Proteomic Profile Of Patients Research Articles

P180 Novel biomarkers associated with inflammatory bowel disease

Abstract Background Inflammatory bowel disease (IBD) is a chronic multi-factorial disease characterized by inflammation of the gastrointestinal tract. Currently, the mechanisms underlying the disease are far from being elucidated. Thus, the study of proteins involved in its pathogenesis would allow further insights into the molecular mechanisms underlying IBD. Methods The serum and intestinal mucosa (ileum and left colon) proteomic profiles of patients with Crohn´s disease (CD) and ulcerative colitis (UC) and healthy controls (HC) were analyzed using a label-free quantitative proteomics approach (Table 1). Data mining and pattern recognition techniques were performed to identify hidden relationships that are not detectable using classical linear classifiers, and thus identify potential markers able to discriminate between the different study groups. Six candidate biomarkers were selected for further validation using enzyme-linked immunosorbent assay (ELISA) and immunohistochemistry (IHC) in serum and intestinal tissue samples, respectively (Table 2). Results Comparison of serum proteins between UC patients and HC revealed statistically lower levels of protein 1 and 2 and higher levels of protein 3. The comparison of potential biomarkers between CD and HC group showed lower levels of protein 1 and higher levels of protein 3. In addition, protein 4 was differentially upregulated in CD patients compared to UC (Figure 1A). Regarding the intestinal biopsies, protein 5 showed higher intensity in the IHC staining of ileum from CD patients compared to HC, whereas protein 6 was significantly decreased in left colon and ileum from CD and UC patients compared to HC (Figure 1B). These proteins are involved in thyroxine transport, regulation of chemotactic chemokine activity, inflammatory processes, triglyceride homeostasis, oxidative stress and regulation of NF-kappa-B activation in the cytosol. Conclusion In this study, we have identified a panel of six potential biomarkers that could help to elucidate mechanisms involved in IBD pathogenesis. Their roles in the pathophysiology need to be clarified in further experiments.

Exploring blood transcriptomic signatures in patients with herpes zoster and postherpetic neuralgia.

Postherpetic neuralgia (PHN) is a common, severe, and hard-to-treat chronic pain condition in clinics. Although PHN is developed from herpes zoster (HZ), the developing mechanism is unknown. A previous study investigated blood metabolomic and proteomic profiling in patients with PHN and HZ. The current study aims to explore the blood transcriptomic signature of PHN compared to HZ patients. Whole blood from eight PHN and 15 HZ patients was used for RNA-Seq analysis. There were 82 and 1,788 genes detected specifically in the PHN and HZ groups, respectively. PHN-specific genes are involved in viral infection, lipid and carbohydrate metabolism, and immune response. For genes coexpressed in PHN and HZ patients, there were 407 differential expression genes (DEGs), including 205 upregulated (UP DEGs) and 202 downregulated (DOWN DEGs) in PHN compared to HZ groups. DEGs are involved in viral infection, type I interferon (IFN), and hemoglobin and oxygen carrier activity. UP DEGs are associated with regulatory T cells (Tregs), activated NK cells, and neutrophils, while DOWN DEGs are associated with Tregs, resting NK cells, and monocytes. The results suggest that the metabolism of lipid, glycan, and nucleotides, type I IFN signaling, and altered neutrophil activation are associated with and might contribute to the development of PHN in HZ. It is also suggested that persistent or altered activation of nonspecific immunity may contribute to the development of PHN from HZ.

Phenotyping patients with ischaemic heart disease at risk of developing heart failure: an analysis of the HOMAGE trial.

We aim to characterize the clinical and proteomic profiles of patients at risk of developing heart failure (HF), with and without coronary artery disease (CAD) or prior myocardial infarction (MI). HOMAGE evaluated the effect of spironolactone on plasma and serum markers of fibrosis over 9months of follow-up in participants with (or at risk of having) CAD, and raised natriuretic peptides. In this post hoc analysis, patients were classified as (i) neither CAD nor MI; (ii) CAD; or (iii) MI. Proteomic between-group differences were evaluated through logistic regression and narrowed using backward stepwise selection and bootstrapping. Among the 527 participants, 28% had neither CAD or MI, 31% had CAD, and 41% had prior MI. Compared with people with neither CAD nor MI, those with CAD had higher baseline plasma concentrations of matrix metalloproteinase-7 (MMP-7), galectin-4 (GAL4), plasminogen activator inhibitor 1 (PAI-1), and lower plasma peptidoglycan recognition protein 1 (PGLYRP1), whilst those with a history of MI had higher plasma MMP-7, neurotrophin-3 (NT3), pulmonary surfactant-associated protein D (PSPD), and lower plasma tumour necrosis factor-related activation-induced cytokine (TRANCE). Proteomic signatures were similar for patients with CAD or prior MI. Treatment with spironolactone was associated with an increase of MMP7, NT3, and PGLYRP1 at 9months. In patients at risk of developing HF, those with CAD or MI had a different proteomic profile regarding inflammatory, immunological, and collagen catabolic processes.

Serum Proteomic Profiling in Patients with Chronic Obstructive Pulmonary Disease.

Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease with high morbidity and mortality rates. This study used proteomic profiling of serum to identify the differentially expressed proteins in COPD patients compared with healthy controls, to expand the knowledge of COPD pathogenesis and to ascertain potential new targets for diagnosis and treatment of COPD. Serum samples were collected from 56 participants (COPD group n = 28; Healthy Control group n = 28). A data-independent acquisition quantitative proteomics approach was used to identify differentially expressed proteins (DEPs) between the two groups. Gene Ontology (GO) functional annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway functional enrichment, and protein-protein interaction analyses of DEPs were conducted to identify their relevant biological processes, cellular components, and related pathways. We used a parallel reaction monitoring (PRM)-based targeted quantitative proteomics approach to validate those findings. Of 8484 peptides identified by searching the UniProtKB/Swiss-Prot knowledgebase, 867 proteins were quantifiable, of which 20 were upregulated and 35 were downregulated in the COPD group. GO functional annotation indicated that the subcellular localization of most DEPs was extracellular. The top three molecular functions of the DEPs were signaling receptor binding, antigen binding, and immunoglobulin receptor binding. The most relevant biological process was immune response. The transforming growth factor-β signaling pathway, Staphylococcus aureus infection, and hematopoietic cell lineage were the top three pathways identified in the KEGG pathway functional enrichment. Our PRM analyses confirmed the identification of 11 DEPs identified in our data-independent acquisition analyses, 8 DEPs were upregulated and 3 DEPs were downregulated. This study using data-independent acquisition analyses with PRM confirmation of findings identified 11 DEPs in the serum of patients with COPD. These DEPs are potential diagnostic or prognostic biomarkers or may be future targets for the treatment of COPD.

Evaluation of the proteomic profile in patients with celiac disease and malabsorption syndrome

The malabsorption syndrome includes many clinical units that lead to chronic diarrhea and malnutrition. In celiac disease and small intestine bacterial overgrowth making the diagnosis is not always straightforward, and the diagnosis often requires combining blood antibody tests, intestinal biopsies, and specific genetic testing. The study aimed to assess patients' protein/peptide profiles with celiac disease (n=31), small intestinal bacterial overgrowth (n=28), and the control group (n=30). Attempts have also been made to identify potential new diagnostic markers. After appropriate preparation, a proteomic analysis of peptides was performed using the MALDI–TOF mass spectrometer. Identified proteins were fibrinogen alpha-chain, kininogen-1, mucin 3A, complement C3, complement C4A, and inter-alpha-trypsin inhibitor heavy chain H4. Performed analyses indicated some proteins that could be potentially involved in the presence of the disease in question and proved that proteomic profiling might serve as a powerful diagnostic tool. Due to the difficulties in celiac disease and small intestine bacterial overgrowth diagnosis, there is a clear need for further investigation of the biological role of proteins potentially involved in the course of the disease.

Plasma Proteomic Profiling Illustrates Endothelial and Complement Signature in Patients with Alcohol-Associated Cirrhosis

INTRODUCTION Cirrhosis related coagulation derangements result in altered hemostasis. Endothelial markers such as von Willebrand factor (VWF) antigen and the factor VIII-to-protein C ratio (FVIII/PC) have prognostic significance in patients with cirrhosis. Additional endothelial markers have not been well described in patients with alcohol-associated cirrhosis. We performed plasma proteomic profiling in patients with alcohol-associated cirrhosis to gain insight into the potential roles of endothelial and hemostatic proteins associated with severity of cirrhosis. METHODS Two independent cohorts of patients with Child-Pugh class A (CPA) and C (CPC) alcohol-associated cirrhosis were recruited. Controls were patients without underlying liver disease. For plasma proteomic profiling, plasma supernatant was frozen, then sent to Eve Technologies (Calgary, Alberta, Canada). Linear discrimination analysis (LDA) was applied to the first cohort to identify a set of proteins that clustered patients based on the severity of liver disease (CPA vs CPC) and controls. Identified proteins were then validated using a second independent cohort of patients with alcohol-associated cirrhosis to determine if the protein signature was replicable. Boruta feature selection was performed on cohort 2 to identify candidate proteins to explain the differences in FVIII/PC ratio. A p-value of < 0.05 was considered statistically significant. RESULTS Cohort 1 included 13 patients: 4 CPA, 9 CPC (median age was 57; 4 women; 9 had dyslipidemia, 2 diabetes mellitus, 2 hypertension, and 2 chronic kidney disease). Cohort 2 included 12 patients: 7 CPA, 5 CPC (median age 50; 5 women; 7 had dyslipidemia, 1 diabetes mellitus, 1 hypertension and 0 chronic kidney disease). For cohort 1 LDA clustered patients based on CPA vs CPC with an endothelial, inflammatory and complement signature (fig.1). The proteins set that achieved robust LDA clustering of CPA, CPC, and control patients in cohort 1 included: sVCAM-1 and PAI-1 (endothelial markers); C3, C4, and CFH (complement cascade factors); IL-8 (inflammatory chemokine), NCAM (neural adhesion maker) and BDNF (neurotrophin); MPO (marker of neutrophilic activation); Eotaxin (eosinophil associated chemokine); MIP-1d (activator of T-cells and monocytes). The same protein profile applied to the validation cohort 2 was also able to cluster CPA, CPC, and control patients (fig. 2). Boruta feature selection for proteins of importance for the FVIII/PC ratio included sVCAM-1; CFI, C4b, C4, C5, CFB (complement factors); IL-6 (inflammatory cytokine), and VWF. CONCLUSIONS Using plasma proteomic profiling we describe a signature of endothelial, complement, hemostatic, and inflammatory activation that distinguishes the severity of liver disease in patients with alcohol-associated cirrhosis. Exploratory analyses suggest that endothelial and complement proteins may also contribute to the differences in the FVIII/PC ratio which has prognostic significance in patients with cirrhosis. Future work should continue to highlight the role of endothelium in the progression of liver disease and describe alternative prognostic markers to help guide clinicians. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Identifying proteomic profiles as indicators of disease severity in arrhythmogenic cardiomyopathy

Abstract Introduction Arrhythmogenic cardiomyopathy (ACM) is an inherited heart muscle disease characterized by progressive fibrofatty replacement of the myocardium and ventricular arrhythmias. Biventricular (BiV) involvement may lead to heart failure. This study aimed to investigate characteristic proteomic patterns in plasma of ACM patients, and correlated them with clinical outcome as well as physical exercise, to assess if key soluble molecules may serve as specific biomarkers for ACM, and whether mechanical stress induced by physical exercise may alter proteomic patterns in ACM patients. Methods In 38 ACM patients clinical parameters and major adverse cardiovascular events (MACE defined as presence of sustained ventricular tachycardia, ventricular fibrillation, appropriate therapy from implantable cardioverter defibrillator, sudden cardiac death, death related to end-stage heart failure or cardiac transplant) were obtained prospectively during a mean follow-up period of 36 months. All patients received genetic testing using next generation DNA sequencing. Plasma protein expression was analysed using the Proximity Extension Assay (PEA) technology, where a pair of oligonucleotide-labelled antibody probe binds to each targeted protein. In a subgroup of 11 patients blood was drawn immediately before and 3 hours after standardised bicycle exercise testing, and plasma protein expression was compared. Results 12 patients had ACM with BiV involvement, and 26 patients had isolated right ventricular (RV) involvement. During the follow-up period, 34 patients had a MACE (30% with RV and 14% with BiV). Over 360 proteins were assessed in all ACM patients and compared to 24 healthy controls. The proteomic signature of ACM patients differed significantly compared to controls, and 32 proteins were upregulated in ACM (Figure 1). The proteomic profiles of patients with RV involvement also differed from those with BiV involvement. Most importantly, after exercise, over 40 proteins were upregulated specifically in ACM patients compared to controls, including key pro-inflammatory, adipogenic molecules and also markers of cardiac fibrosis. Conclusion Our study shows that ACM patients with RV and BiV involvement have different plasma proteomic profiles compared to healthy controls. Furthermore we were able to demonstrate that, specifically in ACM patients, several pro-inflammatory pathways are upregulated after exercise compared to healthy controls, further elucidating the molecular pathways associated with arrhythmogenicity and disease progression and highlighting the key role of physical stress. Our results may enable the identification of potential future biomarkers for diagnosis and risk stratification and may pave the way for personalized patient specific treatments. Funding Acknowledgement Type of funding sources: Foundation. Main funding source(s): Baugarten Foundation ZurichSwiss National Foundation

Tissue-Based Proteomic Profiling in Patients with Hyperplasia and Endometrial Cancer.

Uterine cancers are among the most prevalent gynecological malignancies, and endometrial cancer (EC) is the most common in this group. This study used tissue-based proteomic profiling analysis in patients with endometrial cancer and hyperplasia, and control patients. Conventional 2D gel electrophoresis, followed by a mass spectrometry approach with bioinformatics, including a network pathway analysis pipeline, was used to identify differentially expressed proteins and associated metabolic pathways between the study groups. Thirty-six patients (twelve with endometrial cancer, twelve with hyperplasia, and twelve controls) were enrolled in this study. The mean age of the participants was 46–75 years. Eighty-seven proteins were significantly differentially expressed between the study groups, of which fifty-three were significantly differentially regulated (twenty-eight upregulated and twenty-five downregulated) in the tissue samples of EC patients compared to the control (Ctrl). Furthermore, 26 proteins were significantly dysregulated (8 upregulated and 18 downregulated) in tissue samples of hyperplasia (HY) patients compared to Ctrl. Thirty-two proteins (nineteen upregulated and thirteen downregulated) including desmin, peptidyl prolyl cis-trans isomerase A, and zinc finger protein 844 were downregulated in the EC group compared to the HY group. Additionally, fructose bisphosphate aldolase A, alpha enolase, and keratin type 1 cytoskeletal 10 were upregulated in the EC group compared to those in the HY group. The proteins identified in this study were known to regulate cellular processes (36%), followed by biological regulation (16%). Ingenuity pathway analysis found that proteins that are differentially expressed between EC and HY are linked to AKT, ACTA2, and other signaling pathways. The panels of protein markers identified in this study could be used as potential biomarkers for distinguishing between EC and HY and early diagnosis and progression of EC from hyperplasia and normal patients.

Plasma Proteomic Profile of Patients with Tick-Borne Encephalitis and Co-Infections.

Despite the increasing number of patients suffering from tick-borne encephalitis (TBE), Lyme disease, and their co-infection, the mechanisms of the development of these diseases and their effects on the human body are still unknown. Therefore, the aim of this study was to evaluate the changes in the proteomic profile of human plasma induced by the development of TBE and to compare it with changes in TBE patients co-infected with other tick-borne pathogens. The results obtained by proteomic analysis using a nanoLC-Q Exactive HF mass spectrometer showed that the most highly elevated groups of proteins in the plasma of TBE patients with co-infection were involved in the pro-inflammatory response and protein degradation, while the antioxidant proteins and factors responsible for protein biosynthesis were mainly downregulated. These results were accompanied by enhanced GSH- and 4-HNE-protein adducts formation, observed in TBE and co-infected patients at a higher level than in the case of patients with only TBE. In conclusion, the differences in the proteomic profiles between patients with TBE and co-infected patients indicate that these diseases are significantly diverse and, consequently, require different treatment, which is particularly important for further research, including the development of novel diagnostics tools.

Differences in cord blood extracellular vesicle cargo in preterm and term births.

This study determined the cord plasma-derived extracellular vesicle (exosomes; 30-160nm particles) proteomic profile in patients who had spontaneous preterm birth (PTB) or preterm premature rupture of membranes (pPROM), compared to those who delivered at term regardless of labor status. This is a cross-sectional analysis of a retrospective cohort that quantified and determined the proteomic cargo content of exosomes present in cord blood plasma samples in PTB or pPROM, and normal term in labor (TL) or term not in labor (TNIL) pregnancies. Exosomes were isolated by differential centrifugation followed by size exclusion chromatography. Exosomes were characterized by nanoparticle tracking analysis (quantity and size) and markers (dot blots for exosome markers). The exosomal proteomic profile was identified by liquid chromatography-mass spectrometry (LC-MS/MS). Ingenuity pathway analysis determined canonical pathways and biofunctions associated with dysregulated proteins. Cord plasma exosomes have similar quantity and exhibit both tetraspanin and ESCRT protein markers specific of exosomes regardless of the conditions. Proteomics analysis exhibited several similar markers as well as very unique markers in exosomes from each condition; however, bioinformatics analysis revealed a generalized and non-specific inflammatory condition represented in exosomes from different condition that is not indicative of any specific underlying biological functions indicative of an underlying pathology. Compared to maternal plasma and amniotic fluid exosomes, the value of cord plasma derived exosomes is limited. Quantity, character, and proteomic cargo contents in exosomes or the pathways and functions represented by differentially expressed proteins do not distinguish specific conditions regarding normal and abnormal parturition. The value of cord plasma exosome proteomic cargo has limited value as an indicator of an underlying physiology or as a biomarker of fetal well-being.

Proteomic profiles of patients with atrial fibrillation provide candidate biomarkers for diagnosis

BackgroundAtrial fibrillation (AF) is the most common cardiac arrhythmia worldwide with an increasing risk of heart failure, stroke, and thromboembolic events. Currently distinct pathophysiological mechanisms during AF development and valuable biomarkers for AF management remain unknown. MethodsIn this study, we collected peripheral plasma samples from 18 non-valvular AF patients and 10 controls. A LC-MS/MS-DIA-based quantitative proteomic analysis, as well as bioinformatic analysis, was performed for discovery of differentially expressed proteins (DEPs) and dysregulated pathways. Next, we utilized enzyme-linked immunosorbent assay (ELISA) to validate selected DEPs and assessed their abilities for discrimination in another group of 20 AF patients and 10 controls. ResultsThe plasma proteome provided evidence for vital roles of abnormal inflammation, hemostasis, tissue remodeling and metabolism in AF patients. Differences between paroxysmal and persistent AF mainly lie in proteins or pathways related to hemostasis and cardiac remodeling. In addition, we successfully validated up-regulated proteins of platelet factor 4 variant 1 (PF4V1), thrombospondin-1 (THBS1), platelet basic protein (PBP) and fructose-bisphosphate aldolase A (ALDOA) in another group, which could make discrimination between AF patients and controls. ConclusionsOur pilot proteomic study provided candidate biomarkers of PF4V1, THBS1, PBP and ALODA with the hope of application in AF management. And we showed the differences in pathophysiological mechanisms between paroxysmal and persistent AF. They mainly focused on pathways of hemostasis and cardiac remodeling, which could be a valuable clue for further research on AF progression.

Serum Proteomic Analysis of Cannabis Use Disorder in Male Patients.

Cannabis use has been growing recently and it is legally consumed in many countries. Cannabis has a variety of phytochemicals including cannabinoids, which might impair the peripheral systems responses affecting inflammatory and immunological pathways. However, the exact signaling pathways that induce these effects need further understanding. The objective of this study is to investigate the serum proteomic profiling in patients diagnosed with cannabis use disorder (CUD) as compared with healthy control subjects. The novelty of our study is to highlight the differentially changes proteins in the serum of CUD patients. Certain proteins can be targeted in the future to attenuate the toxicological effects of cannabis. Blood samples were collected from 20 male individuals: 10 healthy controls and 10 CUD patients. An untargeted proteomic technique employing two-dimensional difference in gel electrophoresis coupled with mass spectrometry was employed in this study to assess the differentially expressed proteins. The proteomic analysis identified a total of 121 proteins that showed significant changes in protein expression between CUD patients (experimental group) and healthy individuals (control group). For instance, the serum expression of inactive tyrosine protein kinase PEAK1 and tumor necrosis factor alpha-induced protein 3 were increased in CUD group. In contrast, the serum expression of transthyretin and serotransferrin were reduced in CUD group. Among these proteins, 55 proteins were significantly upregulated and 66 proteins significantly downregulated in CUD patients as compared with healthy control group. Ingenuity pathway analysis (IPA) found that these differentially expressed proteins are linked to p38MAPK, interleukin 12 complex, nuclear factor-κB, and other signaling pathways. Our work indicates that the differentially expressed serum proteins between CUD and control groups are correlated to liver X receptor/retinoid X receptor (RXR), farnesoid X receptor/RXR activation, and acute phase response signaling.

Serum proteomic profiling in patients with advanced Schistosoma japonicum-induced hepatic fibrosis

BackgroundSchistosoma japonicum is a parasitic flatworm that is the aetiological agent of human schistosomiasis, an important cause of hepatic fibrosis. Schistosomiasis-induced hepatic fibrosis is a consequence of the highly fibrogenic nature of egg-induced granulomatous lesions, which are the main pathogenic features of schistosomiasis. Although global awareness of the association between schistosomiasis-induced hepatic fibrosis and S. japonicum infection is increasing, little is known about the molecular differences associated with rapid progression to schistosomiasis in cirrhotic patients.MethodsWe systematically used data-independent acquisition (DIA)-based liquid chromatography-mass spectrometry to identify differentially expressed proteins in serum samples from patients with advanced S. japonicum-induced hepatic fibrosis.ResultsOur analysis identified 1144 proteins, among which 66 were differentially expressed between the healthy control group and the group of patients with advanced S. japonicum-induced hepatic fibrosis stage F2 (SHF-F2) and 214 were differentially expressed between the SHF-F2 and SHF-F4 groups (up- or downregulation of at least 1.5-fold in serum samples). The results also indicated that two selected proteins (C1QA and CFD) are potential biomarkers for distinguishing between patients with SHF-F2 and those with SHF-F4 due to S. japonicum infection.ConclusionsWe provide here the first global proteomic profile of serum samples from patients with advanced S. japonicum-induced hepatic fibrosis. The proteins C1QA and CFD are potential diagnostic markers for patients with SHF-F2 and SHF-F4 due to S. japonicum infection, although further large-scale studies are needed. Our DIA-based quantitative proteomic analysis revealed molecular differences among individuals at different stages of advanced S. japonicum-induced hepatic fibrosis and may provide fundamental information for further detailed investigations.Graphical

MALDI-TOF Protein Profiling Reflects Changes in Type 1 Diabetes Patients Depending on the Increased Amount of Adipose Tissue, Poor Control of Diabetes and the Presence of Chronic Complications.

Introduction: Protein profiling allows the determination of the presence of proteins marking various stages of the disease, and differentiates between people at risk of various diseases. In type 1 diabetes, protein profiling had been previously used to find blood markers other than islet autoantibodies to indicate the pancreatic beta cell destruction process and to reflect the progression of type 1 diabetes mellitus (T1DM). However, T1DM is an auto-immune disease and its clinical presentation changes in time of its duration. The aim of the study: To find differences in protein profiles in patients with type 1 diabetes according to diabetes control (HbA1c > 7%) and with presence of diabetic complications or obesity. It may help to identify subgroups of patients who may need a better clinical supervision and individualized treatment. Material and methods: A group of 103 patients with auto-immunologically confirmed T1DM, and meeting the following inclusion criteria: Caucasian race, duration of diabetes >5 years, were used in the study. Criteria of exclusion: past or present cancer (treated with chemo-/radiotherapy), diseases of the liver (ALT > 3 × ULN) except for people with simple hepatic steatosis, chronic renal disease (eGFR < 30 mL/1.73 m2/min), and acute inflammation (CRP > 5 mg/dL). The study group was divided in terms of the presence of chronic complications, obesity, or poor metabolic control (HbA1c > 7%). Protein profiling was completed by using the MALDI-TOF MS (matrix-assisted laser desorption/ionization-time of flight mass spectrometry) analyzer. Results: Differentiating proteins were identified in all of the groups. The groups burdened with complications, obesity, and poor metabolic control were characterized by increased levels of fibrinogen, complement C4 and C3. Conclusion: The groups of type 1 diabetes patients burdened with complications, obesity, and poor metabolic control were characterized by increased levels of fibrinogen, complement C4 and C3. Further detailed studies are necessary to determine more subtle changes in the proteomic profile of patients with type 1 diabetes.

OMICs AND AI APPROACHES FOR MUSCLE DISEASES: O.07 Proteomic profiling in patients with dermatomyositis

Dermatomyositis (DM) is a rare and systemic autoimmune disease belonging to the idiopathic inflammatory myopathies, primarily affecting skeletal muscle and skin. However, other organs might be affected, like the lung, heart or arteries, and development of cancer might also be associated with DM. For diagnostic and prognostic management, the detection of one of the associated autoantibodies (aAB, e.g. Mi-2, NXP-2, MDA5 TIF1γ and rarely SAE) is of outmost importance, since associations between these antibodies and interstitial lung disease (ILD) or cancer (e.g.

An Integrated Transcriptomic and Proteomic Analysis Identifies Significant Novel Pathways for Henoch-Schönlein Purpura Nephritis Progression.

Background Although Henoch-Schönlein purpura nephritis (HSPN) is characterized by glomerular deposition of aberrantly glycosylated immunoglobulin A1 (IgA1), the underlying mechanism of HSPN progression has not yet been completely elucidated. In this study, we integrated transcriptomic and proteomic analyses to explore the underlying mechanism of HSPN progression. Methods RNA sequencing and tandem mass tag- (TMT-) based quantitative proteomics were used to gain serum transcriptomic and proteomic profiles of patients with different types of HSPN (3 × type 1, 3 × type 2, and 3 × type 3). Student's t-tests were performed to obtain the significance of the differential gene expression. The clusterProfiler package was used to conduct the functional annotation of the DEGs for both Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways. Results A total of 2315 mRNAs and 30 proteins were differentially expressed between the different types of HSPN. 58 mRNAs and one protein changed continuously during HSPN development and are potential biomarkers for HSPN progression. The validation cohort (another 9 patients) confirmed the high-throughput results of the transcriptomic and proteomic analyses. A total of 385 significant pathways were related to HSPN progression, and four of them were closely related to clinical biochemical indicators and may play an important role in the progression of HSPN. Those pathways reveal that HSPN progression may be related to the inhibition of inflammation, promotion of apoptosis, and repair of renal injury. Conclusions Four pathways were found to be closely related to HSPN progression, and it seems that HSPN progression is mainly due to the inhibition of inflammation, promotion of apoptosis, and repair of renal injury.

Salivary proteomic profile of patients with renal cell carcinoma.

622 Background: We aimed to explore the salivary proteomic profile (SPP) of patients undergoing surgery for suspected renal cell carcinoma (RCC), then evaluate any significant findings in a validation cohort. Methods: Prospective IRB approved trial of consecutive patients with suspected RCC undergoing curative surgery. Saliva was collected pre- and postoperatively, and from healthy volunteers. Saliva was mixed with sodium orthovanadate and protease inhibitor, aliquoted, and frozen at -80oC. SPP performed using biomarker concentrated saliva via core-shell hydrogel nanoparticles functionalized with molecular baits coupled to high resolution MS/MS electrospray mass spectrometry analysis; output represented as spectral counts. Wilcoxon Rank Sum test was used for comparisons; p-values were adjusted using false discovery rate (FDR) for multiple testing. Results: Exploratory phase: saliva was collected from 27 volunteers and 34 RCC patients (24 clear cell (cc)RCC, 6 chromophobe (ch)RCC, 4 other). Evaluation of cc vs chRCC revealed differential counts for 56 proteins; none were significant after adjustment by FDR. Comparison of matched pre/post-operative SPP in 14 ccRCC patients identified differential counts of 3 proteins: basic salivary proline-rich protein 3 precursor; prolactin-inducible protein precursor; and submaxillary gland androgen-regulated protein 3B precursor. These were not affected by patient age, partial/radical nephrectomy, or tumor size/stage/grade. Validation phase: power analyses indicated a sample size of 38/53 patients = 90% power = effect size of 0.6/0.5, respectively, 2-sided Type 1 error of 0.025. 49 ccRCC patients were enrolled with pre/postop saliva. 611 proteins were identified; none had differential counts after FDR. Conclusions: Using a unique biomarker technology coupled to high resolution MS, interesting SPP’s were seen between RCC subtypes and before/after ccRCC curative resection. We were unable to show significant differences in pre/post-op levels. More research is needed to further study the SPP in RCC patients and the factors impacting their differential expression. In order to aid such efforts, the raw data will be made available for future researchers.

Salivary proteins as markers of radiation-related oral mucositis

Objectives The aim of this study was to characterize the salivary proteomic profile of patients treated for head and neck cancers (HNCs) and correlate it with the risk of developing severe radiation-related oral mucositis (OM). Study Design Forty-one patients with oral squamous cell carcinoma (OSCC) who underwent adjuvant radiotherapy (RT) or chemoradiotherapy (CRT) were included. All patients were submitted to dental conditioning protocols prior to RT. OM and OM-related pain were evaluated daily during RT and graded according to the Common Toxicity Criteria for Adverse Events (National Cancer Institute, version 4.0, 2010) and the visual analogue scale (VAS). For the molecular analysis, whole saliva was collected immediately before RT and subjected to proteomic analysis by means of liquid chromatography–mass spectrometry (LTQ Orbitrap Velos MS; Thermo Fisher Scientific, Bremen, Germany) and label-free protein quantification. The results obtained from the targeted proteomic analysis were compared with OM clinical outcomes. Statistical analysis was performed by using Wilcoxon's test. Results Of the study patients, 73% presented with stage III/IV OSCC; 58% were submitted to CRT protocols, with a mean RT dose of 66 Gy. Most of the patients (66%) had visible tumor areas at the time of saliva collection; 43.9% had grade 2 and 31.7% had grade 3 as the highest OM grade during RT, with a mean highest reported VAS score of 3.53. For the target proteomics analysis, a total of 65 proteins were observed to be mostly related to biologic processes, such as immune responses, peptidase inhibitor activity, and the inflammatory system. The macrophage migration inhibitory factor (MIF HUMAN) was statistically significant when correlated with OM grade. MIF was observed in patients with grades 1 to 4 OM and showed higher abundance for OM grades 3 and 4 compared with grades 1 and 2 (P = .04). Conclusions The correlation of MIF with the severity of OM is compatible with the role of MIF as a proinflammatory protein. This seems to be the first study to describe this association; therefore, future prospective studies would be ideal to observe pre- and post-RT alterations in salivary MIF levels to validate this result and better understand the role of MIF in the pathogenesis of OM.

Epicardial adipose tissue volume and annexin A2/fetuin-A signalling are linked to coronary calcification in advanced coronary artery disease: Computed tomography and proteomic biomarkers from the EPICHEART study

Background & aimsThe role of epicardial adipose tissue (EAT) in the pathophysiology of late stage-coronary artery disease (CAD) has not been investigated. We explored the association of EAT volume and its proteome with advanced coronary atherosclerosis. MethodsThe EPICHEART Study prospectively enrolled 574 severe aortic stenosis patients referred to cardiac surgery. Before surgery, EAT volume was quantified by computed tomography (CT). During surgery, epicardial, mediastinal (MAT) and subcutaneous (SAT) adipose tissue samples were collected to explore fat phenotype by analyzing the proteomic profile using SWATH-mass spectrometry; pericardial fluid and peripheral venous blood were also collected. CAD presence was defined as coronary artery stenosis ≥50% in invasive angiography and by CT-derived Agatston coronary calcium score (CCS). ResultsEAT volume adjusted for body fat was associated with higher CCS, but not with the presence of coronary stenosis. In comparison with mediastinal and subcutaneous fat depots, EAT exhibited a pro-calcifying proteomic profile in patients with CAD characterized by upregulation of annexin-A2 and downregulation of fetuin-A; annexin-A2 protein levels in EAT samples were also positively correlated with CCS. We confirmed that the annexin-A2 gene was overexpressed in EAT samples of CAD patients and positively correlated with CCS. Fetuin-A gene was not detected in EAT samples, but systemic fetuin-A was higher in CAD than in non-CAD patients, suggesting that fetuin-A was locally downregulated. ConclusionsIn an elderly cohort of stable patients, CCS was associated with EAT volume and annexin-A2/fetuin-A signaling, suggesting that EAT might orchestrate pro-calcifying conditions in the late phases of CAD.

Re: Urine Proteomic Profiling in Patients with Nephrolithiasis and Cystinuria.

No AccessJournal of UrologyUrological Survey1 Jul 2019Re: Urine Proteomic Profiling in Patients with Nephrolithiasis and Cystinuria Dean G. AssimosMD Dean G. AssimosDean G. Assimos More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000000265AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Re: Urine Proteomic Profiling in Patients with Nephrolithiasis and Cystinuria." The Journal of Urology, 202(1), p. 25 Suggested Reading : Do urinary cystine parameters predict clinical stone activity?J Urol 2018; 199: 495. Link, Google Scholar : The interaction of thiol drugs and urine pH in the treatment of cystinuria. J Urol 2013; 189: 2147. Link, Google Scholar : Penicillamine therapy for pediatric cystinuria: experience from a cohort of American children. J Urol 2008; 180: 2620. Link, Google Scholar © 2019 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 202Issue 1July 2019Page: 25-25 Advertisement Copyright & Permissions© 2019 by American Urological Association Education and Research, Inc.MetricsAuthor Information Dean G. Assimos More articles by this author Expand All Advertisement Loading ...