bims-prodis 2019-04-07 papers

bims-prodis

Biomed News

on Proteomics in disease

Issue of 2019‒04‒07
twenty-two papers selected by
Nancy Gough
Bioserendipity

Differential urinary proteomics analysis of myocardial infarction using iTRAQ quantification.
Proteomics Study of Peripheral Blood Mononuclear Cells (PBMCs) in Autistic Children.
Proteomic Profiling of Seminal Plasma Proteins in Varicocele Patients.
Identification of Plasma Proteome Signatures Associated With Surgery Using SOMAscan.
Stratification of asthma phenotypes by airway proteomic signatures.
Unique Protein Profiles of Extracellular Vesicles as Diagnostic Biomarkers for Early and Advanced Non-Small Cell Lung Cancer.
A proteomic signature associated to atypical antipsychotic response in schizophrenia patients: a pilot study.
Impaired testicular signaling of vitamin A and vitamin K contributes to the aberrant composition of the extracellular matrix in idiopathic germ cell aplasia.
Novel biomarkers distinguishing pancreatic head Cancer from distal cholangiocarcinoma based on proteomic analysis.
Using proteomics to advance the search for potential biomarkers for preeclampsia: A systematic review and meta-analysis.
Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia.
iTRAQ-based quantitative proteomic analysis strengthens transcriptomic subtyping of triple-negative breast cancer tumors.
Multi-Omics Approach: New Potential Key Mechanisms Implicated in Cardiorenal Syndromes.
Quantitative mass spectrometric analysis to unravel glycoproteomic signature of follicular fluid in women with polycystic ovary syndrome.
Deciphering the Pharmacological Mechanism of the Herb Radix Ophiopogonis in the Treatment of Nasopharyngeal Carcinoma by Integrating iTRAQ-Coupled 2-D LC-MS/MS Analysis and Network Investigation.
Hemap: An interactive online resource for characterizing molecular phenotypes across hematologic malignancies.
Cannabis allergy: what the clinician needs to know in 2019.
Mass spectrometric analysis of Lewy body-enriched α-synuclein in Parkinson's disease.
Re: Urine Proteomic Profiling in Patients with Nephrolithiasis and Cystinuria.
For Physicians Managing Voiding Dysfunction, Improving the Detection Rate of Early Prostate Cancer and Discrimination From Benign Prostatic Hyperplasia, in a Molecular Biomarker Aspects.
Identification of autoantibodies using human proteome microarrays in patients with IPEX syndrome.
Synthetic standard aided quantification and structural characterization of amyloid-beta glycopeptides enriched from cerebrospinal fluid of Alzheimer's disease patients.

Mol Med Rep. 2019 Mar 26.

Differential urinary proteomics analysis of myocardial infarction using iTRAQ quantification.

Lili Zou, Xubo Wang, Zhengguang Guo, Haidan Sun, Chen Shao, Yehong Yang, Wei Sun.

Myocardial infarction (MI) is a disease characterized by high morbidity and mortality rates. MI biomarkers are frequently used in clinical diagnosis; however, their specificity and sensitivity remain unsatisfactory. Urinary proteome is an easy, efficient and noninvasive source to examine biomarkers associated with various diseases. The present study, to the best of the authors' knowledge, is the first to examine the urinary proteome using the isobaric tags for relative and absolute quantitation (iTRAQ) technology to identify potential diagnostic biomarkers of MI. The urinary proteome was analyzed within 12 h following the first symptoms of early‑onset MI and at day 7 following percutaneous coronary intervention via iTRAQ labeling and two‑dimensional liquid chromatography‑tandem mass spectrometry. Candidate biomarkers were validated by multiple reaction monitoring (MRM) analysis. A total of 233 urinary proteins were differentially expressed. Gene enrichment analysis identified that the urinary proteome in patients with MI was associated with atherosclerosis, abnormal coagulation and abnormal cell metabolism. In total, 12 differentially expressed urinary proteins were validated by MRM analysis, five of which were associated with MI for the first time in the present study. Binary logistic regression analysis suggested that the combination of five urinary proteins (antithrombin‑III, complement C3, α‑1‑acid glycoprotein 1, serotransferrin and cathepsin Z) may be used to diagnose MI with 94% sensitivity and 93% specificity. In addition, the protein expression levels of three proteins were significantly restored to normal levels following surgical treatment. The verified candidate biomarkers may be used for the diagnosis of MI, and for monitoring the disease status and the effects of treatments for MI. The present results may facilitate future clinical applications of the urinary proteome to diagnose MI.

DOI: https://doi.org/10.3892/mmr.2019.10088
Front Cell Neurosci. 2019 ;13 105

Proteomics Study of Peripheral Blood Mononuclear Cells (PBMCs) in Autistic Children.

Liming Shen, Chengyun Feng, Kaoyuan Zhang, Youjiao Chen, Yan Gao, Junyan Ke, Xinqian Chen, Jing Lin, Cuihua Li, Javed Iqbal, Yuxi Zhao, Weibin Wang.

  Autism is one of the most common neurological developmental disorder associated with social isolation and restricted interests in children. The etiology of this disorder is still unknown. There is neither any confirmed laboratory test nor any effective therapeutic strategy to diagnose or cure it. To search for biomarkers for early detection and exploration of the disease mechanisms, here, we investigated the protein expression signatures of peripheral blood mononuclear cells (PBMCs) in autistic children compared with healthy controls by using isobaric tags for relative and absolute quantitation (iTRAQ) proteomics approach. The results showed a total of 41 proteins as differentially expressed in autistic group as compared to control. These proteins are found associated with metabolic pathways, endoplasmic reticulum (ER) stress and protein folding, endocytosis, immune and inflammatory response, plasma lipoprotein particle organization, and cell adhesion. Among these, 17 proteins (13 up-regulated and four down-regulated) are found to be linked with mitochondria. Eight proteins including three already reported proteins in our previous studies were selected to be verified. Five already reported autism associated pro-inflammatory cytokines [interferon-γ (IFN-γ), interleukin-1β (IL-1β), IL-6, IL-12, and tumor necrosis factor-α (TNF-α)] were detected in plasma by enzyme-linked immunosorbent assay (ELISA) analysis. The results were consistent with proteomic results and reports from previous literature. These results proposed that PBMCs from autistic children might be activated, and ER stress, unfolded protein response (UPR), acute-phase response (APR), inflammatory response, and endocytosis may be involved in autism occurrence. These reported proteins may serve as potential biomarkers for early diagnosis of autism. More specifically, simultaneous detection of three proteins [complement C3 (C3), calreticulin (CALR), and SERPINA1] in the plasma and PBMCs could increase the authenticity of detection.

Keywords:  autism; biomarkers; iTRAQ; peripheral blood mononuclear cells; proteomics

DOI:  https://doi.org/10.3389/fncel.2019.00105
World J Mens Health. 2019 Mar 15.

Proteomic Profiling of Seminal Plasma Proteins in Varicocele Patients.

Manesh Kumar Panner Selvam, Ashok Agarwal.

  PURPOSE: Seminal plasma provides a nutritive and protective milieu for spermatozoa. It contains factors/proteins required for sperm maturation, hyperactivation, capacitation and acrosome reaction. Alteration in the expression levels of seminal plasma proteins affect the fertilization process. The main objective of this study is to compare the seminal plasma proteome of healthy fertile men (control group) with varicocele patients in order to identify the differentially expressed seminal plasma proteins.MATERIALS AND METHODS: Pooled seminal plasma samples from control (n=5) and varicocele (unilateral: n=5 and bilateral: n=5) subjects were used for proteomic profiling and functional bioinformatic analysis. Key differentially expressed proteins (DEPs) associated with binding of zona pellucida (acrosin; ACR), protein folding (heat shock related 70 kDa protein 2; HSPA2), oxidative stress (peroxiredoxin 2; PRDX2), lipid peroxidation and DNA fragmentation (apolipoprotein A2; APOA2) were validated by Western blot. Statistical analysis was conducted using Mann-Whitney test.
RESULTS: A total of 412 and 486 proteins were detected in seminal plasma of control group and varicocele patients respectively. Twenty-eight proteins were identified as DEPs between varicocele and control group. Validation of DEPs revealed downregulation of HSPA2 (p=0.0037) as well as APOA2 (p=0.0373), and upregulation of PRDX2 (p=0.0474).
CONCLUSIONS: The seminal plasma protein profile of varicocele patients differ from healthy fertile men. Aberrant expression of seminal plasma proteins serve as an indicator of sperm pathology in varicocele patients.

Keywords:  Infertility, male; Proteomics; Seminal plasma; Varicocele

DOI:  https://doi.org/10.5534/wjmh.180118
Ann Surg. 2019 Mar 26.

Identification of Plasma Proteome Signatures Associated With Surgery Using SOMAscan.

Tamara G Fong, Noel Y Chan, Simon T Dillon, Wenxiao Zhou, Bridget Tripp, Long H Ngo, Hasan H Otu, Sharon K Inouye, Sarinnapha M Vasunilashorn, Zara Cooper, Zhongcong Xie, Edward R Marcantonio, Towia A Libermann.

MINI: In this manuscript, the ability of SOMAscan technology to identify proteins differentially expressed before and after surgery in older adults was evaluated. Systems biology analyses demonstrated that inflammatory proteins and biological functions associated with the inflammatory response and immune cell regulation demonstrated the greatest changes after surgery.OBJECTIVES: To characterize the proteomic signature of surgery in older adults and association with postoperative outcomes.
SUMMARY OF BACKGROUND DATA: Circulating plasma proteins can reflect the physiological response to and clinical outcomes after surgery.
METHODS: Blood plasma from older adults undergoing elective surgery was analyzed for 1305 proteins using SOMAscan. Surgery-associated proteins underwent Ingenuity Pathways Analysis. Selected surgery-associated proteins were independently validated using Luminex or enzyme-linked immunosorbent assay methods. Generalized linear models estimated correlations with postoperative outcomes.
RESULTS: Plasma from a subcohort (n = 36) of the Successful Aging after Elective Surgery (SAGES) study was used for SOMAscan. Systems biology analysis of 110 proteins with Benjamini-Hochberg (BH) corrected P value ≤0.01 and an absolute foldchange (|FC|) ≥1.5 between postoperative day 2 (POD2) and preoperative (PREOP) identified functional pathways with major effects on pro-inflammatory proteins. Chitinase-3-like protein 1 (CHI3L1), C-reactive protein (CRP), and interleukin-6 (IL-6) were independently validated in separate validation cohorts from SAGES (n = 150 for CRP, IL-6; n = 126 for CHI3L1). Foldchange CHI3L1 and IL-6 were associated with increased postoperative complications [relative risk (RR) 1.50, 95% confidence interval (95% CI) 1.21-1.85 and RR 1.63, 95% CI 1.18-2.26, respectively], length of stay (RR 1.35, 95% CI 0.77-1.92 and RR 0.98, 95% CI 0.52-1.45), and risk of discharge to postacute facility (RR 1.15, 95% CI 1.04-1.26 and RR 1.11, 95% CI 1.04-1.18); POD2 and PREOP CRP difference was associated with discharge to postacute facility (RR 1.14, 95% CI 1.04-1.25).
CONCLUSION: SOMAscan can identify novel and clinically relevant surgery-induced protein changes. Ultimately, proteomics may provide insights about pathways by which surgical stress contributes to postoperative outcomes.

DOI: https://doi.org/10.1097/SLA.0000000000003283
J Allergy Clin Immunol. 2019 Mar 27. pii: S0091-6749(19)30415-4. [Epub ahead of print]

Stratification of asthma phenotypes by airway proteomic signatures.

James P R Schofield, Dominic Burg, Ben Nicholas, Fabio Strazzeri, Joost Brandsma, Doroteya Staykova, Caterina Folisi, Aruna T Bansal, Yang Xian, Yike Guo, Anthony Rowe, Julie Corfield, Susan Wilson, Jonathan Ward, Rene Lutter, Dominick E Shaw, Per S Bakke, Massimo Caruso, Sven-Erik Dahlen, Stephen J Fowler, Ildikó Horváth, Peter Howarth, Norbert Krug, Paolo Montuschi, Marek Sanak, Thomas Sandström, Kai Sun, Ioannis Pandis, John Riley, Charles Auffray, Bertrand De Meulder, Diane Lefaudeux, Ana R Sousa, Ian M Adcock, Kian Fan Chung, Peter J Sterk, Paul J Skipp, Ratko Djukanović, .

  BACKGROUND: Stratification by eosinophil and neutrophil counts increases our understanding of asthma and helps target therapy, but there is room for improvement in our accuracy to predict treatment responses and a need for better understanding of the underlying mechanisms.OBJECTIVE: Identify molecular sub-phenotypes of asthma defined by proteomic signatures for improved stratification.
METHODS: Unbiased label-free quantitative mass spectrometry and topological data analysis were used to analyse the proteomes of sputum supernatants from 246 participants (206 asthmatics) as a novel means of asthma stratification. Microarray analysis of sputum cells provided transcriptomics data additionally to inform on underlying mechanisms.
RESULTS: Analysis of the sputum proteome resulted in 10 clusters, proteotypes, based on similarity in proteomics features, representing discrete molecular sub-phenotypes of asthma. Overlaying granulocyte counts onto the 10 clusters as metadata further defined three of these as highly eosinophilic, three as highly neutrophilic, and two as highly atopic with relatively low granulocytic inflammation. For each of these three phenotypes, logistic regression analysis identified candidate protein biomarkers, and matched transcriptomic data pointed to differentially activated underlying mechanisms.
CONCLUSION: This study provides further stratification of asthma currently classified by quantifying granulocytic inflammation and gives additional insight into their underlying mechanisms which could become targets for novel therapies.

Keywords:  asthma; biomarkers; eosinophils; neutrophils; proteomics

DOI:  https://doi.org/10.1016/j.jaci.2019.03.013
Proteomics. 2019 Apr 05. e1800160

Unique Protein Profiles of Extracellular Vesicles as Diagnostic Biomarkers for Early and Advanced Non-Small Cell Lung Cancer.

Taixue An, Sihua Qin, Dehua Sun, Yiyao Huang, Yanwei Hu, Shaopeng Li, Han Zhang, Bo Li, Bo Situ, Linmiao Lie, Yingsong Wu, Lei Zheng.

  Extracellular vesicles (EVs) mediate intercellular communication via transferring proteins and other biological molecules and have been recently investigated as biomarkers of disease. Sensitive and specific biomarkers are required for lung cancer diagnosis and prognosis. The present study screened for abnormal EV proteins in non-small cell lung cancer (NSCLC) using a quantitative proteomics strategy involving LC-MS/MS to identify ideal biomarkers for NSCLC diagnosis. EVs were enriched from the sera of early and advanced NSCLC patients and healthy controls and from cell culture supernatants of lung adenocarcinoma and bronchial epithelial cell lines. In the sera and supernatants, 279 and 632 differentially expressed proteins, respectively, were associated with signaling pathways including extracellular membrane-receptor interaction, focal adhesion, and regulation of the actin cytoskeleton. Thirty-two EV proteins were identified at the intersection of differentially expressed proteins between the NSCLC groups and cell lines. Based on bioinformatics analysis, in silico immunohistochemical and PRM verification, fibronectin was selected for following in vitro studies and validation with an independent cohort. Fibronectin on EVs was estimated to perform well in the diagnosis of NSCLC patients based on AUC, showing great potential for clinical use and demonstrating the efficacy of this method for EV-associated biomarker screening. This article is protected by copyright. All rights reserved.

Keywords:  biomarker; extracellular vesicles; label-free quantification; lung cancer; proteomics

DOI:  https://doi.org/10.1002/pmic.201800160
Eur Arch Psychiatry Clin Neurosci. 2019 Apr 01.

A proteomic signature associated to atypical antipsychotic response in schizophrenia patients: a pilot study.

Daniel Martins-de-Souza, Paul C Guest, Johann Steiner.

  A major hurdle faced by most schizophrenia patients is the poor efficacy of current antipsychotic medications. This stems from a poor understanding of the underlying pathophysiology and the lack of biomarkers for the prediction of a positive medication response. By employing state-of-the-art proteomic analysis of blood plasma from 58 patients who were either drug-naive or drug-free at the time of sample collection, we identified potential biomarkers that were predictive of a positive response after 6 weeks of treatment with antipsychotics. Complement and coagulation cascades were the most over-represented biological pathways among these proteins, consistent with the importance of these processes in schizophrenia. Although preliminary, these findings are novel and may drive future efforts in the development of predictive tests for medication efficacy and thereby have a positive influence on disease outcome.

Keywords:  Atypical antipsychotics; Biomarkers; Drug response; Proteins; Proteome

DOI:  https://doi.org/10.1007/s00406-019-01002-3
Fertil Steril. 2019 Apr;pii: S0015-0282(18)32251-9. [Epub ahead of print]111(4): 687-698

Impaired testicular signaling of vitamin A and vitamin K contributes to the aberrant composition of the extracellular matrix in idiopathic germ cell aplasia.

Massimo Alfano, Filippo Pederzoli, Irene Locatelli, Silvia Ippolito, Erika Longhi, Pietro Zerbi, Maurizio Ferrari, Andrea Brendolan, Francesco Montorsi, Denise Drago, Annapaola Andolfo, Manuela Nebuloni, Andrea Salonia.

  OBJECTIVE: To study pathogenic features of the somatic testicular microenvironment associated with idiopathic germ cell aplasia.DESIGN: Cross-sectional study.
SETTING: Tertiary referral center for reproductive medicine.
PATIENT(S): Testicular specimens from men with idiopathic nonobstructive azoospermia (iNOA) prospectively submitted to microdissection testicular sperm extraction. Of 20 specimens used for histology, 10 were also available for proteomic analysis. Primary Sertoli cells with normal karyotype and phenotype were also used.
INTERVENTION(S): Patients with iNOA were dichotomized according to a positive versus negative sperm retrieval at microdissection testicular sperm extraction, and on the isolated extracellular matrix (ECM) the proteomic analysis was performed.
MAIN OUTCOME MEASURE(S): Proteomic analysis of the ECM from testicular specimens with positive versus negative sperm retrieval. Gene ontology enrichment was used to identify upstream regulators based on the 11 deregulated ECM proteins, which were validated by immunohistochemistry and quantitative polymerase chain reaction. Continuous variables were expressed as medians and interquartile range.
RESULT(S): Germ cell aplasia was characterized by an increased signaling of the retinoic acid in Sertoli cells and associated with decreased expression of the basal membrane markers nidogen-2 and heparan sulfate proteoglycan-2. Decreased levels of the interstitial matrisome-associated factor IX and its regulator VKORC1 were, instead, coupled with decreased signaling of vitamin K in Leydig cells. An altered expression of a further eight ECM proteins was also found, including laminin-4 and laminin-5. Peripheral levels of the two vitamins were within the reference range in the two cohorts of iNOA men.
CONCLUSION(S): We identified the pathogenetic signature of the somatic human testicular microenvironment, providing two vitamin-related mechanistic insights related to the molecular determinants of the idiopathic germ cell aplasia.

Keywords:  Extracellular matrix; azoospermia; male infertility; testis; vitamins

DOI:  https://doi.org/10.1016/j.fertnstert.2018.12.002
BMC Cancer. 2019 Apr 05. 19(1): 318

Novel biomarkers distinguishing pancreatic head Cancer from distal cholangiocarcinoma based on proteomic analysis.

Tsutomu Takenami, Shimpei Maeda, Hideaki Karasawa, Takashi Suzuki, Toru Furukawa, Takanori Morikawa, Tatsuyuki Takadate, Hiroki Hayashi, Kei Nakagawa, Fuyuhiko Motoi, Takeshi Naitoh, Michiaki Unno.

  BACKGROUND: The differentiation between pancreatic head cancer (PHC) and distal cholangiocarcinoma (DCC) can be challenging because of their anatomical and histopathological similarity. This is an important problem, because the distinction has important implications for the treatment of these malignancies. However, there are no biomarkers for the differential diagnosis of PHC and DCC. The present study aimed to identify novel diagnostic immunohistochemical biomarkers to distinguish PHC from DCC.METHODS: Liquid chromatography tandem mass spectrometry (LC-MS/MS) was employed to detect candidate proteins. Ten PHC and 8 DCC specimens were analyzed by LC-MS/MS. Selected proteins were evaluated, using immunohistochemical analysis, to determine whether they would be appropriate biomarkers. Finally, we generated biomarker panels to improve diagnostic accuracy. We applied these panels to clinically difficult cases (cases in which different diagnoses were made before and after operation).
RESULTS: Consequently, 1820 proteins were detected using LC-MS/MS. Fifteen differentially expressed proteins were selected as candidates based on semi-quantitative comparison. We first performed immunohistochemical staining on samples from the small cohort group (12 PHCs and 12 DCCs) using 15 candidates. KRT17, ANXA10, TMEM109, PTMS, and ATP1B1 showed favorable performances and were tested in the next large cohort group (72 PHCs and 74 DCCs). Based on immunohistochemical analysis, KRT17 performed best for the diagnosis of PHC as a single marker; additionally, PTMS exhibited good performance for the diagnosis of DCCs. Moreover, we indicated the KRT17+/ANXA10+/PTMS- staining pattern as a biomarker panel for the correct diagnosis of PHC and KRT17-/ANXA10-/PTMS+ for the diagnosis of DCC. After immunohistochemical staining for examining samples from the clinically difficult cases, these panels showed satisfactory diagnostic performance with 85.7% (6/7) accuracy.
CONCLUSIONS: We conclude that 5 proteins and 2 biomarker panels are promising for distinguishing PHC from DCC, and patients with an equivocal diagnosis would benefit from the application of these biomarkers. Confirmatory studies are needed to generalize these findings to other populations.

Keywords:  Biomarker; Cholangiocarcinoma; Differential diagnosis; Pancreatic cancer; Proteomics

DOI:  https://doi.org/10.1186/s12885-019-5548-x
PLoS One. 2019 ;14(4): e0214671

Using proteomics to advance the search for potential biomarkers for preeclampsia: A systematic review and meta-analysis.

Thy Pham Hoai Nguyen, Cameron James Patrick, Laura Jean Parry, Mary Familari.

BACKGROUND: Preeclampsia (PE) is a leading cause of maternal and perinatal morbidity and mortality worldwide. Although predictive multiparametric screening is being developed, it is not applicable to nulliparous women, and is not applied to low-risk women. As PE is considered a heterogenous disorder, it is unlikely that any single multiparametric screening protocol containing a small group of biomarkers could have the required accuracy to predict all PE subgroups. Given the etiology of PE is complex and not fully understood, it begs the question, whether the search for biomarkers based on the predominant view of impaired placentation involving factors predominately implicated in angiogenesis and inflammation, has been too limiting. Here we highlight the enormous potential of state-of-the-art, high-throughput proteomics, to provide a comprehensive and unbiased approach to biomarker identification.METHODS AND FINDINGS: Our literature search identified 1336 articles; after review, 45 studies with proteomic data from PE women that were eligible for inclusion. From 710 proteins with altered abundance, we identified 13 common circulating proteins, some of which had not been previously considered as prospective biomarkers of PE. An additional search of the literature for original publications testing any of the 13 common proteins using non-proteomic techniques was also undertaken. Strikingly, 9 of these common proteins had been independently evaluated in PE studies as potential biomarkers.
CONCLUSION: This study highlights the potential of using high-throughput data sets, which are comprehensive and without bias, to identify a profile of proteins that may improve predictions of PE and understanding of its etiology. We bring to the attention of the medical and research communities that the strengths and advantages of using data from high-throughput studies for biomarker discovery would be increased dramatically, if first and second trimester samples were collected for proteomics, and if standardized guidelines for patient reporting and data collection were implemented.

DOI: https://doi.org/10.1371/journal.pone.0214671
Nat Commun. 2019 Apr 03. 10(1): 1519

Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia.

Minjun Yang, Mattias Vesterlund, Ioannis Siavelis, Larissa H Moura-Castro, Anders Castor, Thoas Fioretos, Rozbeh Jafari, Henrik Lilljebjörn, Duncan T Odom, Linda Olsson, Naveen Ravi, Eleanor L Woodward, Louise Harewood, Janne Lehtiö, Kajsa Paulsson.

Hyperdiploidy, i.e. gain of whole chromosomes, is one of the most common genetic features of childhood acute lymphoblastic leukemia (ALL), but its pathogenetic impact is poorly understood. Here, we report a proteogenomic analysis on matched datasets from genomic profiling, RNA-sequencing, and mass spectrometry-based analysis of >8,000 genes and proteins as well as Hi-C of primary patient samples from hyperdiploid and ETV6/RUNX1-positive pediatric ALL. We show that CTCF and cohesin, which are master regulators of chromatin architecture, display low expression in hyperdiploid ALL. In line with this, a general genome-wide dysregulation of gene expression in relation to topologically associating domain (TAD) borders were seen in the hyperdiploid group. Furthermore, Hi-C of a limited number of hyperdiploid childhood ALL cases revealed that 2/4 cases displayed a clear loss of TAD boundary strength and 3/4 showed reduced insulation at TAD borders, with putative leukemogenic effects.

DOI: https://doi.org/10.1038/s41467-019-09469-3
Proteomics. 2019 Apr 05. e1800484

iTRAQ-based quantitative proteomic analysis strengthens transcriptomic subtyping of triple-negative breast cancer tumors.

Pascal Jézéquel, Catherine Guette, Hamza Lasla, Wilfried Gouraud, Alice Boissard, Catherine Guérin-Charbonnel, Mario Campone.

  Heterogeneity and lack of targeted therapies represent the two main impediments to precision treatment of triple-negative breast cancer (TNBC). Therefore, molecular subtyping and identification of therapeutic pathways are required to optimize medical care. The aim of the present study was to define robust TNBC subtypes with clinical relevance by means of proteomics and transcriptomics. As a first step, unsupervised analyses were conducted in parallel on proteomics and transcriptomics data of 83 TNBC tumors. Proteomics data unsupervised analysis did not permit separation of TNBC into different subtypes, whereas transcriptomics data was able to clearly and robustly identify three subtypes: molecular apocrine (C1), basal-like immune-suppressed (C2) and basal-like immune response (C3). Supervised analysis of proteomics data was then conducted based on transcriptomics subtyping. Thirty out of 62 proteins differentially expressed between C1, C2 and C3 belonged to biological categories which characterized these TNBC clusters: luminal and androgen-regulated proteins (C1), basal, invasion and extracellular matrix (C2) and basal and immune response (interferon pathway and immunoglobulins) (C3). Although proteomics unsupervised analysis of TNBC tumors was unsuccessful at identifying clusters, our integrated approach is promising. Identification and measurement of 30 proteins strengthen subtyping of TNBC based on robust transcriptomics unsupervised analysis. This article is protected by copyright. All rights reserved.

Keywords:  Integrated analysis; Proteomics; Subtyping; Transcriptomics; Triple-negative breast cancer

DOI:  https://doi.org/10.1002/pmic.201800484
Cardiorenal Med. 2019 Apr 02. 9(4): 201-211

Multi-Omics Approach: New Potential Key Mechanisms Implicated in Cardiorenal Syndromes.

Grazia Maria Virzì, Anna Clementi, Giovanni Giorgio Battaglia, Claudio Ronco.

  Cardiorenal syndromes (CRS) include a scenario of clinical interactions characterized by the heart and kidney dysfunction. The crosstalk between cardiac and renal systems is clearly evidenced but not completely understood. Multi-factorial mechanisms leading to CRS do not involve only hemodynamic parameters. In fact, in recent works on organ crosstalk endothelial injury, the alteration of normal immunologic balance, cell death, inflammatory cascades, cell adhesion molecules, cytokine and chemokine overexpression, neutrophil migration, leukocyte trafficking, caspase-mediated induction of apoptotic mechanisms and oxidative stress has been demonstrated to induce distant organ dysfunction. Furthermore, new alternative mechanisms using the multi-omics approach may be implicated in the pathogenesis of cardiorenal crosstalk. The study of "omics" modifications in the setting of cardiovascular and renal disease represents an emerging area of research. Over the last years, indeed, many studies have elucidated the exact mechanisms involved in gene expression and regulation, cellular communication and organ crosstalk. In this review, we analyze epigenetics, gene expression, small non-coding RNAs, extracellular vesicles, proteomics, and metabolomics in the setting of CRS.

Keywords:  Cardiorenal syndrome; Epigenetics; Extracellular vesicles; Gene expression; Metabolomics; Organ crosstalk; Proteomics; Small non-coding RNAs

DOI:  https://doi.org/10.1159/000497748
PLoS One. 2019 ;14(4): e0214742

Quantitative mass spectrometric analysis to unravel glycoproteomic signature of follicular fluid in women with polycystic ovary syndrome.

Krutika Patil, Soujanya Yelamanchi, Manish Kumar, Indira Hinduja, T S Keshava Prasad, Harsha Gowda, Srabani Mukherjee.

Polycystic ovary syndrome (PCOS) is a complex endocrinopathy affecting women of reproductive age, and whose etiology is not well understood yet. In these women, the follicular growth is arrested at preantral stage leading to cyst formation, consequently resulting in anovulatory infertility in these women. As the follicular fluid provides the conducive microenvironment for the growth of oocytes, molecular profiling of the fluid may provide unique information about pathophysiology associated with follicular development in PCOS. Post-translational addition of oligosaccharide residues is one of the many modifications of secreted proteins influencing their functions. These glycoproteins play a significant role in disease pathology. Despite glycoproteins having such essential functions, very limited information is available on their profiling in human reproductive system, and glycoproteomic profile of follicular fluid of women with PCOS is yet unexplored. In the present study, we performed a comparative glycoproteomic analysis of follicular fluid between women with PCOS and controls undergoing in vitro fertilization, by enrichment of glycoproteins using three different lectins viz. concanavalin A, wheat germ agglutinin and Jacalin. Peptides generated by trypsin digestion were labeled with isobaric tags for relative and absolute quantification reagents and analyzed by liquid chromatography tandem mass spectrometry. We identified 10 differentially expressed glycoproteins, in the follicular fluid of women with PCOS compared to controls. Two important differentially expressed proteins- SERPINA1 and ITIH4, were consistently upregulated and downregulated respectively, upon validation by immunoblotting in follicular fluid and real-time polymerase chain reaction in granulosa cells. These proteins play a role in angiogenesis and extracellular matrix stabilization, vital for follicle maturation. In conclusion, a comparative glycoproteomic profiling of follicular fluid from women with PCOS and controls revealed an altered expression of proteins which may contribute to the defects in follicle development in PCOS pathophysiology.

DOI: https://doi.org/10.1371/journal.pone.0214742
Front Pharmacol. 2019 ;10 253

Deciphering the Pharmacological Mechanism of the Herb Radix Ophiopogonis in the Treatment of Nasopharyngeal Carcinoma by Integrating iTRAQ-Coupled 2-D LC-MS/MS Analysis and Network Investigation.

Xuesong Feng, Hailong Shi, Xu Chao, Fei Zhao, Liang Song, Minhui Wei, Hong Zhang.

  The herb Radix Ophiopogonis (RO) has been used effectively to treat nasopharyngeal carcinoma (NPC) as an adjunctive therapy. Due to the complexity of the traditional Chinese herbs, the pharmacological mechanism of RO's action on NPC remains unclear. To address this problem, an integrative approach bridging proteome experiments with bioinformatics prediction was employed. First, differentially expressed protein profile from NPC serum samples was established using isobaric tag for relative and absolute quantification (iTRAQ) coupled 2-D liquid chromatography (LC)-MS/MS analysis. Second, the RO putative targets were predicted using Traditional Chinese Medicines Integrated Database and known therapeutic targets of NPC were collected from Drugbank and OMIM databases. Then, a network between RO putative targets and NPC known therapeutic targets was constructed. Third, based on pathways enrichment analysis, an integrative network was constructed using DAVID and STRING database in order to identify potential candidate targets of RO against NPC. As a result, we identified 13 differentially expressed proteins from clinical experiments compared with the healthy control. And by bioinformatics investigation, 12 putative targets of RO were selected. Upon interactions between experimental and predicted candidate targets, we identified three key candidate targets of RO against NPC: VEGFA, TP53, and HSPA8, by calculating the nodes' topological features. In conclusion, this integrative pharmacology-based analysis revealed the anti-NPC effects of RO might be related to its regulatory impact via the PI3K-AKT signaling pathway, the Wnt signaling pathway, and the cAMP signaling pathway by targeting VEGFA, TP53, and HSPA8. The findings of potential key targets may provide new clues for NPC's treatments with the RO adjunctive therapy.

Keywords:  Radix Ophiopogonis; iTRAQ; nasopharyngeal carcinoma; network pharmacology; proteomics; traditional Chinese medicine

DOI:  https://doi.org/10.3389/fphar.2019.00253
Cancer Res. 2019 Apr 02. pii: canres.2970.2018. [Epub ahead of print]

Hemap: An interactive online resource for characterizing molecular phenotypes across hematologic malignancies.

Petri Pölönen, Juha Mehtonen, Jake Lin, Thomas Liuksiala, Sergei Häyrynen, Susanna Teppo, Artturi Mäkinen, Ashwini Kumar, Disha Malani, Virva Pohjolainen, Kimmo Porkka, Caroline A Heckman, Patrick May, Ville Hautamäki, Kirsi J Granberg, Olli Lohi, Matti Nykter, Merja Heinäniemi.

Large collections of genome-wide data can facilitate the characterization of disease states and subtypes, permitting pan-cancer analysis of molecular phenotypes and evaluation of disease context for new therapeutic approaches. We analyzed 9,544 transcriptomes from more than 30 hematologic malignancies, normal blood cell types, and cell lines, and showed that disease types could be stratified in a data-driven manner. We then identified cluster-specific pathway activity, new biomarkers and in silico drug target prioritization through interrogation of drug target databases. Using known vulnerabilities and available drug screens, we highlighted the importance of integrating molecular phenotype with drug target expression for in silico prediction of drug responsiveness. Our analysis implicated BCL2 expression level as an important indicator of venetoclax responsiveness and provided a rationale for its targeting in specific leukemia subtypes and multiple myeloma, linked several polycomb group proteins that could be targeted by small molecules (SFMBT1, CBX7 and EZH1) with CLL, and supported CDK6 as a disease-specific target in AML. Through integration with proteomics data, we characterized target protein expression for pre-B leukemia immunotherapy candidates, including DPEP1. These molecular data can be explored using our publicly available interactive resource, Hemap, for expediting therapeutic innovations in hematologic malignancies.

DOI: https://doi.org/10.1158/0008-5472.CAN-18-2970
Expert Rev Clin Immunol. 2019 Apr 04. 1-8

Cannabis allergy: what the clinician needs to know in 2019.

Ine Ilona Decuyper, Hans-Peter Rihs, Athina Ludovica Van Gasse, Jessy Elst, Leander De Puysseleyr, Margaretha Antje Faber, Christel Mertens, Margo Maria Hagendorens, Vito Sabato, Chris Bridts, Luc De Clerck, Didier Gaston Ebo.

  INTRODUCTION: Although the use of cannabis dates back millennia, the first description of cannabis allergy is relatively recent (1971). Recent large-scale data show that cannabis allergy can manifest severe and generalized symptoms with extensive cross-reactions. Thus, it is essential to become familiarized with its clinical presentation, diagnostic aids, and adequate therapeutic guidance. Areas covered: Here we provide a hands-on overview on cannabis allergy focusing on symptomatology and the reliability of diagnostic options. Recent advances in proteomics are discussed in detail, elucidating the link with nsLTP-related allergies. The proteomics advancements have paved the way for more reliable diagnostics, especially component-based tools. Finally, the current experience in treatment options is highlighted. Expert opinion: Cannabis allergy is an allergy entity which can significantly impact the quality of life. For optimal diagnosis, we advise to start with a validated and standardized crude-extract based test such as sIgE hemp complemented by component-based diagnostics such as sIgE Can s 3 quantifications where available. Future research should lift the veil on the true prevalence of cannabis allergy and the importance of other cannabis allergens to further guide our practice.

Keywords:  Can s 3; Cannabis; allergy; basophil activation; hemp; non-specific lipid transfer protein (nsLTP); skin prick test; specific IgE

DOI:  https://doi.org/10.1080/1744666X.2019.1600403
J Proteome Res. 2019 Apr 03.

Mass spectrometric analysis of Lewy body-enriched α-synuclein in Parkinson's disease.

Payel Bhattacharjee, Annika Öhrfelt, Tammaryn Lashley, Kaj Blennow, Ann Brinkmalm, Henrik Zetterberg.

Parkinson's disease (PD) is characterized by intra-neuronal inclusions of aggregated α-synuclein protein (so called Lewy bodies) in distinct brain regions. Multiple posttranslational modifications may affect the structure and function of α-synuclein. Mass spectrometry-based analysis may be useful for the characterization and quantitation of α-synuclein forms, but has proven challenging, mainly due to the insolubility of Lewy bodies in aqueous buffer. In the present study, we developed a novel method by combining differential solubilization with immunoprecipitation and targeted proteomics using liquid chromatography and tandem mass spectrometry. Brain tissue homogenization and sample preparation were modified to facilitate analysis of soluble, detergent soluble and detergent insoluble protein fractions (Lewy body-enriched). The method was used to compare α-synuclein forms from cingulate cortex (affected) and occipital cortex (unaffected) in two study sets of PD patients, and controls. We identified ~20 modified α-synuclein variants, including species with N-terminal acetylation and C-terminal truncations at amino acids 103 and 119. The levels of α-synuclein forms Ac-α-syn1-6, α-syn13-21, α-syn35-43, α-syn46-58, α-syn61-80 and α-syn81-96 except Ac-α-syn103-119 were significantly increased in PD cingulate region compared to controls in the Lewy body-enriched α-synuclein fraction. In the soluble fraction, only Ac-α-syn1-6 was significantly increased in PD compared to controls. None of the detected α-synuclein variants was Lewy body-specific, but acetylated forms should be examined further as potential biomarkers for abnormal α-synuclein accumulation.

DOI: https://doi.org/10.1021/acs.jproteome.8b00982
J Urol. 2019 Apr 01. 101097JU0000000000000265

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

Dean G Assimos.

DOI: https://doi.org/10.1097/JU.0000000000000265
Int Neurourol J. 2019 Mar;23(1): 5-12

For Physicians Managing Voiding Dysfunction, Improving the Detection Rate of Early Prostate Cancer and Discrimination From Benign Prostatic Hyperplasia, in a Molecular Biomarker Aspects.

Won Tae Kim, Seok Joong Yun, Wun-Jae Kim.

  Prostate cancer (CaP) is the most common cancer diagnosed among men in the United States and the fifth most common cancer among men in Korea. Unfortunately, the early stages of CaP may have no symptoms. Thus, early detection is very important and physicians managing voiding dysfunction must have awareness about CaP. The traditional tests used for early detection of CaP are the prostate-specific antigen (PSA) blood test and digital rectal examination. However, a high PSA level is not specific for CaP. Benign prostatic hyperplasia, prostatitis, urinary tract infection, and urinary retention can all cause a high PSA level. Thus, no test shows sufficient accuracy to truly be useful for screening men for CaP. A prostate biopsy is the only method that yields a definitive diagnosis of CaP; however, this test is invasive and uncomfortable. Recently, new biomarkers for CaP detection have been proposed to improve the accuracy of the PSA test. In this review, we summarize our knowledge of various new biomarkers, including PSA-associated biomarkers (the prostate health index and 4Kscore), molecular biomarkers (PCA3, TMPRSS2: ERG fusion gene, and various miRNAs), and proteomics-associated biomarkers, and the ways in which they may improve the detection rate of CaP. Accordingly, this review can raise awareness about CaP to physicians managing voiding dysfunction and be a good reference for them.

Keywords:  Biomarkers; Early detection of cancer; Prostatic neoplasms

DOI:  https://doi.org/10.5213/inj.1836262.131
Clin Immunol. 2019 Apr 02. pii: S1521-6616(18)30466-2. [Epub ahead of print]

Identification of autoantibodies using human proteome microarrays in patients with IPEX syndrome.

Akihiro Hoshino, Hirokazu Kanegane, Masanori Nishi, Ikuya Tsuge, Kiriko Tokuda, Ichiro Kobayashi, Kohsuke Imai, Tomohiro Morio, Masatoshi Takagi.

  Immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome is one of the inborn errors of immunity, characterized by impaired function of the regulatory T cells. Clinical manifestations of IPEX syndrome are characterized by various autoimmune diseases with autoantibodies. The comprehensive analysis for autoantibodies using human proteome microarrays in the four patients with IPEX syndrome was performed. The numbers of the highly expressed autoantibody showing relative log2 ratios greater than 1 were 1876, 513, 234 and 831 (mean: 864), respectively. Some novel autoantibodies which could explain the phenotypes of patients, adrenal dysfunction, muscular hypotonia, afibrinogenemia, enteropathy and pancytopenia were identified. Various kinds of autoantibodies targeting testis-specific antigens were also identified. Human proteome microarray is a powerful tool to understand the pathophysiology of IPEX syndrome. The larger cohort analysis using this method will provide further understanding of the impaired immune tolerance in humans.

Keywords:  Autoantibody; Autoimmune disease; IPEX syndrome; Tolerance

DOI:  https://doi.org/10.1016/j.clim.2019.03.011
Sci Rep. 2019 Apr 02. 9(1): 5522

Synthetic standard aided quantification and structural characterization of amyloid-beta glycopeptides enriched from cerebrospinal fluid of Alzheimer's disease patients.

Jonas Nilsson, Gunnar Brinkmalm, Sherif Ramadan, Lisa Gilborne, Fredrik Noborn, Kaj Blennow, Anders Wallin, Johan Svensson, Mohamed A Abo-Riya, Xuefei Huang, Göran Larson.

An early pathological hallmark of Alzheimer's disease (AD) is amyloid-β (Aβ) deposits in the brain, which largely consist of up to 43 amino acids long Aβ peptides derived from the amyloid precursor protein (APP). We previously identified a series of sialylated Tyr-10 O-glycosylated Aβ peptides, 15-20 residues long, from human cerebrospinal fluid (CSF) and observed a relative increase of those in AD vs non-AD patients. We report here on the synthesis and use of an isotopically double-labeled Aβ1-15 glycopeptide, carrying the core 1 Galβ3GalNAcα1-O-Tyr-10 structure, to (1) identify by HCD LC-MS/MS the definite glycan core 1 structure of immunopurified and desialylated Aβ glycopeptides in human CSF and to (2) establish a LC-MS/MS quantification method for desialylated Aβ1-15 (and Aβ1-17) glycopeptides and to (3) compare the concentrations of these Aβ glycopeptides in CSF from 20 AD patients and 20 healthy controls. Although we unambiguously identified the core 1 structures and Tyr-10 attachment sites of the glycopeptides, we did not observe any quantitative differences, determined through both peptide and oxonium ion fragments, of the desialylated Aβ1-15 or Aβ1-17 glycopeptides between the AD and non-AD group. The new quantitative glycoproteomic approach described, using double-labeled glycopeptide standards, will undoubtedly facilitate future studies of glycopeptides as clinical biomarkers but should also embrace sialylated Aβ standards to reveal specific sialylation patterns of individual Aβ glycopeptides in AD patients and controls.

DOI: https://doi.org/10.1038/s41598-019-41897-5