scholarly journals Proteomic analysis of necroptotic extracellular vesicles

2020 ◽  
Author(s):  
Inbar Shlomovitz ◽  
Gali Yanovich-Arad ◽  
Ziv Erlich ◽  
Liat Edry-Botzer ◽  
Sefi Zargarian ◽  
...  
Keyword(s):  
Extracellular Vesicles ◽  
Antigen Processing ◽  
Early Stage ◽  
Protein Composition ◽  
Kinase Domain ◽  
Adaptive Immune ◽  
And Control ◽  
High Degree ◽  
Antigen Processing And Presentation ◽  
The Impact

AbstractNecroptosis is a regulated and inflammatory form of cell death. We, and others, have previously reported that necroptotic cells release extracellular vesicles (EVs). We have found that necroptotic EVs are loaded with proteins, including the phosphorylated form of the key necroptosis-executing factor, mixed lineage kinase domain-like kinase (MLKL). However, neither the exact protein composition, nor the impact, of necroptotic EVs have been delineated. To characterize their content, EVs from necroptotic and untreated U937 cells were isolated and analyzed by mass spectrometry-based proteomics. A total of 3337 proteins were identified, sharing a high degree of similarity with exosome proteome databases, and clearly distinguishing necroptotic and control EVs. A total of 352 proteins were significantly upregulated in the necroptotic EVs. Among these were MLKL and caspase-8, as validated by immunoblot. Components of the ESCRTIII machinery and inflammatory signaling were also upregulated in the necroptotic EVs, as well as currently unreported components of vesicle formation and transport, and necroptotic signaling pathways. Moreover, we found that necroptotic EVs can be phagocytosed by macrophages to modulate cytokine and chemokine secretion. Finally, we uncovered that necroptotic EVs contain tumor neoantigens, and are enriched with components of antigen processing and presentation. In summary, our study reveals a new layer of regulation during the early stage of necroptosis, mediated by the secretion of specific EVs that influences the microenvironment and may instigate innate and adaptive immune responses. This study sheds light on new potential players in necroptotic signaling and its related EVs, and uncovers the functional tasks accomplished by the cargo of these necroptotic EVs.

scholarly journals Proteomic analysis of necroptotic extracellular vesicles

2021 ◽  
Vol 12 (11) ◽  
Author(s):  
Inbar Shlomovitz ◽  
Ziv Erlich ◽  
Gali Arad ◽  
Liat Edry-Botzer ◽  
Sefi Zargarian ◽  
...  
Keyword(s):  
Extracellular Vesicles ◽  
Antigen Processing ◽  
Early Stage ◽  
Protein Composition ◽  
Kinase Domain ◽  
Adaptive Immune ◽  
And Control ◽  
High Degree ◽  
Antigen Processing And Presentation ◽  
The Impact

AbstractNecroptosis is a regulated and inflammatory form of cell death. We, and others, have previously reported that necroptotic cells release extracellular vesicles (EVs). We have found that necroptotic EVs are loaded with proteins, including the phosphorylated form of the key necroptosis-executing factor, mixed lineage kinase domain-like kinase (MLKL). However, neither the exact protein composition, nor the impact, of necroptotic EVs have been delineated. To characterize their content, EVs from necroptotic and untreated U937 cells were isolated and analyzed by mass spectrometry-based proteomics. A total of 3337 proteins were identified, sharing a high degree of similarity with exosome proteome databases, and clearly distinguishing necroptotic and control EVs. A total of 352 proteins were significantly upregulated in the necroptotic EVs. Among these were MLKL and caspase-8, as validated by immunoblot. Components of the ESCRTIII machinery and inflammatory signaling were also upregulated in the necroptotic EVs, as well as currently unreported components of vesicle formation and transport, and necroptotic signaling pathways. Moreover, we found that necroptotic EVs can be phagocytosed by macrophages to modulate cytokine and chemokine secretion. Finally, we uncovered that necroptotic EVs contain tumor neoantigens, and are enriched with components of antigen processing and presentation. In summary, our study reveals a new layer of regulation during the early stage of necroptosis, mediated by the secretion of specific EVs that influences the microenvironment and may instigate innate and adaptive immune responses. This study sheds light on new potential players in necroptotic signaling and its related EVs, and uncovers the functional tasks accomplished by the cargo of these necroptotic EVs.

scholarly journals The Fatty Acid and Protein Profiles of Circulating CD81-Positive Small Extracellular Vesicles Are Associated with Disease Stage in Melanoma Patients

Cancers ◽  
2021 ◽  
Vol 13 (16) ◽  
pp. 4157
Author(s):  
Giovanni Paolino ◽  
Veronica Huber ◽  
Serena Camerini ◽  
Marialuisa Casella ◽  
Alberto Macone ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Extracellular Vesicles ◽  
Ad Hoc ◽  
Early Stage ◽  
Disease Onset ◽  
Protein Composition ◽  
Disease Stage ◽  
Biological Macromolecules ◽  
Healthy Donors ◽  
Melanoma Patients

The early detection of cutaneous melanoma, a potentially lethal cancer with rising incidence, is fundamental to increasing survival and therapeutic adjustment. In stages II–IV especially, additional indications for adjuvant therapy purposes after resection and for treatment of metastatic patients are urgently needed. We investigated whether the fatty acid (FA) and protein compositions of small extracellular vesicles (sEV) derived from the plasma of stage 0–I, II and III–IV melanoma patients (n = 38) could reflect disease stage. The subpopulation of sEV expressing CD81 EV marker (CD81sEV) was captured by an ad hoc immune affinity technique from plasma depleted of large EV. Biological macromolecules were investigated by gas chromatography and mass spectrometry in CD81sEV. A higher content of FA was detectable in patients with respect to healthy donors (HD). Moreover, a higher C18:0/C18:1 ratio, as a marker of cell membrane fluidity, distinguished early (stage 0–I) from late (III–IV) stages’ CD81sEV. Proteomics detected increases in CD14, PON1, PON3 and APOA5 exclusively in stage II CD81sEV, and RAP1B was decreased in stage III–IV CD81sEV, in comparison to HD. Our results suggest that stage dependent alterations in CD81sEV’ FA and protein composition may occur early after disease onset, strengthening the potential of circulating sEV as a source of discriminatory information for early diagnosis, prediction of metastatic behavior and following up of melanoma patients.

Transcriptional characterization of immune microenvironment and their prediction role for the prognosis of local advanced lung adenocarcinoma.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e20625-e20625
Author(s):  
Yuqiao Chen ◽  
Xinying Shi ◽  
Xue Song ◽  
Lingling Gao ◽  
Beibei Mao ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Survival Data ◽  
Primary Tumor ◽  
Antigen Processing ◽  
Early Stage ◽  
Locally Advanced ◽  
Immune Microenvironment ◽  
Immune Related Genes ◽  
The Impact ◽  
Local Advanced

e20625 Background: The resection of early stage NSCLC offers patients the best hope of a cure. However, the recurrence rate post-resection remains high. As the mechanisms involved in the process is still not clear due to the unavailability of accurate targets, our study was aimed to integrate the impact of different immune context present in lung adenocarcinoma (LUAD) microenvironment on patients’ prognosis. Methods: RNA targeted sequencing was performed on 24 primary tumor specimens from the resected local advanced LUADs . Transcripts of 395 immune related genes expressed in FFPE tumor samples were analyzed. The limma package was used to analyze the different expressed genes (DEGs) between patients with different prognosis. The gene set variance analysis (GSVA) analysis was performed to explore gene sets enrichment related to the prognosis (PFS, progression free survival) post-resection. Results: 23 DEGs were detected in primary tumor between the better (PFS > 18months, n = 12 ) and worse (PFS≤18months, n = 12 ) prognosis group. The combined prediction model containing MPO, IL-6, CXCR2, FCGR3B, ADGRE5 could identify the favorable prognosis of patients. GSVA and Log Rank test of survival data demonstrated that the antigen processing and lymphocyte activation pathway enrichment may associate with better prognosis (p = 0.01), whereas higher Neutrophils cell infiltration in primary tumor demonstrated a shorter PFS (p = 0.008). Conclusions: In LUAD, the immune related genes such as MPO, IL-6, CXCR2, FCGR3B, ADGRE5, can effectively profile the landscape of tumor immune microenvironment and predict the survival in early stage of lung adenocarcinoma. Accordingly immune pathways were correlated with prognosis of these patients. Our findings suggest that immune-related RNA expression pattern in locally advanced LUAD may provide a potential predictive marker for early recurrence after surgical resection.

scholarly journals The impact of the implementation of the quality system (9001) in controlling administrative, financial and logistical matters in the Ministry of Education – An applied study on education in the southern Jordan Valley –: أثر تطبيق نظام الجودة (9001) في ضبط الأمور الإدارية والمالية واللوازمية في وزارة التربية والتعليم – دراسة تطبيقية تربية الأغوار الجنوبية –

2021 ◽  
Vol 5 (48) ◽  
pp. 19-1
Author(s):  
Rakan Atef Al-Dalain Rakan Atef Al-Dalain
Keyword(s):  
Organizational Culture ◽  
Quality System ◽  
Ministry Of Education ◽  
Jordan Valley ◽  
Significance Level ◽  
Applied Study ◽  
Female Employees ◽  
And Control ◽  
High Degree ◽  
The Impact

The aim of the current research is to reveal the impact of the application of the quality system (9001) in controlling administrative, financial and supplies matters in the Ministry of Education, an applied study in the Directorate of Education of the Southern Jordan Valley, and to achieve the objectives of the research, the descriptive analytical method was used, and a questionnaire was developed to collect data from the study sample which consisted of (130) male and female employees working in the Directorate of Education of the Southern Jordan Valley. The research reached a set of results, the most important of which are: the level of apply the quality system came at a high degree with a means of (3.84), and the degree of controlling administrative matters was high with a means of (4.47), and the degree of controlling financial matters was high with a means of (4.26), and the degree of controlling necessary matters was high with a means of (4.09). In addition, there is a statistically significant effect at the significance level (α≤0.05) between the application of the quality system (9001) in all its dimensions (administrative responsibility, procurement, document control, and control of quality records) in controlling administrative and financial, and supplies matters in the Directorate of Education of the Southern Jordan Valley. Based on the results reached, the research recommended the need to constantly develop and update the quality system in line with the quality standards (9001) due to its clear impact on improving the performance of the Directorate of Education in the Southern Jordan Valley and its employees, and working to embody the standards and principles of the quality system (9001) in the organizational culture of the Directorate of Education of the Southern Jordan Valley, so that it becomes a major feature of the organizational culture axis and a fundamental pillar for the success of its performance and achievement of its objectives.

scholarly journals The Oviductal Extracellular Vesicles’ RNA Cargo Regulates the Bovine Embryonic Transcriptome

2020 ◽  
Vol 21 (4) ◽  
pp. 1303 ◽  
Author(s):  
Stefan Bauersachs ◽  
Pascal Mermillod ◽  
Carmen Almiñana
Keyword(s):  
Gene Expression ◽  
Extracellular Vesicles ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
High Throughput Analysis ◽  
Positive Effects ◽  
Early Embryos ◽  
And Control ◽  
The Impact

Oviductal extracellular vesicles (oEVs) are emerging as key players in the gamete/embryo–oviduct interactions that contribute to successful pregnancy. Various positive effects of oEVs on gametes and early embryos have been found in vitro. To determine whether these effects are associated with changes of embryonic gene expression, the transcriptomes of embryos supplemented with bovine fresh (FeEVs) or frozen (FoEVs) oEVs during in vitro culture compared to controls without oEVs were analyzed by low-input RNA sequencing. Analysis of RNA-seq data revealed 221 differentially expressed genes (DEGs) between FoEV treatment and control, 67 DEGs for FeEV and FoEV treatments, and minor differences between FeEV treatment and control (28 DEGs). An integrative analysis of mRNAs and miRNAs contained in oEVs obtained in a previous study with embryonic mRNA alterations pointed to direct effects of oEV cargo on embryos (1) by increasing the concentration of delivered transcripts; (2) by translating delivered mRNAs to proteins that regulate embryonic gene expression; and (3) by oEV-derived miRNAs which downregulate embryonic mRNAs or modify gene expression in other ways. Our study provided the first high-throughput analysis of the embryonic transcriptome regulated by oEVs, increasing our knowledge on the impact of oEVs on the embryo and revealing the oEV RNA components that potentially regulate embryonic development.

scholarly journals The effect of control measures on COVID-19 transmission in Italy: Comparison with Guangdong province in China

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Pei-Yu Liu ◽  
Sha He ◽  
Li-Bin Rong ◽  
San-Yi Tang
Keyword(s):  
Media Coverage ◽  
Early Stage ◽  
Guangdong Province ◽  
Individual Behavior ◽  
Control Measures ◽  
Disease Spread ◽  
Sensitivity Analyses ◽  
And Control ◽  
Parameter Values ◽  
The Impact

Abstract Background COVID-19 has spread all around the world. Italy is one of the worst affected countries in Europe. Although there is a trend of relief, the epidemic situation hasn’t stabilized yet. This study aims to investigate the dynamics of the disease spread in Italy and provide some suggestions on containing the epidemic. Methods We compared Italy’s status at the outbreak stage and control measures with Guangdong Province in China by data observation and analysis. A modified autonomous SEIR model was used to study the COVID-19 epidemic and transmission potential during the early stage of the outbreak in Italy. We also utilized a time-dependent dynamic model to study the future disease dynamics in Italy. The impact of various non-pharmaceutical control measures on epidemic was investigated through uncertainty and sensitivity analyses. Results The comparison of specific measures implemented in the two places and the time when the measures were initiated shows that the initial prevention and control actions in Italy were not sufficiently timely and effective. We estimated parameter values based on available cumulative data and calculated the basic reproduction number to be 4.32 before the national lockdown in Italy. Based on the estimated parameter values, we performed numerical simulations to predict the epidemic trend and evaluate the impact of contact limitation, detection and diagnosis, and individual behavior change due to media coverage on the epidemic. Conclusions Italy was in a severe epidemic status and the control measures were not sufficiently timely and effective in the beginning. Non-pharmaceutical interventions, including contact restrictions and improvement of case recognition, play an important role in containing the COVID-19 epidemic. The effect of individual behavior changes due to media update of the outbreak cannot be ignored. For policy-makers, early and strict blockade measures, fast detection and improving media publicity are key to containing the epidemic.

scholarly journals The effect of control measures on COVID-19 transmission in Italy: Comparison with Guangdong province in China

2020 ◽  
Author(s):  
Pei-Yu Liu ◽  
Sha He ◽  
Li-Bin Rong ◽  
San-Yi Tang
Keyword(s):  
Media Coverage ◽  
Early Stage ◽  
Guangdong Province ◽  
Individual Behavior ◽  
Control Measures ◽  
Disease Spread ◽  
Sensitivity Analyses ◽  
And Control ◽  
Parameter Values ◽  
The Impact

Abstract Background: COVID-19 has spread all around the world. Italy is one of the worst affected countries in Europe. Although there is a trend of relief, the epidemic situation hasn’t stabilized yet. This study aims to investigate the dynamics of the disease spread in Italy and provide some suggestions on containing the epidemic. Methods: We compared Italy’s status at the outbreak stage and control measures with Guangdong Province in China by data observation and analysis. A modified autonomous SEIR model was used to study the COVID-19 epidemic and transmission potential during the early stage of the outbreak in Italy. We also utilized a time-dependent dynamic model to study the future disease dynamics in Italy. The impact of various non-pharmaceutical control measures on epidemic was investigated through uncertainty and sensitivity analyses. Results: The comparison of specific measures implemented in the two places and the time when the measures were initiated shows that the initial prevention and control actions in Italy were not sufficiently timely and effective. We estimated parameter values based on available cumulative data and calculated the basic reproduction number to be 4.32 before the national lockdown in Italy. Based on the estimated parameter values, we performed numerical simulations to predict the epidemic trend and evaluate the impact of contact limitation, detection and diagnosis, and individual behavior change due to media coverage on the epidemic. Conclusions: Italy was in a severe epidemic status and the control measures were not sufficiently timely and effective in the beginning. Non-pharmaceutical interventions, including contact restrictions and improvement of case recognition, play an important role in containing the COVID-19 epidemic. The effect of individual behavior changes due to media update of the outbreak cannot be ignored. For policy-makers, early and strict blockade measures, fast detection and improving media publicity are key to containing the epidemic.

scholarly journals The Impact of Ransomware on Individuals and Organizations in this Modern Era, Ways Forward

2021 ◽  
Vol 10 (04) ◽  
pp. 096-105
Author(s):  
Ike Mgbeafulike ◽  
Ifeose Justin N.
Keyword(s):  
Early Stage ◽  
Security Architecture ◽  
Adaptive Security ◽  
Content Filtering ◽  
Architecture Model ◽  
Signature Detection ◽  
Or Organization ◽  
And Control ◽  
The Impact ◽  
Modern Era

Ransomware is a severe security bottleneck and threat faced by individuals and organizations today in computer and information technology, and ransomware attacks are on the increase by the day. There is no infallible solution for protecting against Ransomware as the malware code uses metamorphic and polymorphic algorithms to generate different versions, thus evading signature detection. Ransomware also uses domain generator algorithms (DGA) to generate new domains for the command and control server (C&C), they constantly exploit new vulnerabilities, and they use various infection vectors. Thus, for an individual or organization to protect itself, an adaptive security architecture must constantly monitor the system to detect new ransomware infections at an early stage such that they block them before encryption of the files done. This approach is a defense in depth approach that supplements the network defenses such as patch management, anti-virus software, intrusion detection, firewalls, and content filtering. A framework for implementing the preempt and preventive security architecture model using open -source software was presented and the proposed framework is tested against the WannaCry and Petya Ransomware. The proposed framework was successfully able to alert of the ransomware attack and, it was even possible to prevent the Petya ransomware from executing on the victim host.

scholarly journals Bioorthogonal antigens allow the unbiased study of antigen processing and presentation

2018 ◽  
Author(s):  
Can Araman ◽  
Linda Pieper-Pournara ◽  
Tyrza van Leeuwen ◽  
Arieke S. B. Kampstra ◽  
Thomas Bakkum ◽  
...  
Keyword(s):  
Immune Response ◽  
Immune System ◽  
Antigen Processing ◽  
Adaptive Immune Response ◽  
Short Peptides ◽  
Biological Processes ◽  
Adaptive Immune ◽  
Major Histocompatibility Complexes ◽  
Antigenic Material ◽  
Antigen Processing And Presentation

AbstractProteolysis is fundamental to many biological processes. In the immune system, it underpins the activation of the adaptive immune response: degradation of antigenic material into short peptides and presentation thereof on major histocompatibility complexes, leads to activation of T-cells. This initiates the adaptive immune response against many pathogens.

scholarly journals SILAC-Based Quantification of TGFBR2-Regulated Protein Expression in Extracellular Vesicles of Microsatellite Unstable Colorectal Cancers

2019 ◽  
Vol 20 (17) ◽  
pp. 4162 ◽  
Author(s):  
Fabia Fricke ◽  
Malwina Michalak ◽  
Uwe Warnken ◽  
Ingrid Hausser ◽  
Martina Schnölzer ◽  
...  
Keyword(s):  
Protein Expression ◽  
Extracellular Vesicles ◽  
Transforming Growth Factor Beta ◽  
Transforming Growth Factor ◽  
Isotope Labeling ◽  
Protein Composition ◽  
Colorectal Cancers ◽  
Gene And Protein Expression ◽  
Associated Proteins ◽  
The Impact

Microsatellite unstable (MSI) colorectal cancers (CRCs) are characterized by mutational inactivation of Transforming Growth Factor Beta Receptor Type 2 (TGFBR2). TGFBR2-deficient CRCs present altered target gene and protein expression. Such cellular alterations modulate the content of CRC-derived extracellular vesicles (EVs). EVs function as couriers of proteins, nucleic acids, and lipids in intercellular communication. At a qualitative level, we have previously shown that TGFBR2 deficiency causes overall alterations in the EV protein content. To deepen the basic understanding of altered protein dynamics, this work aimed to determine TGFBR2-dependent EV protein signatures in a quantitative manner. Using a stable isotope labeling with amino acids in cell culture (SILAC) approach for mass spectrometry-based quantification, 48 TGFBR2-regulated proteins were identified in MSI CRC-derived EVs. Overall, TGFBR2 deficiency caused upregulation of several EV proteins related to the extracellular matrix and nucleosome as well as downregulation of proteasome-associated proteins. The present study emphasizes the general overlap of proteins between EVs and their parental CRC cells but also highlights the impact of TGFBR2 deficiency on EV protein composition. From a clinical perspective, TGFBR2-regulated quantitative differences of protein expression in EVs might nominate novel biomarkers for liquid biopsy-based MSI typing in the future.

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