/2016-leman-swine-conference-material
Dr. Darin Madson - Porcine Epidemic Diarrhea Virus UpdateJohn Blue
Porcine Epidemic Diarrhea Virus Update - Dr. Darin Madson, Iowa State University, Veterinary Diagnostic Lab, from the 2013 Boehringer Ingelheim Swine Health Seminar, August 16-18, 2013, Wrightsville Beach, NC, USA.
More presentations at http://www.swinecast.com/2013-boehringer-ingelheim-carolina-swine-health-seminar
Factors Affecting the Productivity of Small RuminantsOsama Zahid
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
Dr. Elwynn Taylor - Weather Outlook 2016 & BeyondJohn Blue
The document provides an outlook on weather and commodity markets for 2016 and beyond. It discusses current corn and soybean market prices and expected price ranges. It also analyzes the impact of El Niño and La Niña conditions on weather patterns and agricultural yields in the Midwest. The author notes that climate risk in agriculture is expected to increase over the next 20 years and effective risk management will be important.
Dr. Jennie Brown - Weaning Sows Directly into Group Housing: Effects on Aggre...John Blue
Weaning Sows Directly into Group Housing: Effects on Aggression, Physiology and Productivity - Dr. Jennie Brown, from the 2016 Allen D. Leman Swine Conference, September 17-20, 2016, St. Paul, Minnesota, USA.
More presentations at http://www.swinecast.com/2016-leman-swine-conference-material
RNA-Seq Analysis of Blueberry Fruit Development and RipeningAnn Loraine
This document summarizes an RNA-Seq analysis of blueberry fruit development and ripening. Researchers sequenced RNA from five stages of fruit development to generate over 20 million reads per sample. Reads were aligned to the blueberry genome assembly to identify over 50,000 expressed genes and their expression profiles across stages. Analysis identified thousands of differentially expressed genes between stages and clusters of genes with similar expression patterns. Pathway analysis revealed metabolic pathways active during fruit development, including a potential new pathway for bixin biosynthesis with high expression during fruit maturation. Resources from the project include an online blueberry browser and gene expression data.
Slides for a discussion on a brief Nature comment on Bioinformatics Cores and an older Plos One perspective that covers suggested best practices for Bioinformatics Cores.
This document summarizes the process of lipolysis. Lipolysis is the breakdown of triglycerides stored in fat cells into fatty acids and glycerol. It occurs mainly in adipose tissue to release fatty acids for energy. Triglycerides are transported to tissues like adipose and muscle via lipoproteins. Hormones such as epinephrine activate hormone-sensitive lipase in adipose tissue to break down triglycerides into glycerol and fatty acids. Glycerol enters the bloodstream and is converted to glucose by the liver, while fatty acids bind to albumin for transport and are broken down in mitochondria to produce energy.
The document provides guidance on restraining various farm and domestic animals for examination or treatment. It discusses casting large animals onto their side by using ropes and sufficient labor. It also describes leg raising methods for restraining horses and basic knots. For smaller animals, it recommends reclining, stretching, or hugging restraints while immobilizing the injured area. The goal is to minimize stress on the animal while safely exposing areas needing attention.
The document summarizes a study that used the miScript PCR System to profile miRNA expression changes in total RNA samples isolated from FFPE normal and tumor lung tissues. Key points:
1) The miScript PCR System, in conjunction with the miRNeasy FFPE Kit, provides a solution for miRNA expression profiling from archived FFPE samples.
2) The study found significant differences in mature miRNA expression levels between normal and tumor lung tissue, consistent with previous studies.
3) The miRNeasy FFPE Kit efficiently extracts total RNA containing miRNA from FFPE samples, and the miScript PCR System provides highly reproducible results across isolations.
This document discusses microRNAs (miRNAs) and methods for studying their function and regulation of genes. It describes:
1) What miRNAs are, how they work by incorporating into the RISC complex and repressing target mRNAs through translational repression or degradation.
2) Techniques for manipulating miRNAs in cell lines using reporter assays, mimics, inhibitors and target protectors to study their effects on genes.
3) How to screen for miRNAs that regulate a target gene using ready-made cDNA panels and quantitative PCR. Several examples are provided of identifying miRNAs that regulate important cancer genes.
Please note: This presentation accompanies a recorded webinar at:
https://www1.gotomeeting.com/register/347794241
Biomarkers for studying gene regulation and cell function can be efficiently analyzed by multiplexed methods. Dr. Jim Lazar from OriGene Technologies will provide an overview of four different but related detection technologies that can be used to analyze genetic variants, microRNA expression, transcription factor binding, and protein expression on the Luminex xMAP platform. OriGene’s broad panel of assays and tools for discovery, analysis and validation of multiple classes of important biomarkers will allow researcher to develop more accurate descriptions of biologically complex systems.
This document describes miScript miRNA PCR Arrays, which allow for the simultaneous detection of genome-wide or pathway-focused microRNA (miRNA) expression. It provides an overview of miRNA biology and research, details the miScript miRNA PCR Array system workflow from isolation to data analysis, and discusses applications in cancer research, development, differentiation, and genome-wide discovery. The system offers validated miRNA assays, controls, and optimized reagents to enable reproducible and reliable miRNA expression profiling from RNA samples.
Translation converts mRNA into a protein through a multi-step process. The mRNA code is read in triplets and each codon corresponds to a specific amino acid. tRNAs carry amino acids and bind to ribosomes along with mRNA. The ribosome facilitates the chain of amino acids. Translation involves activation, initiation, elongation and termination. Initiation requires assembly of the translation complex on mRNA including ribosomal subunits, initiator tRNA and factors. Ongoing research supports the theory that excess protein translation contributes to autism by showing dampening an overabundant protein reverses social deficits in mouse models.
This study identified protein arginine methyltransferase 6 (PRMT6) as a coactivator of nuclear factor-kappa B (NF-κB) through three main findings:
1. Transgenic mice overexpressing a fusion of PRMT6 and the estrogen receptor displayed increased levels of interleukin 6 (IL-6), an NF-κB target gene, upon tamoxifen treatment.
2. PRMT6 was found to directly interact with the NF-κB subunit RelA and enhance the transcriptional activity of an NF-κB reporter.
3. PRMT6 was recruited by RelA to selective NF-κB target promoters upon TNF-α stimulation and its overexpression led to increased nuclear accumulation of Rel
This document summarizes a webinar series on microRNAs and their role in human disease. It introduces microRNA biogenesis, function, and analysis. The webinar series consists of three parts that will cover microRNA biogenesis and function, advanced microRNA expression analysis, and profiling microRNA expression in different sample types for biomarker development. The document provides an agenda for the first webinar that will discuss microRNA background, genomics, role in disease, isolation technologies, quantification technologies, profiling technologies, and functionalization technologies. It also advertises a newly released product.
This document is an agenda for a webinar on profiling miRNA expression in cells, formalin-fixed paraffin-embedded (FFPE) tissue samples, and serum. The webinar will provide an introduction to miRNAs and disease, discuss sample preparation options for different sample types, and describe the miScript PCR System for profiling miRNA expression. The speaker, Jonathan Shaffer, will summarize the miScript PCR System and take questions at the end of the webinar.
Meeting the challenges of miRNA research: miRNA and its Role in Human Disease...QIAGEN
This document discusses a 4-part webinar series on microRNA (miRNA) research presented by QIAGEN. Part 1 will cover miRNA profiling from biofluids, part 2 will discuss challenges in miRNA research, part 3 will focus on advanced miRNA expression analysis, and part 4 will analyze functional analysis of miRNA. The document provides background on miRNAs and their role in gene expression and disease. It also describes QIAGEN products and solutions for miRNA sample preparation, real-time PCR, data analysis, and functional validation to help researchers overcome challenges in miRNA analysis.
The document describes miScript miRNA PCR Arrays for analyzing miRNA expression patterns. It discusses miRNA biogenesis and function, and how the miScript system allows for genome-wide and pathway-focused miRNA analysis using a qPCR-based approach. The miScript arrays offer high reproducibility, sensitivity, and the ability to discover cancer-related and developmentally regulated miRNAs. They can be used to screen focused miRNA panels or conduct genome-wide screens to discover novel miRNA roles.
Watch the presentation of this webinar here: https://bit.ly/2SWCycq
mRNA has taken center stage. Vaccines and therapeutics based on this versatile biomolecule have the potential to transform disease prevention and treatment. This webinar will explore key considerations for efficient mRNA production, starting from facility design and raw materials selection to technologies and strategies used for manufacturing.
The success of mRNA-based COVID-19 vaccines has created a significant level of interest in this versatile biomolecule for disease prevention and treatment. While production of these vaccines took place in record time, critical decisions must be made when developing novel mRNA applications to ensure manufacturability, reproducibility, and safety. This webinar will explore foundational elements of the mRNA manufacturing workflow and strategies to design the right facilities to ensure success. Topics include collaborative approaches to ensure access to high quality raw materials, application of advanced technologies for manufacturing, options for facility design and key considerations when leveraging a contract development and manufacturing partner.
In this webinar, you will learn:
• Therapeutic potential of mRNA: COVID-19 and beyond
• How mRNA manufacturing workflows and facility design have a significant impact on reproducibility and performance
• Amptec capabilities to accelerate mRNA development and manufacturing
The document discusses microRNAs (miRNAs), a type of non-coding RNA. It describes how miRNAs are produced through transcription and processing, and how they regulate gene expression by targeting mRNAs. It also outlines different types of non-coding RNAs and their functions, miRNA biogenesis pathways, miRNA mechanisms of silencing target genes, and the roles of miRNAs in various cellular processes and diseases like cancer.
Posttranslational modifications and regulation of gene expression are discussed. Protein synthesis involves transcription of DNA to mRNA in the nucleus, then transport of mRNA to the cytoplasm where translation occurs on ribosomes. The genetic code is explained where codons consisting of three nucleotides specify each of the 20 amino acids. Mutations can occur that result in changes to the amino acid sequence of proteins.
Quantitative Analysis of IGF1R/AKT/mTOR Pathway using Multiplex-Immunoprecipi...Thermo Fisher Scientific
Determine the efficacy of multiplex IP to targeted MS (mIP-tMS) technique for measurement of the total and phosphorylated AKT-mTOR pathway targets and to evaluate whether mIP-tMS assays are as effective as the current singleplex immunoassay (Western Blot (WB) and ELISA) and multiplex Luminex assays.
This is a mini-research work presented in partial fulfilment of the requirements for the award of a masters degree in Biochemistry, University of Ibadan.
High-resolution transcriptome of human macrophagesNacho Caballero
This document summarizes a study that used high-resolution transcriptome profiling to analyze human macrophages. The study found that macrophages differentiate from monocytes into two main subtypes, M1 and M2, in response to different stimuli. Transcriptome analysis using both microarrays and RNA sequencing showed that each macrophage subtype expresses a unique gene expression phenotype that can discriminate between the subtypes. RNA sequencing provided advantages over microarrays by enabling detection of alternative splicing and identification of novel macrophage markers.
In molecular biology and genetics, translation is the process in which ribosomes in the cytoplasm or ER synthesize proteins after the process of transcription of DNA to RNA in the cell's nucleus. The entire process is called gene expression.
Mehanism of post Transcription -Cap PolyA kHZ.pptsaqlainsial
The document summarizes several key steps in gene expression after transcription in eukaryotic cells. These include 5' capping, 3' cleavage and polyadenylation of pre-mRNA, splicing, transport of mRNA from the nucleus to cytoplasm, and translation. It focuses on the mechanisms and protein factors involved in RNA capping and 3' end processing, including the AAUAAA polyadenylation signal, GU/U-rich elements, and the roles of CPSF, CstF, PAP, and PAB proteins. Transcription is shown to extend beyond the polyadenylation site, and the polyA tail is added co-transcriptionally in two phases requiring different protein complexes and the AAUAAA
Similar to Liu_Jiangyuan_1201662_Presentation (20)
3. Background information
1. Fat mass and obesity-associated (FTO) protein
An enzyme energy utilization and metabolism
FTO gene body mass index and risk for obesity
FTO, a demethylase N6-methyladenosine (m6A) (most
abundant methylation on mRNA)
4. Background information
2. m6A-specific methylated RNA immunoprecipitation with
next generation sequencing (MeRIP-Seq)
Mapping the m6A RNA methylomes with
a ~100-nucleotide resolution
Steps:
① Fragmentation
② Immunoprecipitation
③ PCR amplification and high-
throughput sequencing
④ m6A peak identification by
comparison between IP and
INPUT signals
5. Background information
Why MeRIP-Seq must require input control samples?
Transcriptome-wide RNA methylation
Transcriptional regulation Enzymatic regulation
It is possible that some peaks exist in both IP and input signal, which is attributed to
transcriptional up-regulation.
Comparison between
the immunoprecipitated
sample and the input
sample
Distinguish m6A peaks from those
peaks caused by transcriptional up-
regulation
m6A RNA immunoprecipitation signal
Signal
Signal
Input signal
Locus Locus
m6A peak
Not m6A peak
6. Background information
A gene set (e.g. differential expression)Different conditions
Influence
Predefined bins called Terms
Classified into
Application:
(e.g. FasR—receptor, apoptosis, plasma membrane)
Compose
GO system of classification
Underlying biological
processes
How it works: (hypergeometric test)
All genes in a Term
All genes in GO system
Input genes that belong to a Term
All input genes ÷Fold enrichment=
Output: GO terms, p-values and fold enrichments.
3. Gene Ontology (GO) Term Enrichment Analysis
7. Methods
1
2
3
4
5
mm10
Wild type: WT IP 1 WT INPUT 1
WT IP 2 WT INPUT 2
WT IP 3 WT INPUT 3
FTO K/O IP 1 FTO K/O INPUT 1
FTO K/O IP 2 FTO K/O INPUT 2
FTO K/O IP 3 FTO K/O INPUT 3
FTO
Knockout:
Mouse midbrain
6
8. Results and analysis
1. Differential mRNA methylation between wild type and FTO
knockout cell lines in mouse midbrain (From exomePeak)
The number of consistent significant differential methylation peaks for three
replicates: 1,129 (hypermethylation peaks) on the mRNAs of 912 genes
The number of transcriptome-wide m6A peaks: 37,968 on the mRNAs of
15,731 genes
912 15,731 ≈ 5.8%
FTO-targeted genes / All genes whose mRNA contain m6A sites:
9. Results and analysis
2. Differential expression between wild type and FTO knockout
cell lines in mouse midbrain (from Cuffdiff and CummeRbund)
The values in x- and y-axis: FPKM, a normalization of gene expression level
No statistically significant
changes of gene expression
level
Why?
FTO can demethylate
m3T in ssDNA, but low
activity
Gene expression
10. Results and analysis
3. Functional enrichment analysis of FTO-targeted genes
(from DAVID)
Neuronal function
11. Results and analysis
4. A web application developed by Shiny
(accessed by http://180.208.58.19:3838/sample-apps/m6A_v2/)
m6A peak search:
13. Conclusion
Results
• Identification of FTO-targeted genes and the positions of m6A sites on their
mRNAs
• FTO might not participate in gene expression.
• FTO is involved in many biological processes (particularly for neuronal function)
Future plans
Two new functions for Term search of the web application:
• Category search (e.g. diseases)
• Upload a gene list