scholarly journals Molecular and proteomic signatures associated with preservation related graft injury: insight from human liver normothermic machine perfusion (NMP)

2021 ◽  
Vol 2 (4) ◽  
Author(s):  
Fungai Dengu
Keyword(s):  
Differential Expression ◽  
Cold Storage ◽  
Liver Perfusion ◽  
Molecular Signature ◽  
Label Free ◽  
Significant Differential Expression ◽  
Tissue Samples ◽  
University Of Oxford ◽  
Novel Technology ◽  
The Impact

Fungai Dengu1; Sadr Shaheed1; Letizia Lo Faro1; Adam Thorne1; Honglei Huang1; Peter Friend1,Rutger Ploeg1. 1. Oxford Organ Perfusion Lab, Nuffield Department of Surgical Sciences and Oxford BiomedicalResearch Centre, University of Oxford, Oxford, UK     BackgroundContinuous liver NMP is a novel technology associated with safe extension of organ preservation time, increased organ utilisation and reduced early graft injury1. Increasingly, it is utilised as a ‘back to base’ application with cold storage for organ transport and NMP initiated at the implanting centre prior to transplantation2. We aimed to evaluate the impact of additional cold ischaemia time (CIT) on the proteomic and molecular signature of NMP livers. Methods Liver tissue samples (N= 57) from a prospective clinical trial of ‘back to base’ NMP were analysed. Collection occurred at the end of cold storage (LT1), end of NMP/total preservation (LT2) and after organ reperfusion (LT3). Unbiased, label-free-quantitative (LFQ) proteomic analysis was conducted using liquid chromatography with tandem mass spectrometry and trapped ion mobility spectrometry (TIMS) to time-of-flight (TOF) mass analysis (LC-MS/MS TIMS-TOF). Differential expression and Gene Ontology/Pathway analysis were performed. Results LT2 samples with prolonged CIT (>6hr) prior to NMP had significant differential expression of proteins associated with liver-specific oxidative stress, cellular haemostasis and removal of damaged or misfolded proteins (e.g. CYP3A5, PSMB1). LT3 samples, similarly, had reduced proteins involved in autophagy and cell-cycle regulation (e.g. STBD1, CD2AP, GADD45GIP1,) and increased expression of proteins involved in neutrophil chemotaxis, adhesion and aggregation (e.g. S100A9). Discussion The molecular signature of grafts at LT2 and LT3 varies depending on the length of CIT prior to NMP. Further exploration of the molecular signatures associated with preservation related graft injury is required to determine how best to apply this novel technology clinically. References: 1. Nasralla, D. et al. A randomized trial of normothermic preservation in liver transplantation. Nature 557, 50–56 (2018).2. Ceresa, C. D. L. et al. Transient Cold Storage Prior to Normothermic Liver Perfusion May Facilitate Adoption of a Novel Technology. Liver Transplant. lt.25584 (2019).doi:10.1002/lt.25584

scholarly journals Molecular and proteomic signatures associated with preservation related graft injury: insight from human liver normothermic achine perfusion (NMP)

2021 ◽  
Vol 2 (4) ◽  
Author(s):  
Fungai Dengu
Keyword(s):  
Differential Expression ◽  
Cold Storage ◽  
Liver Perfusion ◽  
Molecular Signature ◽  
Label Free ◽  
Significant Differential Expression ◽  
Tissue Samples ◽  
University Of Oxford ◽  
Novel Technology ◽  
The Impact

Fungai Dengu1; Sadr Shaheed1; Letizia Lo Faro1; Adam Thorne1; Honglei Huang1; Peter Friend1,Rutger Ploeg1. 1. Oxford Organ Perfusion Lab, Nuffield Department of Surgical Sciences and Oxford BiomedicalResearch Centre, University of Oxford, Oxford, UK BackgroundContinuous liver NMP is a novel technology associated with safe extension of organpreservation time, increased organ utilisation and reduced early graft injury1. Increasingly, it isutilised as a ‘back to base’ application with cold storage for organ transport and NMP initiatedat the implanting centre prior to transplantation2. We aimed to evaluate the impact ofadditional cold ischaemia time (CIT) on the proteomic and molecular signature of NMP livers. MethodsLiver tissue samples (N= 57) from a prospective clinical trial of ‘back to base’ NMP wereanalysed. Collection occurred at the end of cold storage (LT1), end of NMP/total preservation(LT2) and after organ reperfusion (LT3). Unbiased, label-free-quantitative (LFQ) proteomicanalysis was conducted using liquid chromatography with tandem mass spectrometry andtrapped ion mobility spectrometry (TIMS) to time-of-flight (TOF) mass analysis (LC-MS/MS TIMSTOF).Differential expression and Gene Ontology/Pathway analysis were performed. ResultsLT2 samples with prolonged CIT (>6hr) prior to NMP had significant differential expression ofproteins associated with liver-specific oxidative stress, cellular haemostasis and removal ofdamaged or misfolded proteins (e.g. CYP3A5, PSMB1). LT3 samples, similarly, had reducedproteins involved in autophagy and cell-cycle regulation (e.g. STBD1, CD2AP, GADD45GIP1,) andincreased expression of proteins involved in neutrophil chemotaxis, adhesion and aggregation(e.g. S100A9). DiscussionThe molecular signature of grafts at LT2 and LT3 varies depending on the length of CIT prior toNMP. Further exploration of the molecular signatures associated with preservation related graftinjury is required to determine how best to apply this novel technology clinically.   References:1. Nasralla, D. et al. A randomized trial of normothermic preservation in livertransplantation. Nature 557, 50–56 (2018).2. Ceresa, C. D. L. et al. Transient Cold Storage Prior to Normothermic Liver Perfusion MayFacilitate Adoption of a Novel Technology. Liver Transplant. lt.25584 (2019).doi:10.1002/lt.25584

scholarly journals Transient Cold Storage Prior to Normothermic Liver Perfusion May Facilitate Adoption of a Novel Technology

2019 ◽  
Vol 25 (10) ◽  
pp. 1503-1513 ◽  
Author(s):  
Carlo D. L. Ceresa ◽  
David Nasralla ◽  
Christopher J. E. Watson ◽  
Andrew J. Butler ◽  
Constantin C. Coussios ◽  
...  
Keyword(s):  
Cold Storage ◽  
Liver Perfusion ◽  
Novel Technology

Transient Cold Storage Prior to Normothermic Liver Perfusion May Facilitate Adoption of a Novel Technology

2019 ◽  
Vol 26 (1) ◽  
pp. 164-165
Author(s):  
Davide Ghinolfi ◽  
Daniele Pezzati ◽  
Erjon Rreka ◽  
Giandomenico Biancofiore ◽  
Paolo De Simone
Keyword(s):  
Cold Storage ◽  
Liver Perfusion ◽  
Novel Technology

Proper imputation of missing values in proteomics datasets for differential expression analysis

2020 ◽  
Author(s):  
Mingyi Liu ◽  
Ashok Dongre
Keyword(s):  
Differential Expression ◽  
Expression Analysis ◽  
Protein Identification ◽  
Missing Values ◽  
Tissue Sample ◽  
Differential Expression Analysis ◽  
Real Life ◽  
Label Free ◽  
Imputation Methods ◽  
The Impact

Abstract Label-free shotgun proteomics is an important tool in biomedical research, where tandem mass spectrometry with data-dependent acquisition (DDA) is frequently used for protein identification and quantification. However, the DDA datasets contain a significant number of missing values (MVs) that severely hinders proper analysis. Existing literature suggests that different imputation methods should be used for the two types of MVs: missing completely at random or missing not at random. However, the simulated or biased datasets utilized by most of such studies offer few clues about the composition and thus proper imputation of MVs in real-life proteomic datasets. Moreover, the impact of imputation methods on downstream differential expression analysis—a critical goal for many biomedical projects—is largely undetermined. In this study, we investigated public DDA datasets of various tissue/sample types to determine the composition of MVs in them. We then developed simulated datasets that imitate the MV profile of real-life datasets. Using such datasets, we compared the impact of various popular imputation methods on the analysis of differentially expressed proteins. Finally, we make recommendations on which imputation method(s) to use for proteomic data beyond just DDA datasets.

scholarly journals The Role of Surface Chemistry in the Efficacy of Protein and DNA Microarrays for Label-Free Detection: An Overview

Polymers ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1026
Author(s):  
Elisa Chiodi ◽  
Allison M. Marn ◽  
Matthew T. Geib ◽  
M. Selim Ünlü
Keyword(s):  
Surface Chemistry ◽  
Surface Functionalization ◽  
Dna Microarrays ◽  
Label Free ◽  
Polymeric Coatings ◽  
Label Free Detection ◽  
Particle Imaging ◽  
Single Particle Imaging ◽  
The Impact

The importance of microarrays in diagnostics and medicine has drastically increased in the last few years. Nevertheless, the efficiency of a microarray-based assay intrinsically depends on the density and functionality of the biorecognition elements immobilized onto each sensor spot. Recently, researchers have put effort into developing new functionalization strategies and technologies which provide efficient immobilization and stability of any sort of molecule. Here, we present an overview of the most widely used methods of surface functionalization of microarray substrates, as well as the most recent advances in the field, and compare their performance in terms of optimal immobilization of the bioreceptor molecules. We focus on label-free microarrays and, in particular, we aim to describe the impact of surface chemistry on two types of microarray-based sensors: microarrays for single particle imaging and for label-free measurements of binding kinetics. Both protein and DNA microarrays are taken into consideration, and the effect of different polymeric coatings on the molecules’ functionalities is critically analyzed.

scholarly journals The Impact of Health Policies and Sociodemographic Factors on Doubling Time of the COVID-19 Pandemic in Mexico

2021 ◽  
Vol 18 (5) ◽  
pp. 2354
Author(s):  
Lina Díaz-Castro ◽  
Héctor Cabello-Rangel ◽  
Kurt Hoffman
Keyword(s):  
Population Density ◽  
Doubling Time ◽  
Sociodemographic Factors ◽  
Health Policies ◽  
Government Response ◽  
University Of Oxford ◽  
Negative Effect ◽  
Population Sizes ◽  
The University ◽  
The Impact

Background. The doubling time is the best indicator of the course of the current COVID-19 pandemic. The aim of the present investigation was to determine the impact of policies and several sociodemographic factors on the COVID-19 doubling time in Mexico. Methods. A retrospective longitudinal study was carried out across March–August, 2020. Policies issued by each of the 32 Mexican states during each week of this period were classified according to the University of Oxford Coronavirus Government Response Tracker (OxCGRT), and the doubling time of COVID-19 cases was calculated. Additionally, variables such as population size and density, poverty and mobility were included. A panel data model was applied to measure the effect of these variables on doubling time. Results. States with larger population sizes issued a larger number of policies. Delay in the issuance of policies was associated with accelerated propagation. The policy index (coefficient 0.60, p < 0.01) and the income per capita (coefficient 3.36, p < 0.01) had a positive effect on doubling time; by contrast, the population density (coefficient −0.012, p < 0.05), the mobility in parks (coefficient −1.10, p < 0.01) and the residential mobility (coefficient −4.14, p < 0.01) had a negative effect. Conclusions. Health policies had an effect on slowing the pandemic’s propagation, but population density and mobility played a fundamental role. Therefore, it is necessary to implement policies that consider these variables.

scholarly journals O-GlcNAcylation protein disruption by Thiamet G promotes changes on the GBM U87-MG cells secretome molecular signature

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Maria Cecilia Oliveira-Nunes ◽  
Glaucia Julião ◽  
Aline Menezes ◽  
Fernanda Mariath ◽  
John A. Hanover ◽  
...  
Keyword(s):  
Experimental Evidence ◽  
Critical Role ◽  
Molecular Signature ◽  
Label Free ◽  
Intercellular Signaling ◽  
Tumor Aggressiveness ◽  
Signaling Axis ◽  
Literature Evidence ◽  
Therapeutic Tools

AbstractGlioblastoma (GBM) is a grade IV glioma highly aggressive and refractory to the therapeutic approaches currently in use. O-GlcNAcylation plays a key role for tumor aggressiveness and progression in different types of cancer; however, experimental evidence of its involvement in GBM are still lacking. Here, we show that O-GlcNAcylation plays a critical role in maintaining the composition of the GBM secretome, whereas inhibition of OGA activity disrupts the intercellular signaling via microvesicles. Using a label-free quantitative proteomics methodology, we identified 51 proteins in the GBM secretome whose abundance was significantly altered by activity inhibition of O-GlcNAcase (iOGA). Among these proteins, we observed that proteins related to proteasome activity and to regulation of immune response in the tumor microenvironment were consistently downregulated in GBM cells upon iOGA. While the proteins IGFBP3, IL-6 and HSPA5 were downregulated in GBM iOGA cells, the protein SQSTM1/p62 was exclusively found in GBM cells under iOGA. These findings were in line with literature evidence on the role of p62/IL-6 signaling axis in suppressing tumor aggressiveness and our experimental evidence showing a decrease in radioresistance potential of these cells. Taken together, our findings provide evidence that OGA activity may regulate the p62 and IL-6 abundance in the GBM secretome. We propose that the assessment of tumor status from the main proteins present in its secretome may contribute to the advancement of diagnostic, prognostic and even therapeutic tools to approach this relevant malignancy.

scholarly journals Expression profiling of ileal mucosa in asthma reveals upregulation of innate immunity and genes characteristic of Paneth and goblet cells

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Jan K. Nowak ◽  
Marzena Dworacka ◽  
Nazgul Gubaj ◽  
Arystan Dossimov ◽  
Zhumabek Dossimov ◽  
...  
Keyword(s):  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Differential Expression ◽  
Expression Profiles ◽  
Differential Expression Analysis ◽  
Goblet Cells ◽  
Ileal Mucosa ◽  
Significant Differential Expression ◽  
Immune Genes ◽  
Asthma Patients

Abstract Background The expression profiles of the intestinal mucosa have not been comprehensively investigated in asthma. We aimed to explore this in the Correlated Expression and Disease Association Research (CEDAR) patient cohort. Methods Differential expression analysis of ileal, transverse colon, and rectal biopsies were supplemented by a comparison of transcriptomes from platelets and leukocytes subsets, including CD4+, CD8+, CD14+, CD15+, and CD19+ cells. Asthma patients (n = 15) and controls (n = 15) had similar age (p = 0.967), body mass index (p = 0.870), similar numbers of females (80%) and smoking rates (13.3%). Results Significant differential expression was found in the ileum alone, and not in any other cell/tissue types. More genes were found to be overexpressed (1,150) than under-expressed (380). The most overexpressed genes included Fc Fragment of IgG Binding Protein (FCGBP, logFC = 3.01, pFDR = 0.015), Mucin 2 (MUC2, logFC = 2.78, pFDR = 0.015), and Alpha 1B Defensin (DEFA1B, logFC = 2.73, pFDR = 0.024). Gene ontology implicated the immune system, including interleukins 4 and 13, as well as antimicrobial peptides in this overexpression. There was concordance of gene over- (STAT1, XBP1) and underexpression (NELF, RARA) in asthma and Crohn’s disease ileum when our results were compared to another dataset (p = 3.66 × 10–7). Conclusion Ileal mucosa in asthma exhibits a specific transcriptomic profile, which includes the overexpression of innate immune genes, mostly characteristic of Paneth and goblet cells, in addition to other changes that may resemble Crohn’s disease.

scholarly journals Combining tissue and circulating tumor DNA increases the detection rate of a CTNNB1 mutation in hepatocellular carcinoma

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Stine Karlsen Oversoe ◽  
Michelle Simone Clement ◽  
Britta Weber ◽  
Henning Grønbæk ◽  
Stephen Jacques Hamilton-Dutoit ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Mutation Rate ◽  
Detection Rate ◽  
Tumor Tissue ◽  
Circulating Tumor Dna ◽  
Treatment Modalities ◽  
Advanced Hepatocellular Carcinoma ◽  
Tissue Samples ◽  
The Impact ◽  
Tumor Dna

Abstract Background and aims Studies suggest that mutations in the CTNNB1 gene are predictive of response to immunotherapy, an emerging therapy for advanced hepatocellular carcinoma (HCC). Analysis of circulating tumor DNA (ctDNA) offers the possibility of serial non-invasive mutational profiling of tumors. Combining tumor tissue and ctDNA analysis may increase the detection rate of mutations. This study aimed to evaluate the frequency of the CTNNB1 p.T41A mutation in ctDNA and tumor samples from HCC patients and to evaluate the concordance rates between plasma and tissue. We further evaluated changes in ctDNA after various HCC treatment modalities and the impact of the CTNNB1 p.T41A mutation on the clinical course of HCC. Methods We used droplet digital PCR to analyze plasma from 95 patients and the corresponding tumor samples from 37 patients during 3 years follow up. Results In tumor tissue samples, the mutation rate was 8.1% (3/37). In ctDNA from HCC patients, the CTNNB1 mutation rate was 9.5% (9/95) in the pre-treatment samples. Adding results from plasma analysis to the subgroup of patients with available tissue samples, the mutation detection rate increased to 13.5% (5/37). There was no difference in overall survival according to CTNNB1 mutational status. Serial testing of ctDNA suggested a possible clonal evolution of HCC or arising multicentric tumors with separate genetic profiles in individual patients. Conclusion Combining analysis of ctDNA and tumor tissue increased the detection rate of CTNNB1 mutation in HCC patients. A liquid biopsy approach may be useful in a tailored therapy of HCC.

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