bims-prodis 2019-01-13 papers

bims-prodis

Biomed News

on Proteomics in disease

Issue of 2019–01–13
39 papers selected by
Nancy Gough, Bioserendipity

Effects of APOE Genotype on Brain Proteomic Network and Cell Type Changes in Alzheimer's Disease.
Plasma Protein Biomarkers for the Prediction of CSF Amyloid and Tau and [18F]-Flutemetamol PET Scan Result.
Multiplexed LC/ESI-MRM-MS-based Assay for Identification of Coronary Artery Disease Biomarkers in Human Plasma.
High-density peptide arrays help to identify linear immunogenic B cell epitopes in individuals naturally exposed to malaria infection.
Quantitative mass spectrometry to interrogate proteomic heterogeneity in metastatic lung adenocarcinoma and validate a novel somatic mutation CDK12-G879V.
Proteomic pattern of cervico-vaginal fluid (CVF) in an ovarian cancer diagnosis - pilot study.
Proteomic Signatures Reveal Differences in Stress Response, Antioxidant Defense and Proteasomal Activity in Fertile Men with High Seminal ROS Levels.
Functional pathways associated with human carotid atheroma: a proteomics analysis.
Urinary Peptidomic Biomarker for Personalized Prevention and Treatment of Diastolic Left Ventricular Dysfunction.
Proteomics analysis indicated the protein expression pattern related to the development of fetal conotruncal defects.
Sample Pooling and Inflammation Linked to the False Selection of Biomarkers for Neurodegenerative Diseases in Top-Down Proteomics: A Pilot Study.
Cancer biomarkers in atherosclerotic plaque: Evidenced from structural and proteomic analyses.
Proteome analysis of human neutrophil granulocytes from patients with monogenic disease using data-independent acquisition.
Exosome proteomic analyses identify inflammatory phenotype and novel biomarkers in African American prostate cancer patients.
Urinary Proteomics as a tool to Identify Kidney Responders to Dipeptidyl Peptidase-4 Inhibition. A Hypothesis-Generating Analysis from the MARLINA-T2D Trial.
In vitro chondrogenic potency of surplus chondrocytes from autologous transplantation procedures does not predict short-term clinical outcomes.
Improved Differential Diagnosis of Alzheimer's Disease by Integrating ELISA and Mass Spectrometry-Based Cerebrospinal Fluid Biomarkers.
Blood-Derived Plasma Protein Biomarkers for Alzheimer's Disease in Han Chinese.
Mass Spectrometry-Based Comprehensive Analysis of Pancreatic Cyst Fluids.
Proteomic Screening for Serum Biomarkers for Cervical Cancer and Their Clinical Significance.
Multiplex assay for multiomics advances in personalized-precision medicine.
[Quantitative proteomics of human blood exosomes].
The SNAP25 interactome in ventromedial caudate in schizophrenia includes the mitochondrial protein ARF1.
Endometrial stromal cell proteome mapping in repeated implantation failure and recurrent pregnancy loss cases and fertile women.
Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae.
AXIN1 in Plasma or Serum Is a Potential New Biomarker for Endometriosis.
Human PAH is characterized by a pattern of lipid-related insulin resistance.
High accuracy differentiating autoimmune pancreatitis from pancreatic ductal adenocarcinoma by immunoglobulin G glycosylation.
Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis.
Ultra-high-performance liquid chromatography-mass spectrometry method for neutrophil gelatinase-associated lipocalin as a predictive biomarker in acute kidney injury.
Peptidome profiling dataset of ovarian cancer and non-cancer proximal fluids: Ascites and blood sera.
Molecular evidence of field cancerization initiated by diabetes in colon cancer patients.
A novel contribution to clubfoot pathogenesis: the possible role of extracellular matrix proteins.
Identification of Novel Autoantibodies Associated with Psoriatic Arthritis.
Probing the endogenous peptidomes of cancer for biomarkers: A new endeavor.
Close association between abnormal expressed enzymes of energy metabolism and diarrhea-predominant irritable bowel syndrome.
Molecular changes during extended neoadjuvant letrozole treatment of breast cancer: distinguishing acquired resistance from dormant tumours.
Urinary proteomics and precision medicine for chronic kidney disease: Current status and future perspectives.
Data-driven discovery and validation of circulating blood-based biomarkers associated with prevalent atrial fibrillation.

Front Mol Neurosci. 2018 ;11 454

Effects of APOE Genotype on Brain Proteomic Network and Cell Type Changes in Alzheimer's Disease.

Jingting Dai, Erik C B Johnson, Eric B Dammer, Duc M Duong, Marla Gearing, James J Lah, Allan I Levey, Thomas S Wingo, Nicholas T Seyfried.

  Polymorphic alleles in the apolipoprotein E (APOE) gene are the main genetic determinants of late-onset Alzheimer's disease (AD) risk. Individuals carrying the APOE E4 allele are at increased risk to develop AD compared to those carrying the more common E3 allele, whereas those carrying the E2 allele are at decreased risk for developing AD. How ApoE isoforms influence risk for AD remains unclear. To help fill this gap in knowledge, we performed a comparative unbiased mass spectrometry-based proteomic analysis of post-mortem brain cortical tissues from pathologically-defined AD or control cases of different APOE genotypes. Control cases (n = 10) were homozygous for the common E3 allele, whereas AD cases (n = 24) were equally distributed among E2/3, E3/3, and E4/4 genotypes. We used differential protein expression and co-expression analytical approaches to assess how changes in the brain proteome are related to APOE genotype. We observed similar levels of amyloid-β, but reduced levels of neurofibrillary tau, in E2/3 brains compared to E3/3 and E4/4 AD brains. Weighted co-expression network analysis revealed 33 modules of co-expressed proteins, 12 of which were significantly different by APOE genotype in AD. The modules that were significantly different by APOE genotype were associated with synaptic transmission and inflammation, among other biological processes. Deconvolution and analysis of brain cell type changes revealed that the E2 allele suppressed homeostatic and disease-associated cell type changes in astrocytes, microglia, oligodendroglia, and endothelia. The E2 allele-specific effect on brain cell type changes was validated in a separate cohort of 130 brains. Our systems-level proteomic analyses of AD brain reveal alterations in the brain proteome and brain cell types associated with allelic variants in APOE, and suggest further areas for investigation into the upstream mechanisms that drive ApoE-associated risk for AD.

Keywords:  Alzheimer's disease; apolipoprotein E; deconvolution; inflammation; proteomics

DOI:  https://doi.org/10.3389/fnmol.2018.00454
Front Aging Neurosci. 2018 ;10 409

Plasma Protein Biomarkers for the Prediction of CSF Amyloid and Tau and [18F]-Flutemetamol PET Scan Result.

Sarah Westwood, Alison L Baird, Abdul Hye, Nicholas J Ashton, Alejo J Nevado-Holgado, Sneha N Anand, Benjamine Liu, Danielle Newby, Chantal Bazenet, Steven J Kiddle, Malcolm Ward, Ben Newton, Keyur Desai, Cristina Tan Hehir, Michelle Zanette, Daniela Galimberti, Lucilla Parnetti, Alberto Lleó, Susan Baker, Vaibhav A Narayan, Wiesje M van der Flier, Philip Scheltens, Charlotte E Teunissen, Pieter Jelle Visser, Simon Lovestone.

  Background: Blood biomarkers may aid in recruitment to clinical trials of Alzheimer's disease (AD) modifying therapeutics by triaging potential trials participants for amyloid positron emission tomography (PET) or cerebrospinal fluid (CSF) Aβ and tau tests. Objective: To discover a plasma proteomic signature associated with CSF and PET measures of AD pathology. Methods: Liquid chromatography-tandem mass spectrometry (LC-MS/MS) based proteomics were performed in plasma from participants with subjective cognitive decline (SCD), mild cognitive impairment (MCI), and AD, recruited to the Amsterdam Dementia Cohort, stratified by CSF Tau/Aβ42 (n = 50). Technical replication and independent validation were performed by immunoassay in plasma from SCD, MCI, and AD participants recruited to the Amsterdam Dementia Cohort with CSF measures (n = 100), MCI participants enrolled in the GE067-005 study with [18F]-Flutemetamol PET amyloid measures (n = 173), and AD, MCI and cognitively healthy participants from the EMIF 500 study with CSF Aβ42 measurements (n = 494). Results: 25 discovery proteins were nominally associated with CSF Tau/Aβ42 (P < 0.05) with associations of ficolin-2 (FCN2), apolipoprotein C-IV and fibrinogen β chain confirmed by immunoassay (P < 0.05). In the GE067-005 cohort, FCN2 was nominally associated with PET amyloid (P < 0.05) replicating the association with CSF Tau/Aβ42. There were nominally significant associations of complement component 3 with PET amyloid, and apolipoprotein(a), apolipoprotein A-I, ceruloplasmin, and PPY with MCI conversion to AD (all P < 0.05). In the EMIF 500 cohort FCN2 was trending toward a significant relationship with CSF Aβ42 (P ≈ 0.05), while both A1AT and clusterin were nominally significantly associated with CSF Aβ42 (both P < 0.05). Conclusion: Associations of plasma proteins with multiple measures of AD pathology and progression are demonstrated. To our knowledge this is the first study to report an association of FCN2 with AD pathology. Further testing of the proteins in larger independent cohorts will be important.

Keywords:  Alzheimer’s disease; amyloid; biomarkers; blood; ficolin-2; plasma; proteomics; tau

DOI:  https://doi.org/10.3389/fnagi.2018.00409
Proteomics Clin Appl. 2019 Jan 11. e1700111

Multiplexed LC/ESI-MRM-MS-based Assay for Identification of Coronary Artery Disease Biomarkers in Human Plasma.

Mohammad A Anwar, Darlene Liying Dai, Janet Wilson-McManus, Derek Smith, Gordon A Francis, Christoph H Borchers, Bruce M McManus, John S Hill, Gabriela V Cohen Freue.

   PURPOSE: A highly-multiplexed LC/ESI-MRM-MS based assay was developed for the identification of coronary artery disease (CAD) biomarkers in human plasma.
EXPERIMENTAL DESIGN: The assay was used to measure 107 stable isotope labeled peptide standards and native peptides from 64 putative biomarkers of cardiovascular diseases in tryptic digests of plasma from subjects with (n = 70) and without (n = 45) angiographic evidence of CAD and no subsequent cardiovascular mortality during follow-up.
RESULTS: Extensive computational and statistical analysis revealed 6 plasma proteins associated with CAD, namely apolipoprotein CII, C reactive protein, CD5 antigen-like, fibronectin, inter alpha trypsin inhibitor heavy chain H1, and protein S. The identified proteins were combined into a LASSO-logistic score with high classification performance (cross-validated AUC = 0.74). When combined with a separate score computed from markers currently used in the clinic with similar performance, the AUC increased to 0.84. Similar results were observed in an independent set of subjects (n = 87).
CONCLUSIONS AND CLINICAL RELEVANCE: If externally validated, the assay and identified biomarkers can improve CAD risk stratification. This article is protected by copyright. All rights reserved.

Keywords:  MRM-MS; biomarkers; classification; coronary artery disease; proteomics

DOI:  https://doi.org/10.1002/prca.201700111
Mol Cell Proteomics. 2019 Jan 10. pii: mcp.RA118.000992. [Epub ahead of print]

High-density peptide arrays help to identify linear immunogenic B cell epitopes in individuals naturally exposed to malaria infection.

Thomas Jaenisch, Kirsten Heiss, Nico Fischer, Carolin Geiger, F Ralf Bischoff, Gerhard Moldenhauer, Leszek Rychlewski, Ali Sié, Boubacar Coulibaly, Peter H Seeberger, Lucjan S Wyrwicz, Frank Breitling, Felix F Loeffler.

  High-density peptide arrays are an excellent means to profile anti-plasmodial antibody responses. Different protein intrinsic epitopes can be distinguished and additional insights are gained, when compared to assays involving the full-length protein. Distinct reactivities to specific epitopes within one protein may explain differences in published results, regarding immunity or susceptibility to malaria. We pursued three approaches to find specific epitopes within important plasmodial proteins, (1) twelve leading vaccine candidates were mapped as overlapping 15-mer peptides, (2) a bioinformatical approach served to predict immunogenic malaria epitopes which were subsequently validated in the assay, and (3) randomly selected peptides from the malaria proteome were screened as a control. Several peptide array replicas were prepared, employing particle-based laser printing, and were used to screen 27 serum samples from a malaria-endemic area in Burkina Faso, West Africa. The immunological status of the individuals was classified as 'protected' or 'unprotected' based on clinical symptoms, parasite density, and age. The vaccine candidate screening approach resulted in significant hits in all twelve proteins and allowed us (i) to verify many known immunogenic structures, (ii) to map B cell epitopes across the entire sequence of each antigen and (iii) to uncover novel immunogenic epitopes. Predicting immunogenic regions in the proteome of the human malaria parasite Plasmodium falciparum, via the bioinformatics approach and subsequent array screening, confirmed known immunogenic sequences, such as in the leading malaria vaccine candidate CSP and discovered immunogenic epitopes derived from hypothetical or unknown proteins.

Keywords:  Antibodies*; Biomarker: Diagnostic; Malaria; Peptide array; Peptidomics; epitope mapping

DOI:  https://doi.org/10.1074/mcp.RA118.000992
Mol Cell Proteomics. 2019 Jan 07. pii: mcp.RA118.001266. [Epub ahead of print]

Quantitative mass spectrometry to interrogate proteomic heterogeneity in metastatic lung adenocarcinoma and validate a novel somatic mutation CDK12-G879V.

Xu Zhang, Khoa Dang Nguyen, Paul Rudnick, Nitin Roper, Emily Kawaler, Tapan K Maity, Shivangi Awasthi, Shaojian Gao, Romi Biswas, Abhilash Venugopalan, Constance M Cultraro, David Fenyö, Udayan Guha.

  Lung cancer is the leading cause of cancer death in both men and women. Tumor heterogeneity is an impediment to targeted treatment of all cancers, including lung cancer. Here, we sought to characterize tumor proteome and phosphoproteome changes by longitudinal, prospective collection of tumor tissue from an exceptional responder lung adenocarcinoma patient who survived with metastatic lung adenocarcinoma for over seven years while undergoing HER2-directed therapy in combination with chemotherapy. We employed "Super-SILAC" and TMT labeling strategies to quantify the proteome and phosphoproteome of a lung metastatic site and eight distinct metastatic progressive lymph nodes collected during these seven years, including five lymph nodes procured at autopsy. We identified specific signaling networks enriched in lung in comparison to the lymph node metastatic sites. We correlated the changes in protein abundance with changes in copy number alteration (CNA) and transcript expression. ERBB2/HER2 protein expression was higher in lung, consistent with a higher degree of ERBB2 amplification in lung compared to the lymph node metastatic sites. To further interrogate the mass spectrometry data, a patient-specific database was built by incorporating all the somatic and germline variants identified by whole genome sequencing (WGS) of genomic DNA from the lung, one lymph node metastatic site and blood. An extensive validation pipeline was built to confirm variant peptides. We validated 360 spectra corresponding to 55 germline and 6 somatic variant peptides. Targeted MRM assays revealed two novel variant somatic peptides, CDK12-G879V and FASN-R1439Q, expressed in lung and lymph node metastatic sites, respectively. The CDK12-G879V mutation likely results in a nonfunctional CDK12 kinase and chemotherapy susceptibility in lung metastatic sites. Knockdown of CDK12 in lung adenocarcinoma cells increased chemotherapy sensitivity which was rescued by wild type, but not CDK12-G879V expression, consistent with the complete resolution of the lung metastatic sites in this patient.

Keywords:  Cancer Biology*; Database design; Lung cancer; Mass Spectrometry; Multiple reaction monitoring; Tumor Heterogeneity

DOI:  https://doi.org/10.1074/mcp.RA118.001266
Ginekol Pol. 2018 ;89(12): 688-694

Proteomic pattern of cervico-vaginal fluid (CVF) in an ovarian cancer diagnosis - pilot study.

Emilia Gasiorowska, Bartosz Urbaniak, Jakub Lorek, Jan Matysiak, Ewa Nowak-Markwitz.

   OBJECTIVES: High grade serous ovarian cancer (HGSC) is the most common type of ovarian cancer and is responsible for about 90% of ovarian cancer deaths. The diagnostic tests currently used do not increase the detection rates for ovarian cancer. There is a great necessity to develop new and non-invasive diagnostic tests for ovarian cancer (OC). Cervico-vaginal fluid (CVF) seems to be a potential and valuable source of biomarkers for genital tract diseases including ovarian cancer. The aim of our pilot study was to undertake a preliminary proteomic analysis of CVF derived from ovarian cancer patients and to compare these with results from a control group.
MATERIAL AND METHODS: We analysed and compared samples from a group of ovarian cancer patients and a control group of healthy patients. The study used MALDI-TOF coupled with nanoLC and ClinProTools software for MS, MS/MS spectra collection and proteomic analysis.
RESULTS: We identified 404 different proteins in the OC group and 417 proteins in the control group. 239 of the proteins were found to be common to both study groups, 165 proteins were unique to the OC subjects, and 178 proteins were unique to the control subjects. We selected three proteins as the OC markers with the greatest potential: cysteine-rich secretory protein 3, fibronectin and Ly6/PLAUR domain-containing protein 3.
CONCLUSIONS: The proteins we selected seem to possess great potential as markers for the screening and early detection of OC, especially in non-invasive and low-cost diagnostic tests. However, our findings require more advanced and validated proteomic analysis to confirm the suitability of the selected proteins in everyday medical diagnoses.

Keywords:  cervico-vaginal fluid; ovarian cancer; proteomic pattern; tumor markers

DOI:  https://doi.org/10.5603/GP.a2018.0116
Int J Mol Sci. 2019 Jan 08. pii: E203. [Epub ahead of print]20(1):

Proteomic Signatures Reveal Differences in Stress Response, Antioxidant Defense and Proteasomal Activity in Fertile Men with High Seminal ROS Levels.

Tânia R Dias, Luna Samanta, Ashok Agarwal, Peter N Pushparaj, Manesh Kumar Panner Selvam, Rakesh Sharma.

  Elevated levels of reactive oxygen species (ROS) are a major cause of male infertility. However, some men with high seminal ROS levels are still fertile. The main objective of this study was to understand the molecular mechanism(s) responsible for the preservation of fertility in those men. Semen samples from fertile men were divided into two groups: control (n = 10, ROS < 102.2 RLU/s/10⁶ sperm) and ROS+ (n = 10, ROS > 102.2 RLU/s/10⁶ sperm). Proteomic analysis of seminal plasma and spermatozoa was used to identify the differentially expressed proteins (DEPs) between the experimental groups, from which some proteins were validated by Western blot (WB). A total of 44 and 371 DEPs were identified between the study groups in the seminal plasma and spermatozoa, respectively. The identified DEPs were primarily involved in oxidoreductase, endopeptidase inhibitor, and antioxidant activities. We validated by WB the underexpression of NADH:ubiquinone oxidoreductase core subunit S1 (p = 0.01), as well as the overexpression of superoxide dismutase 1 (p = 0.03) and peroxiredoxin 4 (p = 0.04) in spermatozoa of ROS+ group. Our data suggest that fertile men with high ROS levels possess an effective antioxidant defense system that protects sperm proteins, as well as an active proteasomal system for degradation of defective proteins.

Keywords:  Western blot; antioxidants; bioinformatics; chemiluminescence; differentially expressed proteins; proteomics; reactive oxygen species; seminal plasma; spermatozoa

DOI:  https://doi.org/10.3390/ijms20010203
Hypertens Res. 2019 Jan 07.

Functional pathways associated with human carotid atheroma: a proteomics analysis.

Ali Nehme, Firas Kobeissy, Jingfu Zhao, Rui Zhu, Patrick Feugier, Yehia Mechref, Kazem Zibara.

  Advances in large-scale analysis are becoming very useful in understanding health and disease. Here, we used high-throughput mass spectrometry to identify differentially expressed proteins between early and advanced lesions. Carotid endarterectomy samples were collected and dissected into early and advanced atherosclerotic lesion portions. Proteins were extracted and subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Differentially expressed proteins were identified and verified using multiple reaction monitoring (MRM), on which advanced systems biology and enrichment analyses were performed. The identified proteins were further compared to the transcriptomic data of 32 paired samples obtained from early and advanced atherosclerotic lesions. A total of 95 proteins were upregulated, and 117 proteins were downregulated in advanced lesions compared to early atherosclerotic lesions (p < 0.05). The upregulated proteins were associated with proatherogenic processes, whereas downregulated proteins were involved in extracellular matrix organization and vascular smooth muscle cytoskeleton. Many of the identified proteins were linked to various "upstream regulators", among which TGFβ had the highest connections. Specifically, a total of 19 genes were commonly upregulated, and 30 genes were downregulated at the mRNA and protein levels. These genes were involved in vascular smooth muscle cell activity, for which enriched transcription factors were identified. This study deciphers altered pathways in atherosclerosis and identifies upstream regulators that could be candidate targets for treatment.

Keywords:  Atherosclerosis; Carotid artery; Proteome; Transcription regulators; Transcriptome

DOI:  https://doi.org/10.1038/s41440-018-0192-4
Proteomics Clin Appl. 2019 Jan 11. e1800174

Urinary Peptidomic Biomarker for Personalized Prevention and Treatment of Diastolic Left Ventricular Dysfunction.

Zhen-Yu Zhang, Esther Nkuipou-Kenfack, Jan A Staessen.

  Diastolic heart failure (DHF) is characterized by slow left ventricular (LV) relaxation, increased LV stiffness, interstitial deposition of collagen, and a modified extracellular matrix proteins. Among Europeans, the frequency of asymptomatic diastolic LV dysfunction (DD) is 25%. This constitutes a large pool of people at high risk of DHF. The goal of this review was to describe the discovery and the initial validation of new multidimensional urinary peptidomic biomarkers (UPB) indicative of DD, mainly consisting of collagen fragments, and to describe a roadmap for their introduction in to clinical practice. The availability of new drugs creates a window of opportunity for mounting a randomized clinical trial consolidating the clinical applicability of UPB to screen for DD. If successfully completed, such trial will benefit ∼25% of all people older than 50 years and open a large market for a UPB diagnostic tool and the drug tested. Moreover, sequenced peptides making up UPB will generate novel insights in the pathophysiology of DD and facilitate personalized treatment of patients with DHF for whom prevention came too late. If proven cost-effective, the clinical application of UPB will contribute to the sustainability of health care in ageing population in epidemiologic transition. This article is protected by copyright. All rights reserved.

Keywords:  diastolic heart failure; diastolic left ventricular dysfunction; population science; urinary peptidomics

DOI:  https://doi.org/10.1002/prca.201800174
J Cell Physiol. 2019 Jan 12.

Proteomics analysis indicated the protein expression pattern related to the development of fetal conotruncal defects.

Yun Wu, Jingjing Zhang, Mei Wang, Ling Yang, Yongmei Wang, Tao Hu, An Liu, Qing Cheng, Ziyi Fu, Pingyang Zhang, Li Cao.

  Abnormal development of embryonic conus arteriosus could lead to conotruncal defects in fetal heart, and increase the incidence of fetal congenital heart disease. Tetralogy of Fallot (TOF) is one of the most common forms of congenital heart disease. It may be helpful for us to solve this clinical problem through exploring the molecular mechanisms of development in embryonic congenital heart disease. Proteomics has attracted much attention in understanding the development of human diseases during the past decades. However, there is still little information about the relationship between protein expression pattern and TOF. In this study, we aimed to explore the potential linkage of proteomics and TOF development. Briefly, 121 differentially expressed proteins were identified from a TOF group, compared with a control group. The expression levels of 34 of these proteins were significantly different (>1.5 absolute fold change, p < 0.05) between the two groups. Gene ontology (GO) and pathway analysis showed that these proteins were mainly associated with carbon metabolism, biosynthesis of antibodies, positive regulation of transcription from RNA polymerase II promoter, nucleus, ATP binding, and so on. The ingenuity pathway analysis (IPA) results indicated that 435 of upstream regulators were identified of these differentially expressed proteins, which might be involved in the development of TOF. Data of string analysis showed the protein-protein interaction network among the differentially expressed proteins and regulators, which are related to TOF. In conclusion, our study explored the protein expression pattern of TOF, which might provide new insights into understanding the mechanism of TOF development and afford potential targets for TOF diagnosis and therapy.

Keywords:  conotruncal defects (CTD); protein expression pattern; proteomics; tetralogy of fallot (TOF)

DOI:  https://doi.org/10.1002/jcp.28033
Front Mol Neurosci. 2018 ;11 477

Sample Pooling and Inflammation Linked to the False Selection of Biomarkers for Neurodegenerative Diseases in Top-Down Proteomics: A Pilot Study.

Nicolas Molinari, Stéphane Roche, Katell Peoc'h, Laurent Tiers, Martial Séveno, Christophe Hirtz, Sylvain Lehmann.

  Proteomic technologies have been recently adapted to the new field of clinical proteomics. The origin of errors and biases has been well-identified in the pre-analytical steps, leading to the measurement of clinical analytes. One possible source of inadequacy in clinical proteomics is linked to sample pooling. This practice is usually related to low sample availability, variability, experiment time/cost. In this study, we first asked whether sample pooling in top-down proteomics is suitable to obtain a relevant biological average. Our second objective was to identify inflammatory biomarkers of outlier samples in our population of Creutzfeldt-Jakob disease patients. Our results demonstrated that, in a proteomics study, sample pooling as well as the inflammation status was an important source of errors: missed detection of biomarkers and false identification of others. Pooled samples were not equivalent to the average of biological values. In addition, this procedure reduced the statistical value of the identified biomarkers due to a stabilization of their standard deviation and rendered outlier samples difficult to detect. We identified serum amyloid A as a candidate biomarker of outlier samples. The presence of this protein, which could be explained by inflammatory processes, induced major modifications in the sample profiles.

Keywords:  CRP; SAA; clinical proteomics; neurodegenerative disease; sample pooling; serum; top–down

DOI:  https://doi.org/10.3389/fnmol.2018.00477
Biochem Biophys Res Commun. 2019 Jan 04. pii: S0006-291X(18)32841-9. [Epub ahead of print]

Cancer biomarkers in atherosclerotic plaque: Evidenced from structural and proteomic analyses.

Hamidreza Fasehee, Mahsa Fakhraee, Saeed Davoudi, Hojatollah Vali, Shahab Faghihi.

  Atherosclerosis and cancer are the leading causes of mortality around the world that share common pathogenic pathways. The aim of this study is the investigation of the protein profile of atherosclerotic plaque in order to find similar biomarker between cancer and atherosclerosis. The small pieces of human coronary artery containing advanced atherosclerotic plaque is obtained from patients during bypass surgery. Structural characterization of type V plaque, including fibrous connective tissue, necrotic lipid core, cholesterol clefts and calcium deposits are performed using high resolution transmission electron microscopy (HR-TEM). The protein profile of atherosclerosis plaque is also analyzed using 2-dimensional electrophoresis and matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF). TEM analysis shows that vascular smooth muscle cells (VSMCs) exhibit different and uncommon morphologies in atherosclerotic plaque which is correlated to the proliferative state of the cells. The proteomics analysis reveals proteins related to atherosclerosis formation including Mimecan, Ras Suppressor Protein-1 (RSUP-1) and Cathepsin D which identified as biomarker of cancerous tumors. The expression of Mimecan and RSUP-1 is down-regulated in atherosclerotic plaque while the expression of Cathepsin D is up-regulated. These data support that atherosclerotic plaque presents some degree of tumorgenesis with the significant activity of VSMCs as the key player in atherogenesis.

Keywords:  2D electrophoresis; Atherosclerosis; Cancer; Coronary artery; TEM

DOI:  https://doi.org/10.1016/j.bbrc.2018.12.160
Mol Cell Proteomics. 2019 Jan 10. pii: mcp.RA118.001141. [Epub ahead of print]

Proteome analysis of human neutrophil granulocytes from patients with monogenic disease using data-independent acquisition.

Piotr Grabowski, Sebastian Hesse, Sebastian Hollizeck, Meino Rohlfs, Uta Behrends, Roya Sherkat, Hannah Tamary, Ekrem Ünal, Raz Somech, Türkan Patıroğlu, Stefan Canzar, Jutte van der Werff Ten Bosch, Christoph Klein, Juri Rappsilber.

  Neutrophil granulocytes are critical mediators of innate immunity and tissue regeneration. Rare diseases of neutrophil granulocytes may affect their differentiation and/or functions. However, there are very few validated diagnostic tests assessing the functions of neutrophil granulocytes in these diseases. Here, we set out to probe omics analysis as a novel diagnostic platform for patients with defective differentiation and function of neutrophil granulocytes. We analyzed highly purified neutrophil granulocytes from 68 healthy individuals and 16 patients with rare monogenic diseases. Cells were isolated from fresh venous blood (purity >99%) and used to create a spectral library covering almost 8000 proteins using strong cation exchange fractionation. Patient neutrophil samples were then analyzed by data-independent acquisition proteomics, quantifying 4154 proteins in each sample. Neutrophils with mutations in the neutrophil elastase gene ELANE, showed large proteome changes that suggest these mutations may affect maturation of neutrophil granulocytes and initiate misfolded protein response and cellular stress mechanisms. In contrast, only few proteins changed in patients with leukocyte adhesion deficiency (LAD) and chronic granulomatous disease (CGD). Strikingly, neutrophil transcriptome analysis showed no correlation with its proteome. In case of two patients with undetermined genetic causes, proteome analysis guided the targeted genetic diagnostics and uncovered the underlying genomic mutations. Data-independent acquisition proteomics may help to define novel pathomechanisms in neutrophil diseases and provide a clinically useful diagnostic dimension.

Keywords:  Diagnostic; Immunology*; Omics; Personalized medicine; Proteogenomics; data-independent acquisition; neutrophil granulocyte; primary immunodeficiency diseases; systems medicine; whole exome sequencing

DOI:  https://doi.org/10.1074/mcp.RA118.001141
Cancer Med. 2019 Jan 08.

Exosome proteomic analyses identify inflammatory phenotype and novel biomarkers in African American prostate cancer patients.

Gati K Panigrahi, Prakash P Praharaj, Hiroki Kittaka, Asit R Mridha, Olen M Black, Rakesh Singh, Roger Mercer, Adrie van Bokhoven, Kathleen C Torkko, Chapla Agarwal, Rajesh Agarwal, Zakaria Y Abd Elmageed, Hariom Yadav, Santosh K Mishra, Gagan Deep.

  African American men face a stark prostate cancer (PCa)-related health disparity, with the highest incidence and mortality rates compared to other races. Additional and innovative measures are warranted to reduce this health disparity. Here, we focused on the identification of a novel serum exosome-based "protein signature" for potential use in the early detection and better prognosis of PCa in African American men. Nanoparticle tracking analyses showed that compared to healthy individuals, exosome concentration (number/ml) was increased by ~3.2-fold (P ˂ 0.05) in the sera of African American men with PCa. Mass spectrometry-based proteomic analysis of serum exosomes identified seven unique and fifty-five overlapping proteins (up- or downregulated) in African Americans with PCa compared to healthy African Americans. Furthermore, ingenuity pathway analyses identified the inflammatory acute-phase response signaling as the top pathway associated with proteins loaded in exosomes from African American PCa patients. Interestingly, African American PCa E006AA-hT cells secreted exosomes strongly induced a proinflammatory M2-phenotype in macrophages and showed calcium response on sensory neurons, suggesting a neuroinflammatory response. Additionally, proteomic analyses showed that the protein Isoform 2 of Filamin A has higher loading (2.6-fold) in exosomes from African Americans with PCa, but a lesser loading (0.6-fold) was observed in exosomes from Caucasian men with PCa compared to race-matched healthy individuals. Interestingly, TCGA and Taylor's dataset as well as IHC analyses of PCa tissue showed a lower Filamin A expression in tissues of PCa patients compared with normal subjects. Overall, these results support the usefulness of serum exosomes to noninvasively detect inflammatory phenotype and to discover novel biomarkers associated with PCa in African American men.

Keywords:  biomarker; exosomes; health disparity; inflammation; prostate cancer

DOI:  https://doi.org/10.1002/cam4.1885
Proteomics Clin Appl. 2019 Jan 11. e1800144

Urinary Proteomics as a tool to Identify Kidney Responders to Dipeptidyl Peptidase-4 Inhibition. A Hypothesis-Generating Analysis from the MARLINA-T2D Trial.

Justyna Siwy, Thomas Klein, Marcel Rosler, Maximilan von Eynatten.

   PURPOSE: Chronic kidney disease (CKD) is a serious complication of hyperglycemia and treatment options to slow its progression are scarce. Dipeptidyl peptidase-4 (DPP-4) inhibitors are commonly used glucose-lowering drugs in type 2 diabetes (T2D). Among these, linagliptin has been suggested to exert kidney protective effects. We investigated whether a potential effect of linagliptin on kidney function could be unmasked by characterizing the urinary proteome profile (UPP) in T2D individuals with prevalent albuminuria.
EXPERIMENTAL DESIGN: This study was performed based on data and samples available from the previously reported MARLINA-T2D trail (NCT01792518). Study participants were randomized 1:1 to receive either linagliptin 5mg or placebo for 24 weeks. A previously developed urinary proteome-based classifier, CKD273, was assessed.
RESULTS: Our results confirm previous studies of a significant correlation between CKD273 and clinical kidney parameters as well as with eGFR decline. Patient stratification using CKD273 at baseline, showed a trend towards attenuation of renal function loss in high CKD-risk patients treated with linagliptin. We further characterized linagliptin affected peptides of which the majority contained a DPP-4 target sequence and some also correlated with urinary DPP-4 activity.
CONCLUSIONS AND CLINICAL RELEVANCE: CKD273 is a promising tool for identifying patients at high risk for kidney disease progression and may unmask a potential of linagliptin to slow progressive kidney function loss in high CKD-risk patients. UPP characterization revealed a significant impact of linagliptin on urinary peptides. This article is protected by copyright. All rights reserved.

Keywords:  biomarker; chronic kidney disease; diabetes; linagliptin; proteomics

DOI:  https://doi.org/10.1002/prca.201800144
BMC Musculoskelet Disord. 2019 Jan 10. 20(1): 19

In vitro chondrogenic potency of surplus chondrocytes from autologous transplantation procedures does not predict short-term clinical outcomes.

Ashraful Islam, Vegard Fossum, Ann Kristin Hansen, Ilona Urbarova, Gunnar Knutsen, Inigo Martinez-Zubiaurre.

   BACKGROUND: Autologous chondrocyte implantation (ACI) has been used over the last two decades to treat focal cartilage lesions aiming to delay or prevent the onset of osteoarthritis; however, some patients do not respond adequately to the procedure. A number of biomarkers that can forecast the clinical potency of the cells have been proposed, but evidence for the relationship between in vitro chondrogenic potential and clinical outcomes is missing. In this study, we explored if the ability of cells to make cartilage in vitro correlates with ACI clinical outcomes. Additionally, we evaluated previously proposed chondrogenic biomarkers and searched for new biomarkers in the chondrocyte proteome capable of predicting clinical success or failure after ACI.
METHODS: The chondrogenic capacity of chondrocytes derived from 14 different donors was defined based on proteoglycans staining and visual histological grading of tissues generated using the pellet culture system. A Lysholm score of 65 two years post-ACI was used as a cut-off to categorise "success" and "failure" clinical groups. A set of predefined biomarkers were investigated in the chondrogenic and clinical outcomes groups using flow cytometry and qPCR. High-throughput proteomics of cell lysates was used to search for putative biomarkers to predict chondrogenesis and clinical outcomes.
RESULTS: Visual histological grading of pellets categorised donors into "high" and "low" chondrogenic groups. Direct comparison between donor-matched in vitro chondrogenic potential and clinical outcomes revealed no significant associations. Comparative analyses of selected biomarkers revealed that expression of CD106 and TGF-β-receptor-3 was enhanced in the low chondrogenic group, while expression of integrin-α1 and integrin-β1 was significantly upregulated in the high chondrogenic group. Additionally, increased surface expression of CD166 was observed in the clinical success group, while the gene expression of cartilage oligomeric matrix protein was downregulated. High throughput proteomics revealed no differentially expressed proteins from success and failure clinical groups, whereas seven proteins including prolyl-4-hydroxylase 1 were differentially expressed when comparing chondrogenic groups.
CONCLUSION: In our limited material, we found no correlation between in vitro cartilage-forming capacity and clinical outcomes, and argue on the limitations of using the chondrogenic potential of cells or markers for chondrogenesis as predictors of clinical outcomes.

Keywords:  3D culture; ACI; Biomarkers; CD166; Cartilage; Chondrocytes; Clinical outcome; In vitro chondrogenesis; P4HA1; Proteomics

DOI:  https://doi.org/10.1186/s12891-018-2380-4
J Alzheimers Dis. 2019 Jan 03.

Improved Differential Diagnosis of Alzheimer's Disease by Integrating ELISA and Mass Spectrometry-Based Cerebrospinal Fluid Biomarkers.

Payam Emami Khoonsari, Ganna Shevchenko, Stephanie Herman, Julia Remnestål, Vilmantas Giedraitis, RoseMarie Brundin, Malin Degerman Gunnarsson, Lena Kilander, Henrik Zetterberg, Peter Nilsson, Lars Lannfelt, Martin Ingelsson, Kim Kultima.

   BACKGROUND: Alzheimer's disease (AD) is diagnosed based on a clinical evaluation as well as analyses of classical biomarkers: Aβ42, total tau (t-tau), and phosphorylated tau (p-tau) in cerebrospinal fluid (CSF). Although the sensitivities and specificities of the classical biomarkers are fairly good for detection of AD, there is still a need to develop novel biochemical markers for early detection of AD.
OBJECTIVE: We explored if integration of novel proteins with classical biomarkers in CSF can better discriminate AD from non-AD subjects.
METHODS: We applied ELISA, mass spectrometry, and multivariate modeling to investigate classical biomarkers and the CSF proteome in subjects (n = 206) with 76 AD patients, 74 mild cognitive impairment (MCI) patients, 11 frontotemporal dementia (FTD) patients, and 45 non-dementia controls. The MCI patients were followed for 4-9 years and 21 of these converted to AD, whereas 53 remained stable.
RESULTS: By combining classical CSF biomarkers with twelve novel markers, the area of the ROC curves (AUROCS) of distinguishing AD and MCI/AD converters from non-AD were 93% and 96%, respectively. The FTDs and non-dementia controls were identified versus all other groups with AUROCS of 96% and 87%, respectively.
CONCLUSIONS: Integration of new and classical CSF biomarkers in a model-based approach can improve the identification of AD, FTD, and non-dementia control subjects.

Keywords:  Alzheimer’s disease; ELISA; cerebrospinal fluid; mass spectrometry; mild cognitive impairment; proteomics

DOI:  https://doi.org/10.3233/JAD-180855
Front Aging Neurosci. 2018 ;10 414

Blood-Derived Plasma Protein Biomarkers for Alzheimer's Disease in Han Chinese.

Zaohuo Cheng, Jiajun Yin, Hongwei Yuan, Chunhui Jin, Fuquan Zhang, Zhiqiang Wang, Xiaowei Liu, Yue Wu, Tao Wang, Shifu Xiao.

  It is well known that Alzheimer's disease (AD) is one of the most common progressive neurodegenerative diseases; it begins gradually, and therefore no effective medicine is administered in the beginning. Thus, early diagnosis and prevention of AD are crucial. The present study focused on comparing the plasma protein changes between patients with AD and their healthy counterparts, aiming to explore a specific protein panel as a potential biomarker for AD patients in Han Chinese. Hence, we recruited and collected plasma samples from 98 AD patients and 101 elderly healthy controls from Wuxi and Shanghai Mental Health Centers. Using a Luminex assay, we investigated the expression levels of fifty plasma proteins in these samples. Thirty-two out of 50 proteins were found to be significantly different between AD patients and healthy controls (P < 0.05). Furthermore, an eight-protein panel that included brain-derived neurotrophic factor (BDNF), angiotensinogen (AGT), insulin-like growth factor binding protein 2 (IGFBP-2), osteopontin (OPN), cathepsin D, serum amyloid P component (SAP), complement C4, and prealbumin (transthyretin, TTR) showed the highest determinative score for AD and healthy controls (all P = 0.00). In conclusion, these findings suggest that a combination of eight plasma proteins can serve as a promising diagnostic biomarker for AD with high sensitivity and specificity in Han Chinese populations; the eight plasma proteins were proven important for AD diagnosis by further cross-validation studies within the AD cohort.

Keywords:  Alzheimer’s disease; Han Chinese; biomarker; early diagnosis; plasma protein

DOI:  https://doi.org/10.3389/fnagi.2018.00414
Biomed Res Int. 2018 ;2018 7169595

Mass Spectrometry-Based Comprehensive Analysis of Pancreatic Cyst Fluids.

Agnieszka Paziewska, Marcin Polkowski, Tymon Rubel, Jakub Karczmarski, Anna Wiechowska-Kozlowska, Michalina Dabrowska, Michal Mikula, Michal Dadlez, Jerzy Ostrowski.

Pancreatic cyst fluids (PCFs) enriched in tumour-derived proteins are considered a potential source of new biomarkers. This study aimed to determine compositional and quantitative differences between the degradome and proteome of PCFs aspirated from different types of pancreatic cyst lesions (PCLs). 91 patients who underwent endoscopic ultrasound-fine needle aspiration under routine clinical diagnosis of PCLs were enrolled. Four cysts were malignant (CAs), and 87 were nonmalignant and consisted of 18 intraductal papillary mucinous neoplasms (IPMNs), 14 mucinous cystic neoplasms (MCNs), nine serous cystic neoplasms (SCNs), 29 pseudocysts (PCs), and 17 unclassified. Profiles of the <5 kDa fraction, the degradome, and the trypsin-digested proteome were analysed using an LTQ-Orbitrap Elite mass spectrometer coupled with a nanoACQUITY LC system. Qualitative analyses identified 796 and 366 proteins in degradome and proteome, respectively, and 689 (77%) and 285 (78%) of them were present in the Plasma Proteome Database. Gene Ontology analysis showed a significant overrepresentation of peptidases and peptidases inhibitors in both datasets. In the degradome fraction, quantitative values were obtained for 6996 peptides originating from 657 proteins. Of these, 2287 peptides were unique to a single type, and 515 peptides, derived from 126 proteins, were shared across cyst types. 32 peptides originating from 12 proteins had differential (adjusted p-value ≤0.05, FC ≥1.5) abundance in at least one of the five cysts types. In proteome, relative expression was measured for 330 proteins. Of them, 33 proteins had significantly (adjusted p-value ≤0.05, FC ≥1.5) altered abundance in at least one of the studied groups and 19 proteins appeared to be unique to a given cyst type. PCFs are dominated by blood proteins and proteolytic enzymes. Although differences in PCF peptide composition and abundance could aid classification of PCLs, the unpredictable inherent PCF proteolytic activity may limit the practical applications of PCF protein profiling.

DOI: https://doi.org/10.1155/2018/7169595
Med Sci Monit. 2019 Jan 09. 25 288-297

Proteomic Screening for Serum Biomarkers for Cervical Cancer and Their Clinical Significance.

Yani Chen, Xiaofan Xiong, Yanfeng Wang, Junmei Zhao, Haiyan Shi, Huahua Zhang, Yu Wang, Yameng Wei, Wanjuan Xue, Jing Zhang.

BACKGROUND The present study aimed to determine serum markers for cervical cancer (CC) and to provide valuable references for clinical diagnosis and treatment. MATERIAL AND METHODS Serum samples were collected from age-matched healthy control women, and from female CC patients before and after surgery. Serum biomarkers were selected by comparing serum peptides profiles among the 3 groups by magnetic bead-based weak cation - exchange chromatography fractionation combined with matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Probable serum biomarkers for cervical cancer were then further identified by liquid chromatography-electrospray ionization-tandem mass spectrometry system and the identified proteins were verified by enzyme-linked immunosorbent assay (ELISA). RESULTS Three peptide biomarkers were identified for distinguishing CC patients from normal individuals, and distinguishing preoperative CC patients from postoperative CC patients. Of these 3 identified protein peptide regions, 2 peptide regions - TKT (Peak 2, 2435.63 m/z, 499-524) and FGA (Peak 4, 2761.79 m/z, 603-629) - were identified as upregulated markers, and peptide region of APOA1 (Peak 9, 2575.3 m/z, 245-260) was identified as a downregulated biomarker in preoperative CC patients compared with healthy women. CONCLUSIONS The present study provides a new method for identifying potential serum biomarkers for CC patients.

DOI: https://doi.org/10.12659/MSM.911478
J Immunoassay Immunochem. 2019 Jan 11. 1-23

Multiplex assay for multiomics advances in personalized-precision medicine.

Maria-Linda Popa, Radu Albulescu, Monica Neagu, Mihail Eugen Hinescu, Cristiana Tanase.

  Building the future of precision medicine is the main focus in cancer domain. Clinical trials are moving toward an array of studies that are more adapted to precision medicine. In this domain, there is an enhanced need for biomarkers, monitoring devices, and data-analysis methods. Omics profiling using whole genome, epigenome, transcriptome, proteome, and metabolome can offer detailed information of the human body in an integrative manner. Omes profiles reflect more accurately real-time physiological status. Personalized omics analyses both disease as a whole and the main disease processes, for a better understanding of the individualized health. Through this, multi-omic approaches for health monitoring, preventative medicine, and personalized treatment can be targeted simultaneously and can lead clinicians to have a comprehensive view on the diseasome.

Keywords:  Precision medicine; omics technology; personalized medicine; target therapy

DOI:  https://doi.org/10.1080/15321819.2018.1562940
Biomed Khim. 2018 Nov;64(6): 496-504

[Quantitative proteomics of human blood exosomes].

N A Shushkova, N E Vavilov, S E Novikova, T E Farafonova, O V Tikhonova, P-C Liao, V G Zgoda.

  Exosomes are extracellular membrane vesicles secreted by cells into biological fluids. The outer membrane of exosomes protects their content from degradation and contains markers of the parent cell. Almost all cells of the body produce exosomes, however, tumor cells secrete them more intensively. Due to fact that exosomes contain proteins of cells secreting them, these vesicles could be a valuable source for biomarkers discovery. Currently, a number of studies prove the participation of exosomes in carcinogenesis. However, there is a problem of isolating pure and characterized exosomes for further use in investigation of functions or identification of tumor protein biomarkers. In this work, we have performed experiments on exosomes isolation from human plasma by three methods: differential ultracentrifugation, ultracentrifugation in sucrose cushion, sedimentation of the exosomal fraction from serum by using a commercial kit. The protein composition of the obtained samples was determined by mass spectrometric methods of selected reactions monitoring (SRM) and shotgun proteomic analysis. The obtained exosomal samples were searched for the presence of exosomal markers (CD9, CD82, HSPA8, CD63). In the samples of exosomes isolated by ultracentrifugation with the sucrose cushion, the content of the above markers was determined as 32.85, 15.59, 6.07 fmol/mg of total protein, correspondently. It was shown that the centrifugation method with the sucrose cushion was optimal for the isolation of exosomes.

Keywords:  biomarkers; exosome; mass-spectrometry; methods of isolation; ultracentrifugation

DOI:  https://doi.org/10.18097/PBMC20186406496
Neuroscience. 2019 Jan 02. pii: S0306-4522(18)30871-6. [Epub ahead of print]

The SNAP25 interactome in ventromedial caudate in schizophrenia includes the mitochondrial protein ARF1.

Alfredo Ramos-Miguel, Vilte Barakauskas, Jehan Alamri, Masatoshi Miyauchi, Alasdair M Barr, Clare L Beasley, Gorazd Rosoklija, J John Mann, Andrew J Dwork, Annie Moradian, Gregg B Morin, William G Honer.

  Abnormalities of SNAP25 (synaptosomal-associated protein 25) amount and protein-protein interactions occur in schizophrenia, and may contribute to abnormalities of neurotransmitter release in patients. However, presynaptic terminal function depends on multiple subcellular mechanisms, including energy provided by mitochondria. To explore the SNAP25 interactome in schizophrenia, we immunoprecipitated SNAP25 along with interacting proteins from the ventromedial caudate of 15 cases of schizophrenia and 13 controls. Proteins were identified with mass spectrometry-based proteomics. As well as 15 SNARE- (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) associated proteins, we identified 17 mitochondrial-associated and 4 other proteins. The mitochondrial small GTPase ARF1 (ADP-ribosylation factor 1) was identified in 8 schizophrenia SNAP25 immunoprecipitates and none from controls (P = 0.004). Although the ARF1-SNAP25 interaction may be increased, immunoblotting demonstrated 21% lower ARF1-21 (21 kiloDaltons) in schizophrenia samples (P = 0.04). In contrast, the mitochondrial protein UQCRC1 (ubiquinol-cytochrome c reductase core protein 1) did not differ. Lower ARF1-21 levels were associated with the previously reported increased SNAP25-syntaxin interaction in schizophrenia (r = -0.39, P = 0.04). Additional immunoprecipitation studies confirmed the ARF1-21-SNAP25 interaction, independent of UQCRC1. Both ARF1 and SNAP25 were localized to synaptosomes. Confocal microscopy demonstrated co-localization of ARF1 and SNAP25, and further suggested 5-fold enrichment of ARF1 in synaptosomes containing an excitatory marker (vesicular glutamate transporter) compared with synaptosomes containing an inhibitory marker (vesicular GABA transporter). The present findings suggest an association between abnormalities of SNARE proteins involved with vesicular neurotransmission and the mitochondrial protein ARF1 that may contribute to the pathophysiology of schizophrenia.

Keywords:  Mitochondria; Postmortem brain; Presynaptic; Proteomics; Schizophrenia

DOI:  https://doi.org/10.1016/j.neuroscience.2018.12.045
Reprod Biomed Online. 2018 Dec 23. pii: S1472-6483(18)30646-1. [Epub ahead of print]

Endometrial stromal cell proteome mapping in repeated implantation failure and recurrent pregnancy loss cases and fertile women.

Lien Dhaenens, Sylvie Lierman, Laura De Clerck, Elisabeth Govaert, Dieter Deforce, Kelly Tilleman, Petra De Sutter.

   RESEARCH QUESTION: Are there proteomic differences between endometrial stromal cells of repeated implantation failure (RIF), recurrent pregnancy loss (RPL) and normal fertile women, and is there differential protein expression upon decidualization?
DESIGN: This exploratory study investigated the proteome of in-vitro cultured endometrial stromal cells of women with RIF (n = 4), women with RPL (n = 3) and normal fertile women (n = 4), comparing day 0 with 5 days of decidualization. Total proteins extracted from cell lysates were analysed by high-definition mass spectrometry. Data analysis was performed using significance analysis of microarray in R (P < 0.05; false discovery rate [FDR] 10%).
RESULTS: In the RIF group, ANXA6, PSMC5 and FSCN1 were up-regulated (1.9-fold, 2.5-fold and 1.9-fold, respectively), whereas PBXIP1 was down-regulated (7.7-fold) upon decidualization. In the RPL group, RPS25 and ACADVL were down-regulated (1.9-fold and 2.4-fold, respectively; FDR 10%) between the non-decidualized and the decidualized samples. In the normal fertile group VIM and RPL23A were down-regulated (1.9-fold and 2.4-fold, respectively). Comparing ratios of expression of decidualized over non-decidualized samples in the different groups revealed six differentially expressed proteins: DUX4L2, CNPY4, PDE7A, CTSK, PCBP2 and PSMD4. Comparison of RPL versus normal fertile in the decidualized condition revealed serotransferrin to be differentially expressed. The changes in expression levels for serotransferrin, ANX6, ACDVL and VIM were confirmed by western blot.
CONCLUSIONS: Results show a varying response of endometrial stromal cells in distinct clinical groups (RIF, RPL and normal fertile) upon in-vitro decidualization. Serotransferrin could serve as a marker for the aberrant decidualization process in RPL.

Keywords:  Decidualization; Endometrial receptivity; Recurrent pregnancy loss; Repeated implantation failure; Stromal cell proteome

DOI:  https://doi.org/10.1016/j.rbmo.2018.11.022
Proteomes. 2019 Jan 08. pii: E2. [Epub ahead of print]7(1):

Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae.

Julia Rechenberger, Patroklos Samaras, Anna Jarzab, Juergen Behr, Martin Frejno, Ana Djukovic, Jaime Sanz, Eva M González-Barberá, Miguel Salavert, Jose Luis López-Hontangas, Karina B Xavier, Laurent Debrauwer, Jean-Marc Rolain, Miguel Sanz, Marc Garcia-Garcera, Mathias Wilhelm, Carles Ubeda, Bernhard Kuster.

  The microbiome has a strong impact on human health and disease and is, therefore, increasingly studied in a clinical context. Metaproteomics is also attracting considerable attention, and such data can be efficiently generated today owing to improvements in mass spectrometry-based proteomics. As we will discuss in this study, there are still major challenges notably in data analysis that need to be overcome. Here, we analyzed 212 fecal samples from 56 hospitalized acute leukemia patients with multidrug-resistant Enterobactericeae (MRE) gut colonization using metagenomics and metaproteomics. This is one of the largest clinical metaproteomic studies to date, and the first metaproteomic study addressing the gut microbiome in MRE colonized acute leukemia patients. Based on this substantial data set, we discuss major current limitations in clinical metaproteomic data analysis to provide guidance to researchers in the field. Notably, the results show that public metagenome databases are incomplete and that sample-specific metagenomes improve results. Furthermore, biological variation is tremendous which challenges clinical study designs and argues that longitudinal measurements of individual patients are a valuable future addition to the analysis of patient cohorts.

Keywords:  clinical proteomics; data analysis; human gut microbiome; mass spectrometry; metaproteome; multi-omics; multidrug-resistant Enterobacteriaceae; proteomics

DOI:  https://doi.org/10.3390/proteomes7010002
Int J Mol Sci. 2019 Jan 07. pii: E189. [Epub ahead of print]20(1):

AXIN1 in Plasma or Serum Is a Potential New Biomarker for Endometriosis.

Malin Ek, Bodil Roth, Gunnar Engström, Bodil Ohlsson.

  Although endometriosis is considered an inflammatory disease, no reliable diagnostic biomarkers exist for use in clinical practice. The aim was to investigate the inflammatory profile in endometriosis using an exploratory approach of inflammation-related proteins. Patients with laparoscopy-verified endometriosis (N = 172), women with microscopic colitis (N = 50), healthy controls (N = 31), and age-matched controls from the general population (N = 100) were enrolled and questionnaires regarding socioeconomic factors, lifestyle habits, and medical history were completed. Sera from patients and healthy controls were analyzed for 92 inflammatory biomarkers using Proximity Extension Assay technology (PEA). Plasma AXIN1 levels were analyzed in patients with endometriosis and controls from the general population by ELISA. General linear model adjusted for age, Mann⁻Whitney U-test, and principal component analysis (PCA) were used for statistical calculations. Serum levels of AXIN1 and ST1A1 were increased in endometriosis compared with MC (p < 0.001) and healthy controls (p = 0.001), whereas CXCL9 levels were decreased. Plasma levels of AXIN1 were elevated in endometriosis compared with age-matched controls from the general population (30.0 (17.0⁻38.0) pg/mL vs. 19.5 (15.0⁻28.0) pg/mL, p < 0.001). PCA analysis identified four clusters of proteins, where one cluster differed between endometriosis and controls, with strong correlations for AXIN1 and ST1A1. Plasma/serum AXIN1 is an interesting biomarker to be further evaluated in endometriosis.

Keywords:  AXIN1; ST1A1; endometriosis; gastrointestinal symptoms; inflammatory profile

DOI:  https://doi.org/10.3390/ijms20010189
JCI Insight. 2019 Jan 10. pii: 123611. [Epub ahead of print]4(1):

Human PAH is characterized by a pattern of lipid-related insulin resistance.

Anna R Hemnes, J Matthew Luther, Christopher J Rhodes, Jason P Burgess, James Carlson, Run Fan, Joshua P Fessel, Niki Fortune, Robert E Gerszten, Stephen J Halliday, Rezzan Hekmat, Luke Howard, John H Newman, Kevin D Niswender, Meredith E Pugh, Ivan M Robbins, Quanhu Sheng, Cyndya A Shibao, Yu Shyr, Susan Sumner, Megha Talati, John Wharton, Martin R Wilkins, Fei Ye, Chang Yu, James West, Evan L Brittain.

   BACKGROUND: Pulmonary arterial hypertension (PAH) is a deadly disease of the small pulmonary vasculature with an increased prevalence of insulin resistance (IR). Insulin regulates both glucose and lipid homeostasis. We sought to quantify glucose- and lipid-related IR in human PAH, testing the hypothesis that lipoprotein indices are more sensitive indices of IR in PAH.
METHODS: Oral glucose tolerance testing in PAH patients and triglyceride-matched (TG-matched) controls and proteomic, metabolomics, and lipoprotein analyses were performed in PAH and controls. Results were validated in an external cohort and in explanted human PAH lungs.
RESULTS: PAH patients were similarly glucose intolerant or IR by glucose homeostasis metrics compared with control patients when matched for the metabolic syndrome. Using the insulin-sensitive lipoprotein index, TG/HDL ratio, PAH patients were more commonly IR than controls. Proteomic and metabolomic analysis demonstrated separation between PAH and controls, driven by differences in lipid species. We observed a significant increase in long-chain acylcarnitines, phosphatidylcholines, insulin metabolism-related proteins, and in oxidized LDL receptor 1 (OLR1) in PAH plasma in both a discovery and validation cohort. PAH patients had higher lipoprotein axis-related IR and lipoprotein-based inflammation scores compared with controls. PAH patient lung tissue showed enhanced OLR1 immunostaining within plexiform lesions and oxidized LDL accumulation within macrophages.
CONCLUSIONS: IR in PAH is characterized by alterations in lipid and lipoprotein homeostasis axes, manifest by elevated TG/HDL ratio, and elevated circulating medium- and long-chain acylcarnitines and lipoproteins. Oxidized LDL and its receptor OLR1 may play a role in a proinflammatory phenotype in PAH.
FUNDING: NIH DK096994, HL060906, UL1 RR024975-01, UL1 TR000445-06, DK020593, P01 HL108800-01A1, and UL1 TR002243; American Heart Association 13FTF16070002.

Keywords:  Cardiology; Hypertension; Insulin; Proteomics; Pulmonology

DOI:  https://doi.org/10.1172/jci.insight.123611
Clin Proteomics. 2019 ;16 1

High accuracy differentiating autoimmune pancreatitis from pancreatic ductal adenocarcinoma by immunoglobulin G glycosylation.

Hsi-Chang Shih, Ming-Chu Chang, Chein-Hung Chen, I-Lin Tsai, San-Yuan Wang, Ya-Po Kuo, Chung-Hsuan Chen, Yu-Ting Chang.

   Background: Misdiagnosis of autoimmune pancreatitis (AIP) as pancreatic cancer (PDAC) or vice versa can cause dismal patents' outcomes. Changes in IgG glycosylation are associated with cancers and autoimmune diseases. This study investigated the IgG glycosylation profiles as diagnostic and prognostic biomarkers in PDAC and AIP.
Methods: Serum IgG-glycosylation profiles from 86 AIP patients, 115 PDAC patients, and 57 controls were analyzed using liquid chromatography-electrospray ionization mass spectrometry. Classification and regression tree (CART) analysis was applied to build a decision tree for discriminating PDAC from AIP. The result was validated in an independent cohort.
Results: Compared with AIP patients and controls, PDAC patients had significantly higher agalactosylation, lower fucosylation, and sialylation of IgG1, a higher agalactosylation ratio of IgG1 and a higher agalactosylation ratio of IgG2. AIP patients had significantly higher fucosylation of IgG1 and a higher sialylation ratio of IgG subclasses 1, 2 and 4. Using the CART analysis of agalactosylation and sialylation ratios in the IgG to discriminate AIP from PDAC, the diagnostic accuracy of the glycan markers was 93.8% with 94.6% sensitivity and 92.9% specificity. There were no statistically significant difference of IgG-glycosylation profiles between diffuse type and focal type AIP.
Conclusions: AIP and PDAC patients have distinct IgG-glycosylation profilings. IgG-glycosylation could different PDAC from AIP with high accuracy.

Keywords:  Autoimmune pancreatitis (AIP); Glycosylation; Immunoglobulin G (IgG); Pancreatic cancer

DOI:  https://doi.org/10.1186/s12014-018-9221-1
PLoS One. 2019 ;14(1): e0208646

Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis.

Mukesh Bansal, Jing He, Michael Peyton, Manjunath Kustagi, Archana Iyer, Michael Comb, Michael White, John D Minna, Andrea Califano.

To understand drug combination effect, it is necessary to decipher the interactions between drug targets-many of which are signaling molecules. Previously, such signaling pathway models are largely based on the compilation of literature data from heterogeneous cellular contexts. Indeed, de novo reconstruction of signaling interactions from large-scale molecular profiling is still lagging, compared to similar efforts in transcriptional and protein-protein interaction networks. To address this challenge, we introduce a novel algorithm for the systematic inference of protein kinase pathways, and applied it to published mass spectrometry-based phosphotyrosine profile data from 250 lung adenocarcinoma (LUAD) samples. The resulting network includes 43 TKs and 415 inferred, LUAD-specific substrates, which were validated at >60% accuracy by SILAC assays, including "novel' substrates of the EGFR and c-MET TKs, which play a critical oncogenic role in lung cancer. This systematic, data-driven model supported drug response prediction on an individual sample basis, including accurate prediction and validation of synergistic EGFR and c-MET inhibitor activity in cells lacking mutations in either gene, thus contributing to current precision oncology efforts.

DOI: https://doi.org/10.1371/journal.pone.0208646
Talanta. 2019 Apr 01. pii: S0039-9140(18)31201-3. [Epub ahead of print]195 668-675

Ultra-high-performance liquid chromatography-mass spectrometry method for neutrophil gelatinase-associated lipocalin as a predictive biomarker in acute kidney injury.

Valentin Ion, Gwenaël Nys, Gaël Cobraiville, Etienne Cavalier, Jacques Crommen, Anne-Catherine Servais, Daniela-Lucia Muntean, Marianne Fillet.

  Neutrophil gelatinase associated lipocalin (NGAL) is a protein that was found to be overexpressed in acute kidney injury (AKI). The rise in NGAL concentration, both in urine or plasma, appears earlier than for other classical renal function markers such as serum creatinine, thus making it a suitable marker for early pathology detection. The aim of this study was to develop a method involving tryptic digestion, solid phase extraction and LC-MS/MS analysis to analyze NGAL in plasma medium using an isotope labeled surrogate protein, containing NGAL signature tags, as internal standard (QPrEST). The method was validated for the analysis of NGAL in an analytical range from 50 to 1250 ng/mL using two different proteotypic peptides. The method was further used to quantify the NGAL in human plasma samples for whom elevated NGAL values were expected. NGAL values were between 190.8 and 242.6 ng/mL for control group and between 228.1 and 3526.2 ng/mL for patient group. This study proved that the selection of the right internal standard is of utmost importance in targeted proteomics studies as the digestion steps might cause high variability. This study also confirmed that, although NGAL is highly resistant to proteases such as trypsin, the method could be fully validated according to FDA guidelines and subsequently used to assess NGAL levels in patient plasma with high analytical confidence.

Keywords:  AKI; NGAL; Targeted proteomics; UHPLC-MS/MS

DOI:  https://doi.org/10.1016/j.talanta.2018.11.050
Data Brief. 2019 Feb;22 557-562

Peptidome profiling dataset of ovarian cancer and non-cancer proximal fluids: Ascites and blood sera.

Victoria Shender, Georgij Arapidi, Ivan Butenko, Nikolay Anikanov, Olga Ivanova, Vadim Govorun.

Despite a large number of proteomic studies of biological fluids from ovarian cancer patients, there is a lack of sensitive screening methods in clinical practice (Kim et al., 2016) (DOI:https://doi.org/10.1111/cas.12987[1]). Low molecular weight endogenous peptides more easily diffuse across endothelial barriers than proteins and can be more relevant biomarker candidates (Meo et al., 2016) (DOI:https://doi.org/10.18632/oncotarget.8931[2], (Bery et al., 2014) DOI:https://doi.org/10.1186/1559-0275-11-13[3], (Huang et al., 2018) DOI:https://doi.org/10.1097/IGC.0000000000001166[4]). Detailed peptidomic analysis of 26 ovarian cancer and 15 non-cancer samples of biological fluids (ascites and sera) were performed using TripleTOF 5600+ mass-spectrometer. Prior to LC-MS/MS analysis, peptides were extracted from biological fluids using anion exchange sorbent with subsequent peptide desorption from the surface of highly abundant proteins. In total, we identified 4874 peptides; 3123 peptides were specific for the ovarian cancer samples. The mass-spectrometry peptidomics data presented in this data article have been deposited to the ProteomeXchange Consortium (Deutsch et al., 2017) (DOI:https://doi.org/10.1093/nar/gkw936[5]) via the PRIDE partner repository with the dataset identifier PXD009382 and https://doi.org/10.6019/PXD009382, http://www.ebi.ac.uk/pride/archive/projects/PXD009382.

DOI: https://doi.org/10.1016/j.dib.2018.12.056
Mol Oncol. 2019 Jan 09.

Molecular evidence of field cancerization initiated by diabetes in colon cancer patients.

DiabetesCancerConnect Consortium

  The potential involvement of type 2 diabetes mellitus (T2DM) as a risk factor for colon cancer (CC) has been previously reported. While several clinical studies show a higher incidence of CC and a lower survival rate in diabetics, others report no association. Our own experience indicates that diabetes does not seem to worsen the prognosis once the tumor is present. Despite this controversy, there are no wide spectrum molecular studies that delve into the impact of T2DM-related mechanisms in colon carcinogenesis. Here we present a transcriptomic and proteomic profiling of paired tumor and normal colon mucosa samples in a cohort of 42 CC patients, 23 of which have T2DM. We used gene set enrichment and network approaches to extract relevant pathways in diabetics, referenced them to current knowledge and tested them using in vitro techniques. Through our transcriptomics approach, we identified an unexpected overlap of pathways over-represented in diabetics compared to non-diabetics, both in tumor and normal mucosa, including diabetes-related metabolic and signaling processes. Proteomic approaches highlighted several cancer-related signaling routes in diabetics found only in normal mucosa, not in tumors. An integration of the transcriptome and proteome analyses suggested the deregulation of key pathways related to colon carcinogenesis which converged on tumor initiation axis TEAD/YAP-TAZ as a potential initiator of the process. In vitro studies confirmed up-regulation of this pathway in non-tumor colon cells under high glucose conditions. In conclusion, T2DM associates with deregulation of cancer-related processes in normal colon mucosa adjacent to tissue which has undergone a malignant transformation. These data support that in diabetic patients, the local micro-environment in normal colon mucosa may be a factor driving field cancerization promoting carcinogenesis. Our results set a new framework to study links between diabetes and colon cancer, including a new role of the TEAD/YAP-TAZ complex as a potential driver.

Keywords:  Colon cancer; carcinogenesis; diabetes; field cancerization; high glucose; omics; systems biology

DOI:  https://doi.org/10.1002/1878-0261.12438
J Orthop Res. 2019 Jan 07.

A novel contribution to clubfoot pathogenesis: the possible role of extracellular matrix proteins.

Adam Eckhardt, Tomas Novotny, Ivan Miksik, Lucia Hronkova, Ludek Vajner, Statis Pataridis, Daniel Hadraba, Lucie Kulhava, Martin Plencner, Jarmila Knitlova, Jana Liskova, Jiri Uhlik, Marie Zaloudikova, David Vondrasek, Martina Doubkova, Martin Ostadal.

  Idiopathic pes equinovarus (clubfoot) is a congenital deformity of the feet and lower legs. Clubfoot belongs to a group of fibro proliferative disorders but its origin remains unknown. Our study aimed to achieve the first complex proteomic comparison of clubfoot contracted tissue of the foot (medial side; n = 16), with non contracted tissue (lateral side; n = 13). We used label free mass spectrometry quantification and immunohistochemistry. Seven proteins were observed to be significantly upregulated in the medial side (asporin, collagen type III, V, and VI, versican, tenascin C, and transforming growth factor beta induced protein) and four in the lateral side (collagen types XII and XIV, fibromodulin, and cartilage intermediate layer protein 2) of the clubfoot. Comparison of control samples from cadavers brought only two different protein concentrations (collagen types I and VI). We also revealed pathological calcification and intracellular positivity of transforming growth factor beta only in the contracted tissue of clubfoot. Most of the 11 differently expressed proteins are strongly related to the extracellular matrix architecture and we assume that they may play specific roles in the pathogenesis of this deformity. These proteins seem to be promising targets for future investigations and treatment of this disease.

Keywords:  clubfoot; collagen; extracellular matrix; fibrosis; proteomics

DOI:  https://doi.org/10.1002/jor.24211
Arthritis Rheumatol. 2019 Jan 07.

Identification of Novel Autoantibodies Associated with Psoriatic Arthritis.

Yulin Yuan, Jingyi Qiu, Zuan-Tao Lin, Wen Li, Christopher Haley, Uyen Ngoc Mui, Jing Ning, Stephen K Tyring, Tianfu Wu.

OBJECTIVE: The autoimmune etiology in psoriasis is not very clear, we aim to identify autoantigens and autoantibodies in psoriasis, which may shed light on the molecular and cellular basis of the pathogenesis of psoriasis and psoriatic arthritis.
METHODS: In this study, we developed an autoantigen array system harboring a variety of antigens including typical autoantigens in rheumatic diseases as well as skin antigens, inflammatory mediators and putative autoantigens in psoriasis. Sera from psoriasis patients (N = 73) were used to interrogate antigens on the array. Individual ELISA was also used in validation studies.
RESULTS: We found several serum autoantibodies were elevated in psoriasis patients compared to healthy controls; particularly, IgG autoantibodies against two novel antigens, LL37 and ADAMTSL5, were significantly increased in the psoriasis patients compared to healthy controls. Importantly, serum levels of IgG autoantibodies against LL37 and ADAMTSL5 were correlated with Psoriasis Area and Severity Index (PASI), and reflected disease progression in longitudinally collected samples from psoriasis patients. Importantly, we found both anti-ADAMTSL5 and anti-LL-37 autoantibodies were significantly elevated in psoriatic arthritis (PsA) compared to Non-PsA, suggesting that these molecules may be involved in the pathogenesis of psoriatic arthritis.
CONCLUSION: Our findings suggest that these autoantibodies may be useful biomarkers and indicative of therapeutic targets of psoriasis and psoriatic arthritis. This article is protected by copyright. All rights reserved.

DOI: https://doi.org/10.1002/art.40830
Adv Clin Chem. 2019 ;pii: S0065-2423(18)30056-8. [Epub ahead of print]88 67-89

Probing the endogenous peptidomes of cancer for biomarkers: A new endeavor.

Pey Yee Lee, Teck Yew Low, Rahman Jamal.

  The life span of cancer patients can be prolonged with appropriate therapies if detected early. Mass screening for early detection of cancer, however, requires sensitive and specific biomarkers obtainable from body fluids such as blood or urine. To date, most biomarker discovery programs focus on the proteome rather than the endogenous peptidome. It has been long-established that tumor cells and stromal cells produce tumor resident proteases (TRPs) to remodel the surrounding tumor microenvironment in support of tumor progression. In fact, proteolytic products of TRPs have been shown to correlate with malignant behavior. Being of low molecular weight, these unique peptides can pass through the endothelial barrier of the vasculature into the bloodstream. As such, the cancer peptidome has increasingly become a focus for biomarker discovery. In this review, we discuss on the various aspects of the peptidome in cancer biomarker research.

Keywords:  Biomarker; Cancer; Peptidomics; Proteolysis

DOI:  https://doi.org/10.1016/bs.acc.2018.10.004
Chin Med J (Engl). 2019 Jan 03.

Close association between abnormal expressed enzymes of energy metabolism and diarrhea-predominant irritable bowel syndrome.

Chun-Yan Zhang, Xin Yao, Gang Sun, Yun-Sheng Yang.

BACKGROUND: Irritable bowel syndrome (IBS) is one of the most common functional intestinal diseases, but its pathogenesis is still unknown. The present study aimed to screen the differentially expressed proteins in the mucosa of colon between IBS with diarrhea (IBS-D) patients and the healthy controls.
METHODS: Forty-two IBS-D patients meeting the Rome III diagnostic criteria and 40 control subjects from July 2007 to June 2009 in Chinese PLA General Hospital were enrolled in the present study. We examined the protein expression profiles in mucosa of colon corresponding to IBS-D patients (n = 5) and controls (n = 5) using 2-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS). Secondly, Western blot and immunohistochemical analysis were carried out to validate the screened proteins in 27 IBS-D patients and 27 controls. Thirdly, high-performance liquid chromatography (HPLC) was further carried out to determine ATP concentration in the mucosa of colon between 10 IBS-D patients and 8 controls. Comparisons between 2 groups were performed by Student's t-test or Mann-Whitney U-test.
RESULTS: Twelve differentially expressed proteins were screened out. The α-enolase (ENOA) in the sigmoid colon (0.917 ± 0.007 vs 1.310 ± 0.100, t = 2.643, P = 0.017) and caecum (0.765 ± 0.060 vs 1.212 ± 0.122, t = 2.225, P = 0.023), Isobutyryl-CoA dehydrogenase (ACAD8) in the sigmoid colon (1.127 ± 0.201 vs 1.497 ± 0.392, t = 7.093, P = 0.008) of the IBS-D group were significantly lower while acetyl-CoA acetyltransferase (CT) in the caecum (2.453 ± 0.422 vs 0.931 ± 0.652, t = 8.363, P = 0.015) and ATP synthase subunit d (ATP5H) in the sigmoid (0.843 ± 0.042 vs 0.631 ± 0.042, t = 8.613,P = 0.007) of the IBS-D group was significantly higher, compared with the controls. The ATP concentration in the mucosa of the sigmoid colon in IBS-D group was significantly lower than that of control group (0.470 [0.180, 1.360] vs 5.350 [2.230, 7.900], U = 55, P < 0.001).
CONCLUSIONS: Many proteins related to energy metabolism presented differential expression patterns in the mucosa of colon of the IBS-D patients. The abnormalities in energy metabolism may be involved in the pathogenesis of IBS which deserves more studies to elucidate.This is an open access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal. http://creativecommons.org/licenses/by-nc-nd/4.0.

DOI: https://doi.org/10.1097/CM9.0000000000000003
Breast Cancer Res. 2019 Jan 07. 21(1): 2

Molecular changes during extended neoadjuvant letrozole treatment of breast cancer: distinguishing acquired resistance from dormant tumours.

Cigdem Selli, Arran K Turnbull, Dominic A Pearce, Ang Li, Anu Fernando, Jimi Wills, Lorna Renshaw, Jeremy S Thomas, J Michael Dixon, Andrew H Sims.

   BACKGROUND: The risk of recurrence for endocrine-treated breast cancer patients persists for many years or even decades following surgery and apparently successful adjuvant therapy. This period of dormancy and acquired resistance is inherently difficult to investigate; previous efforts have been limited to in-vitro or in-vivo approaches. In this study, sequential tumour samples from patients receiving extended neoadjuvant aromatase inhibitor therapy were characterised as a novel clinical model.
METHODS: Consecutive tumour samples from 62 patients undergoing extended (4-45 months) neoadjuvant aromatase inhibitor therapy with letrozole were subjected to transcriptomic and proteomic analysis, representing before (≤ 0), early (13-120 days), and long-term (> 120 days) neoadjuvant aromatase inhibitor therapy with letrozole. Patients with at least a 40% initial reduction in tumour size by 4 months of treatment were included. Of these, 42 patients with no subsequent progression were classified as "dormant", and the remaining 20 patients as "acquired resistant".
RESULTS: Changes in gene expression in dormant tumours begin early and become more pronounced at later time points. Therapy-induced changes in resistant tumours were common features of treatment, rather than being specific to the resistant phenotype. Comparative analysis of long-term treated dormant and resistant tumours highlighted changes in epigenetics pathways including DNA methylation and histone acetylation. The DNA methylation marks 5-methylcytosine and 5-hydroxymethylcytosine were significantly reduced in resistant tumours compared with dormant tissues after extended letrozole treatment.
CONCLUSIONS: This is the first patient-matched gene expression study investigating long-term aromatase inhibitor-induced dormancy and acquired resistance in breast cancer. Dormant tumours continue to change during treatment whereas acquired resistant tumours more closely resemble their diagnostic samples. Global loss of DNA methylation was observed in resistant tumours under extended treatment. Epigenetic alterations may lead to escape from dormancy and drive acquired resistance in a subset of patients, supporting a potential role for therapy targeted at these epigenetic alterations in the management of resistance to oestrogen deprivation therapy.

Keywords:  Dormancy; Epigenetics; Letrozole; Microarray; Oestrogen deprivation therapy; Proteomics; Resistance; Sequential samples

DOI:  https://doi.org/10.1186/s13058-018-1089-5
Proteomics Clin Appl. 2019 Jan 11. e1800176

Urinary proteomics and precision medicine for chronic kidney disease: Current status and future perspectives.

Frederik Persson, Peter Rossing.

  Precision medicine is since long an ongoing refinement of classical medicine, integrating improved and more detailed pathophysiological understanding with rapid technological advances. In the heterogenous are of chronic kidney disease there seems to be a high potential for improvement in treatment and prognosis for several causes, with new technologies under development, that have yet to be introduced in clinical practice. As in other medical disciplines, investigation of abundant peptide patterns (proteomics) has gained recent interest. Especially relevant for kidney disease, urinary proteomics may provide both improved diagnosis and as reviewed here, also holds promise for personalized treatment in the future. So far, capillary electrophoresis coupled to mass spectrometry (CE-MS) is the most widely applied technique, and in addition to several cross-sectional and cohort studies, there is even an ongoing randomized controlled trial that will soon report on the concept used as a method of personalizing treatment. In addition, there is hope that urinary proteomics can turn into a "liquid biopsy", replacing the invasive diagnostic procedure. The next couple of years will provide more answers on the topic. This article is protected by copyright. All rights reserved.

Keywords:  albuminuria; chronic kidney disease; diabetes; glomerular filtration; urinary proteomics

DOI:  https://doi.org/10.1002/prca.201800176
Eur Heart J. 2019 Jan 07.

Data-driven discovery and validation of circulating blood-based biomarkers associated with prevalent atrial fibrillation.

Winnie Chua, Yanish Purmah, Victor R Cardoso, Georgios V Gkoutos, Samantha P Tull, Georgiana Neculau, Mark R Thomas, Dipak Kotecha, Gregory Y H Lip, Paulus Kirchhof, Larissa Fabritz.

Aims: Undetected atrial fibrillation (AF) is a major health concern. Blood biomarkers associated with AF could simplify patient selection for screening and further inform ongoing research towards stratified prevention and treatment of AF.
Methods and results: Forty common cardiovascular biomarkers were quantified in 638 consecutive patients referred to hospital [mean ± standard deviation age 70 ± 12 years, 398 (62%) male, 294 (46%) with AF] with known AF or ≥2 CHA2DS2-VASc risk factors. Paroxysmal or silent AF was ruled out by 7-day ECG monitoring. Logistic regression with forward selection and machine learning algorithms were used to determine clinical risk factors, imaging parameters, and biomarkers associated with AF. Atrial fibrillation was significantly associated with age [bootstrapped odds ratio (OR) per year = 1.060, 95% confidence interval (1.04-1.10); P = 0.001], male sex [OR = 2.022 (1.28-3.56); P = 0.008], body mass index [BMI, OR per unit = 1.060 (1.02-1.12); P = 0.003], elevated brain natriuretic peptide [BNP, OR per fold change = 1.293 (1.11-1.63); P = 0.002], elevated fibroblast growth factor-23 [FGF-23, OR = 1.667 (1.36-2.34); P = 0.001], and reduced TNF-related apoptosis-induced ligand-receptor 2 [TRAIL-R2, OR = 0.242 (0.14-0.32); P = 0.001], but not other biomarkers. Biomarkers improved the prediction of AF compared with clinical risk factors alone (net reclassification improvement = 0.178; P < 0.001). Both logistic regression and machine learning predicted AF well during validation [area under the receiver-operator curve = 0.684 (0.62-0.75) and 0.697 (0.63-0.76), respectively].
Conclusion: Three simple clinical risk factors (age, sex, and BMI) and two biomarkers (elevated BNP and elevated FGF-23) identify patients with AF. Further research is warranted to elucidate FGF-23 dependent mechanisms of AF.

DOI: https://doi.org/10.1093/eurheartj/ehy815