bims-prodis 2019-01-20 papers

bims-prodis

Biomed News

on Proteomics in disease

Issue of 2019–01–20
27 papers selected by
Nancy Gough, Bioserendipity

Proteomic Profiling of Acute Promyelocytic Leukemia Identifies Two Protein Signatures Associated with Relapse.
The proteomic profile of keratinocytes and lymphocytes in psoriatic patients.
Label-free quantitative proteomic analysis reveals potential biomarkers for early healing in cutaneous leishmaniasis.
GPVI surface expression and signalling pathway activation are increased in platelets from obese patients: Elucidating potential anti-atherothrombotic targets in obesity.
[Serum Proteomic Analysis and Construction of Protein-protein Interaction Networks about Ejaculation Praecox with Shen-yang Deficiency].
Quantitative proteomics reveals key roles for post-transcriptional gene regulation in the molecular pathology of FSHD.
Altered expression of metabolic pathways in CLL detected by unlabelled quantitative mass spectrometry analysis.
Molecular signatures of chronic periodontitis in gingiva: A genomic and proteomic analysis.
Current and future biomarkers for risk-stratification and treatment personalisation in multiple myeloma.
Proteomic analysis of stratum corneum in Cutaneous T-Cell Lymphomas and psoriasis.
Exosomes harbor B cell targets in pancreatic adenocarcinoma and exert decoy function against complement-mediated cytotoxicity.
Understanding the role of chondrocytes in osteoarthritis: utilizing proteomics.
Phosphorylated proteomics analysis of human coronary artery endothelial cells stimulated by Kawasaki disease patients serum.
Differential expression of serum proteins in multiple myeloma.
Novel Biomarkers for the Precisive Diagnosis and Activity Classification of Takayasu Arteritis.
[Study on proteomic profiling changes of workers exposed to methylbenzene and healthy individuals].
Multi-omics analysis of synovial fluid: a promising approach in the study of osteoarthritis.
Proteogenomic Characterization of Human Early-Onset Gastric Cancer.
Modulation of blood inflammatory markers by benralizumab in patients with eosinophilic airway diseases.
The end of omics? High dimensional single cell analysis in precision medicine.
From Omics Technologies to Personalized Transfusion Medicine.
Differences in serum biomarkers between combined glucosamine and chondroitin versus celecoxib in a randomized, double-blind trial in osteoarthritis patients.
GZFLW Induces Apoptosis of Ectopic Endometrial Stromal Cells via Promoting VPS53 Protein Stability.
VCAN Canonical Splice Site Mutation is Associated With Vitreoretinal Degeneration and Disrupts an MMP Proteolytic Site.
Unlocking bone for proteomic analysis and FISH.
Artificially intelligent proteomics improves cardiovascular risk assessment.
Big data in IBD: a look into the future.

Proteomics Clin Appl. 2019 Jan 16. e1800133

Proteomic Profiling of Acute Promyelocytic Leukemia Identifies Two Protein Signatures Associated with Relapse.

Fieke W Hoff, Chenyue W Hu, Amina A Qutub, Yihua Qiu, Marisa J Hornbaker, Carlos Bueso-Ramos, Hussein A Abbas, Sean M Post, Eveline S J M de Bont, Steven M Kornblau.

   PURPOSE: Acute promyelocytic leukemia (APL) is the most prognostically favorable subtype of AML. Defining the features that allow identification of acute promyelocytic leukemia (APL) patients likely to relapse after therapy remains challenging.
EXPERIMENTAL DESIGN: Proteomic profiling was performed on 20 newly diagnosed APL, 205 non-APL acute myeloid leukemia (AML), and 10 normal CD34+ samples using Reverse Phase Protein Arrays probed with 230 antibodies.
RESULTS: Comparison between APL and non-APL AML samples identified 8.3% of the proteins to be differentially expressed. Proteins higher expressed in APL were involved in the pro-apoptotic pathways or were linked to higher proliferation. The ''MetaGalaxy'' approach that considers proteins in relation to other assayed proteins, stratified the APL patients into two protein signatures. All of the relapse patients (n = 4/4) were in protein signature 2 (S2). Comparison of proteins between the signatures showed significant differences in relative expression for 38 proteins. Protein expression summary plots suggested less translational activity in combination with a less proliferative character for S2 compared to signature 1.
CONCLUSIONS AND CLINICAL RELEVANCE: This study provides a potential proteomic-based classification of APL patients that may be useful for risk stratification and therapeutic guidance. Validation in a larger independent cohort in required. This article is protected by copyright. All rights reserved.

Keywords:  AML; APL; leukemia; proteomics reverse phase protein array

DOI:  https://doi.org/10.1002/prca.201800133
Proteomics Clin Appl. 2019 Jan 16. e1800119

The proteomic profile of keratinocytes and lymphocytes in psoriatic patients.

Agnieszka Gęgotek, Pedro Domingues, Adam Wroński, Ewa Ambrożewicz, Elżbieta Skrzydlewska.

   PURPOSE: Psoriatic skin lesions are associated with chronic inflammation related to immune cell activity. Therefore, the aim of this study was to compare changes in the proteome of psoriatic keratinocytes and lymphocytes.
EXPERIMENTAL DESIGN: A proteomics approach (nanoflow LC-MS/MS) was used to analyze the expression of proteins in keratinocytes and lymphocytes from psoriatic patients and healthy controls.
RESULTS: As a result 2119 proteins for keratinocytes and 1235 proteins for lymphocytes were identified, quantified, and assigned for further analysis. Psoriatic keratinocytes had 68 downregulated and 7 upregulated proteins and psoriatic lymphocytes had 106 downregulated and 67 upregulated proteins compared to healthy individuals. The list of proteins that expression was downregulated included proteins involved in antioxidant homeostasis, transcription regulation, and ATP hydrolysis; proteins with an upregulated expression were involved in glycolytic processes and RNA translation. These changes in both cell types were accompanied by an increased level of 4-HNE-protein adducts; control cells were characterized by 4-HNE-Lysine adducts formed with structural and binding proteins, while in psoriatic cells 4-HNE-Lysine, 4-HNE-Histidine, and 4-HNE-Cysteine adducts with various molecular function proteins occurred at a significant level.
CONCLUSION: This study highlighting the changes in psoriatic keratinocytes and lymphocytes that can be directly involved in the development of psoriasis. In both cell types the most significant changes were associated with upregulation of phosphoglycerate mutase 1 and downregulation of thioredoxin reductase. This article is protected by copyright. All rights reserved.

Keywords:  4-HNE-protein adducts; Keratinocytes; Lymphocytes; Proteome; Psoriasis

DOI:  https://doi.org/10.1002/prca.201800119
PeerJ. 2019 ;6 e6228

Label-free quantitative proteomic analysis reveals potential biomarkers for early healing in cutaneous leishmaniasis.

Andrés Montoya, Manuel Carlos López, Ivan D Vélez, Sara M Robledo.

   Background: Leishmaniasis is a parasitic disease caused by more than 20 species of the Leishmania genus. The disease is globally distributed and is endemic in 97 countries and three territories in the tropical and subtropical regions. The efficacy of the current treatments is becoming increasingly low either due to incomplete treatment or resistant parasites. Failure of treatment is frequent, and therefore, the search for early biomarkers of therapeutic response in cutaneous leishmaniasis (CL) is urgently needed.
Objective: The aim of this study was to compare the proteomic profiles in patients with CL before and after 7 days of treatment and identify early biomarkers of curative response.
Methods: Four patients with a parasitological diagnosis of leishmaniasis with confirmation of species by PCR-RFLP were recruited. All patients had a single lesion, and a protein from the middle of the ulcer was quantified by liquid chromatography and mass spectrometry.
Results: A total of 12 proteins showed differential expression in the comparative LC-electrospray ionization MS/MS (LC-ESI-MS/MS) triplicate analysis. Seven of them were up-regulated and five of them were down-regulated. Calcium binding proteins A2, A8, and A9 and hemoglobin subunits alpha-2 and delta showed high correlation with epidermis development and immune response.
Conclusion: We identified changes in the profiles of proteins that had a positive therapeutic response to the treatment. The proteins identified with differential expression are related to the reduction of inflammation and increased tissue repair. These proteins can be useful as biomarkers for early monitoring of therapeutic response in CL.

Keywords:  Biomarkers; Cutaneous leishmaniasis; Label-free proteome; Therapeutic response

DOI:  https://doi.org/10.7717/peerj.6228
Atherosclerosis. 2018 Dec 25. pii: S0021-9150(18)31554-5. [Epub ahead of print]281 62-70

GPVI surface expression and signalling pathway activation are increased in platelets from obese patients: Elucidating potential anti-atherothrombotic targets in obesity.

María N Barrachina, Aurelio M Sueiro, Irene Izquierdo, Lidia Hermida-Nogueira, Esteban Guitián, Felipe F Casanueva, Richard W Farndale, Masaaki Moroi, Stephanie M Jung, María Pardo, Ángel García.

   BACKGROUND AND AIMS: Platelets play a fundamental role in the increased atherothrombotic risk related to central obesity since they show hyperactivation and lower sensitivity to antiplatelet therapy in obese patients. The main goal of this study was to identify platelet biomarkers related to the risk of atherothrombosis in obese patients, confirm platelet activation levels in these patients, and identify altered activation pathways.
METHODS: Platelets were obtained from cohorts of obese patients and age- and sex-matched lean controls. Biochemical and proteome analyses were done by two-dimensional differential in-gel electrophoresis (2D-DIGE), mass spectrometry, and immunoblotting. Functional and mechanistic studies were conducted with aggregation assays and flow cytometry.
RESULTS: We confirmed an up-regulation of αIIb and fibrinogen isoforms in platelets from obese patients. A complementary platelet aggregation approach showed platelets from obese patients are hyper-reactive in response to collagen and collagen-related peptide (CRP), revealing the collagen receptor Glycoprotein VI (GPVI) signalling as one of the altered pathways. We also found the active form of Src (pTyr418) is up-regulated in platelets from obese individuals, which links proteomics to aggregation data. Moreover, we showed that CRP-activated platelets present higher levels of tyrosine phosphorylated PLCγ2 in obese patients, confirming alterations in GPVI signalling. In line with the above, flow cytometry studies show higher surface expression levels of total GPVI and GPVI-dimer in obese platelets, both correlating with BMI.
CONCLUSIONS: Our results suggest a higher activation state of SFKs-mediated signalling pathways in platelets from obese patients, with a primary involvement of GPVI signalling.

Keywords:  Drug targets; GPVI signalling; Obesity; Platelets; Proteomics; SFK-Mediated signalling pathways

DOI:  https://doi.org/10.1016/j.atherosclerosis.2018.12.023
Zhongguo Zhong Xi Yi Jie He Za Zhi. 2017 04;37(4): 438-442

[Serum Proteomic Analysis and Construction of Protein-protein Interaction Networks about Ejaculation Praecox with Shen-yang Deficiency].

Cong-E Tan, Xiang-Yun Huang, Mi-Qu Wang.

Objective To identify serum proteome of ejaculation praecox(EP) with Shen-yang de- ficiency, and to explore its pathogenesis of EP in the protein-protein interaction ( PPI) network. Methods The serum samples were respectively collected from 4 EP with Shen-yang deficiency patients and 4 healthy controls. After the serum proteome of EP with Shen-yang deficiency was obtained, the technology of isobaric tags for relative and absolute quantitation (iTRAQ) was adopted for identification. The STRING data- base was applied to construct the PPI network whose function was analyzed through bioinformatics meth- ods. Results A group of 238 serum proteins were identified in total, of which, 162 proteins reached the strict quantitative standard. Nine proteins were differently expressed, including 1 up-regulated and 8 down-regulated. The constructed PPI network was constituted by 72 protein nodes and 283 protein couples, and could be clustered to 16 clusters, in which 10 clusters were composed of 3 or more proteins. Each cluster could be found with a core protein correspondingly. The core protein of C3,C5,C1S and MASP2 were all main constituents of complement system, whose function involves in biological process of complement ac- tivation. Conclusions The protein models in PPI network of differently expressed serum proteome about EP with Shen-yang deficiency were functional enriched in the biological process of complement activa-, tion; which indicate that a immune dysfuction dominated by abnormal process of complent activation may' be one of the main mechanisms of EP with Shen-yang deficiency.
Elife. 2019 Jan 15. pii: e41740. [Epub ahead of print]8

Quantitative proteomics reveals key roles for post-transcriptional gene regulation in the molecular pathology of FSHD.

Sujatha Jagannathan, Yuko Ogata, Philip R Gafken, Stephen J Tapscott, Robert K Bradley.

  DUX4 is a transcription factor whose misexpression in skeletal muscle causes facioscapulohumeral muscular dystrophy (FSHD). While DUX4's transcriptional activity has been extensively characterized, the DUX4-induced proteome remains undescribed. Here, we report concurrent measurement of RNA and protein levels in DUX4-expressing cells via RNA-seq and quantitative mass spectrometry. DUX4 transcriptional targets were robustly translated, confirming the likely clinical relevance of proposed FSHD biomarkers. However, a multitude of mRNAs and proteins exhibited discordant expression changes upon DUX4 expression. Our dataset revealed unexpected proteomic, but not transcriptomic, dysregulation of diverse molecular pathways, including Golgi apparatus fragmentation, as well as extensive post-transcriptional buffering of stress response genes. Key components of RNA degradation machineries, including UPF1, UPF3B, and XRN1, exhibited suppressed protein, but not mRNA, levels, explaining the build-up of aberrant RNAs that characterizes DUX4-expressing cells. Our results provide a resource for the FSHD community and illustrate the importance of post-transcriptional processes to DUX4-induced pathology.

Keywords:  genetics; genomics; human; human biology; medicine

DOI:  https://doi.org/10.7554/eLife.41740
Br J Haematol. 2019 Jan 17.

Altered expression of metabolic pathways in CLL detected by unlabelled quantitative mass spectrometry analysis.

Lauren A Thurgood, Eveline S Dwyer, Karen M Lower, Tim K Chataway, Bryone J Kuss.

  Chronic lymphocytic leukaemia (CLL) remains the most common incurable malignancy of B cells in the western world. Patient outcomes are heterogeneous and can be difficult to predict with current prognostic markers. Here, we used a quantitative label-free proteomic technique to ascertain differences in the B-cell proteome from healthy donors and CLL patients with either mutated (M-CLL) or unmutated (UM-CLL) IGHV to identify new prognostic markers. In peripheral B-CLL cells, 349 (22%) proteins were differentially expressed between normal B cells and B-CLL cells and 189 (12%) were differentially expressed between M-CLL and UM-CLL. We also examined the proteome of proliferating CLL cells in the lymph nodes, and identified 76 (~8%) differentially expressed proteins between healthy and CLL lymph nodes. B-CLL cells show over-expression of proteins involved in lipid and cholesterol metabolism. A comprehensive lipidomic analysis highlighted large differences in glycolipids and sphingolipids. A shift was observed from the pro-apoptotic lipid ceramide towards the anti-apoptotic/chemoresistant lipid, glucosylceramide, which was more evident in patients with aggressive disease (UM-CLL). This study details a novel quantitative proteomic technique applied for the first time to primary patient samples in CLL and highlights that primary CLL lymphocytes display markers of a metabolic shift towards lipid synthesis and breakdown.

Keywords:   CLL ; SWATH ; lipidomics; metabolism; proteomics

DOI:  https://doi.org/10.1111/bjh.15751
J Periodontol. 2019 Jan 17.

Molecular signatures of chronic periodontitis in gingiva: A genomic and proteomic analysis.

Esra Guzeldemir-Akcakanat, Begum Alkan, Deniz Sunnetci-Akkoyunlu, Busra Güral, V Merve Balta, Bahadir Kan, Emel Akgun, Elif Busra Yilmaz, Ahmet Tarik Baykal, Naci Cine, Vakur Olgac, Esen Gumuslu, Hakan Savlı.

   BACKGROUND: To elucidate molecular signatures of chronic periodontitis (CP) using gingival tissue samples through omics-based whole-genome transcriptomic and whole protein profiling.
METHODS: Gingival tissues from 18 CP and 25 controls were analysed using gene expression microarrays to identify gene expression patterns and the proteins isolated from these samples were subjected to comparative proteomic analysis by LC-MS/MS. The data from transcriptomics and proteomics were integrated to reveal common shared genes and proteins.
RESULTS: The most upregulated genes in CP compared to controls were found as MZB1, BMS1P20, IGLL1/IGLL5, TNFRSF17, ALDH1A1, KIAA0125, MMP7, PRL, MGC16025, ADAM11, and the most upregulated proteins in CP compared to controls were BPI, ITGAM, CAP37, PCM1, MMP-9, MZB1, UGTT1, PLG, RAB1B, HSP90B1. Functions of the identified genes were involved cell death/survival, DNA replication, recombination/repair, gene expression, organismal development, cell-to-cell signalling/interaction, cellular development, cellular growth/proliferation, cellular assembly/organization, cellular function/maintenance, cellular movement, B-cell development and identified proteins were involved in protein folding, response to stress, single-organism catabolic process, regulation of peptidase activity, and negative regulation of cell death. The integration and validation analysis of the transcriptomics and proteomics data revealed two common shared genes and proteins, MZB1 and ECH1.
CONCLUSIONS: Integrative data from transcriptomics and proteomics revealed MZB1 as a potent candidate for chronic periodontitis. This article is protected by copyright. All rights reserved.

Keywords:  chronic periodontitis; enoyl-CoA Hydratase; genomics; gingiva; inflammation; pERp1 ; proteogenomics; proteomics

DOI:  https://doi.org/10.1002/JPER.18-0477
Mol Omics. 2019 Jan 17.

Current and future biomarkers for risk-stratification and treatment personalisation in multiple myeloma.

Giao N Lê, Jonathan Bones, Mark Coyne, Despina Bazou, Paul Dowling, Peter O'Gorman, Anne-Marie Larkin.

Multiple myeloma, an incurable malignancy of the plasma cells in the bone marrow, has a complex pathogenesis due to clonal heterogeneity. Over the years, many clinical trials and researches have led to the development of effective myeloma treatments, resulting in survival prolongation. Molecular prognostic markers for risk-stratification to predict survival, and predictive markers for treatment response are being extensively explored. This review discusses the current risk-adaptive strategies based on genetic and molecular risk signatures that are in practice to predict survival and describes the future prognostic and predictive biomarkers across the fields of genomics, proteomics, and glycomics in myeloma. Gene expression profiling and next generation sequencing are coming to the forefront of risk-stratification and therapeutic-response prediction. Similarly, proteomic and glycomic-based platforms are gaining momentum in biomarker discovery to predict drug resistance and disease progression.

DOI: https://doi.org/10.1039/c8mo00193f
Exp Dermatol. 2019 Jan 13.

Proteomic analysis of stratum corneum in Cutaneous T-Cell Lymphomas and psoriasis.

Bruno Méhul, Corinne Ménigot, Paul Fogel, Alexia Seraidaris, Alexandre Genette, Thierry Pascual, Madeleine Duvic, Johannes J Voegel.

  Stratum corneum collected by tape stripping from 10 and 24 subjects with Cutaneous T-Cell Lymphomas (CTCL) or psoriasis, respectively, were compared using quantitative label-free mass spectrometry analysis. A non-supervised statistical analysis (Posneg NMF) based on 352 differentially expressed proteins in both CTCL and psoriasis samples was able to separate the two disease groups and finally able to identify a set of 112 proteins that contributed most and significantly to the separation when compared to non-lesional samples. In addition, Luminex assay revealed that the increase in the amount of chemokines related to the inflammatory response, and immune cell infiltration and recruitment in lesional stratum corneum in CTCL, including CXCL8, CXCL9, CXCL10, CCL27, TNF and sICAM-1 was in agreement with published data on entire skin biopsies. Proteome analysis using quantitative methods including mass spectrometry and Luminex technology offered the possibility to investigate the relevant protein signature in CTCL and may be helpful to diagnose and investigate the efficacy of treatments in clinical investigations using non-invasive methods in the future. This article is protected by copyright. All rights reserved.

Keywords:   CTCL ; Stratum corneum ; Luminex; Mass spectrometry; Psoriasis

DOI:  https://doi.org/10.1111/exd.13880
Nat Commun. 2019 Jan 16. 10(1): 254

Exosomes harbor B cell targets in pancreatic adenocarcinoma and exert decoy function against complement-mediated cytotoxicity.

Michela Capello, Jody V Vykoukal, Hiroyuki Katayama, Leonidas E Bantis, Hong Wang, Deepali L Kundnani, Clemente Aguilar-Bonavides, Mitzi Aguilar, Satyendra C Tripathi, Dilsher S Dhillon, Amin A Momin, Haley Peters, Matthew H Katz, Hector Alvarez, Vincent Bernard, Sammy Ferri-Borgogno, Randall Brand, Douglas G Adler, Matthew A Firpo, Sean J Mulvihill, Jeffrey J Molldrem, Ziding Feng, Ayumu Taguchi, Anirban Maitra, Samir M Hanash.

Although B cell response is frequently found in cancer, there is little evidence that it alters tumor development or progression. The process through which tumor-associated antigens trigger humoral response is not well delineated. We investigate the repertoire of antigens associated with humoral immune response in pancreatic ductal adenocarcinoma (PDAC) using in-depth proteomic profiling of immunoglobulin-bound proteins from PDAC patient plasmas and identify tumor antigens that induce antibody response together with exosome hallmark proteins. Additional profiling of PDAC cell-derived exosomes reveals significant overlap in their protein content with immunoglobulin-bound proteins in PDAC plasmas, and significant autoantibody reactivity is observed between PDAC cell-derived exosomes and patient plasmas compared to healthy controls. Importantly, PDAC-derived exosomes induce a dose-dependent inhibition of PDAC serum-mediated complement-dependent cytotoxicity towards cancer cells. In summary, we provide evidence that exosomes display a large repertoire of tumor antigens that induce autoantibodies and exert a decoy function against complement-mediated cytotoxicity.

DOI: https://doi.org/10.1038/s41467-018-08109-6
Expert Rev Proteomics. 2019 Jan 17.

Understanding the role of chondrocytes in osteoarthritis: utilizing proteomics.

Varvara Trachana, Evanthia Mourmoura, Ioanna Papathanasiou, Aspasia Tsezou.

   INTRODUCTION: Proteomic analyses have been acknowledged to carry a significant prospective in elucidating the pathogenesis of several diseases, including osteoarthritis (OA). But it hasn't been an easy road: major technical issues, mainly derived from the complex and rigid nature of the cartilage tissue, had to be faced; an obstacle that led to the development of different approaches. Areas covered: In this review, we categorized the proteomic studies undertaken (proteomic analyses of the cartilage, cartilage explants, cultured chondrocytes and chondrocytes' secretome) as are part of the different strategies developed in order to overcome tissue and disease specific challenges. Essentially these approaches aimed at identifying differences in the proteome of healthy vs diseased tissue. Our aim was to point out the novel players that have emerged from these analyses and highlight the associated mechanism(s) suggested to play a role in the pathogenesis of OA. Expert Commentary: The identified factors indicate the implication of age-associated mechanisms, such as metabolic deregulation, inflammation and redox imbalance, in OA onset and/or progression. Taken together these results outline the causal network of the disease and place chondrocytes' senescence at the center of the emerging aetiopathological atlas.

Keywords:  Aging; cartilage; chondrocyte; extracellular matrix (ECM); osteoarthritis; proteomics; secretome; senescence

DOI:  https://doi.org/10.1080/14789450.2019.1571918
BMC Cardiovasc Disord. 2019 Jan 17. 19(1): 21

Phosphorylated proteomics analysis of human coronary artery endothelial cells stimulated by Kawasaki disease patients serum.

Shui-Ming Li, Wan-Ting Liu, Fang Yang, Qi-Jian Yi, Shuai Zhang, Hong-Ling Jia.

   BACKGROUND: Kawasaki disease (KD) is an acute febrile childhood systemic vasculitis that disturbs coronary arteries. The pathogenesis remains unknown. The study of phosphorylated proteins helps to elucidate the relevant pathophysiological mechanisms of cardiovascular disease. However, few researches explored phosphorylated proteins in KD patients.
METHODS: We compared phosphoprotein profiles of HCAECs stimulated by the serum of KD patients and normal children using iTRAQ technology, TiO2 enrichment phosphorylated peptide and MS analysis. Then we conducted the functional analysis by ClueGO and the biological interaction networking analysis by ReactomeFIViz. Western blotting was performed to identify the hub proteins.
RESULTS: Our results revealed that phosphorylation of 148 proteins showed different intensities between the two HCAECs groups, which are enriched in MAPK, VEGFR, EGFR, Angiopoietin receptor, mTOR, FAK signaling pathway and so on. Through the Network Analyzer analysis, the hub proteins are CDKN1A, MAPK1 and POLR2A, which were experimentally validated.
CONCLUSION: In summary, we provided evidence addressing the valuable phosphorylation signaling that could be useful resource to understand the molecular mechanism and the potential targets for novel therapy of KD.

Keywords:  HCAECs; Hub proteins; KD; Network analyzer analysis; Phosphorylated proteomics

DOI:  https://doi.org/10.1186/s12872-018-0982-2
Exp Ther Med. 2019 Jan;17(1): 649-656

Differential expression of serum proteins in multiple myeloma.

Tian-Ze Ma, Zhe Piao, Sheng-Yu Jin, Yong-Geun Kwak.

  The exact cause instigating multiple myeloma (MM) has not been fully elucidated, and the disease has a median survival of 6 months without any treatment. To identify potential biomarkers of MM, serum proteins reflecting alteration in their proteomes were analyzed in 6 patients with MM compared with 6 healthy controls using two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time-of flight mass spectrometry. The most notable differentially expressed proteins were validated by immunoblotting and changes in mRNA expression were evaluated by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). A total of 11 differentially expressed protein spots were found. The expression levels of 7 proteins [Immunoglobulin heavy constant µ; proto-oncogene diffuse B-cell lymphoma (DBL2); 26S protease regulatory subunit 4 (P26s4); serum albumin; haptoglobin; and two unknown proteins with isoelectronic point (pI) of 6.41 and molecular weight of 35.4 kDa, and pI of 8.05 and molecular weight of 27.4 kDa, respectively] were downregulated in MM compared with healthy controls. Expression of gel actin-related protein 2/3 complex subunit 1A (ARPC1A); immunoglobulin heavy constant γ 1; fibrinogen α chain (FGA) fragment D; and zinc finger protein 70 were increased in serum of MM patients. Protein expressions of ARPC1A, FGA, P26s4 and DBL2 were measured by immunoblotting in an independent cohort of 12 MM patients and 10 healthy controls. RT-qPCR analysis demonstrated that ARPC1A expression only mimicked protein expression, whereas FGA, PSMC1 (encoding P26s4) and MCF2 (encoding DBL2) did not exhibit significant changes in mRNA expression between control and MM samples. These proteins represent putative serological biomarkers for patients with MM.

Keywords:  A clonal B cell malignancy; biomarkers; multiple myeloma; serum protein; somatic mutations

DOI:  https://doi.org/10.3892/etm.2018.7010
Circ Genom Precis Med. 2019 Jan;12(1): e002080

Novel Biomarkers for the Precisive Diagnosis and Activity Classification of Takayasu Arteritis.

Xiao Cui, Fang Qin, Lei Song, Tian Wang, Bin Geng, Weili Zhang, Ling Jin, Wenjie Wang, Shuangyue Li, Xinping Tian, Huimin Zhang, Jun Cai.

   BACKGROUND: Establishing the diagnosis and determining disease activity of Takayasu arteritis (TA) remains challenging. Novel biomarkers might help to solve this problem.
METHODS: In the screening phase, by using large-scale protein arrays detecting samples from 90 subjects (TA active, 29; TA inactive 31; and controls, 30). In the validation phase, by using enzyme-linked immunosorbent assay (ELISA), potential biomarkers for TA diagnosis, and activity classification were measured in independent cohorts, respectively.
RESULTS: In the screening phase, 18 cytokines significantly differentially enriched between TA patients and controls and another 15 cytokines significantly differentially enriched between TA patient in active and inactive status were identified (adjusted P<0.05). In the validation phase, TIMP (tissue inhibitor of metalloproteinases)-1 was identified as a specific biomarker for TA diagnosis that a cutoff value of 221.86 μg/L could provide a specificity of 89.58% and a positive predictive value of 0.92. Meanwhile, we found it unreliable to use a single biomarker for TA activity classification. Considering this, we further built a logistic regression model based on multiple cytokines, including CA (cancer antigen) 125, FLRG (follistatin-related protein), IGFBP (insulin-like growth factor-binding protein)-2, CA15-3, GROa (growth-regulated alpha protein), LYVE (lymphatic vessel endothelial hyaluronic acid receptor)-1, ULBP (UL16-binding protein)-2, and CD (cluster of differentiation) 99, with an area under the curve reaching 0.909 for discriminating TA activity status.
CONCLUSIONS: This study suggested TIMP-1 as a specific biomarker for TA diagnosis with a cutoff value of 221.86 μg/L. Furthermore, we provided a logistic regression model based on 8 biomarkers for the precisive activity classification of TA with an area under the curve of 0.909.

Keywords:  arteritis; biomarker; cytokines; proteomics

DOI:  https://doi.org/10.1161/CIRCGEN.117.002080
Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi. 2018 Nov 20. 36(11): 824-826

[Study on proteomic profiling changes of workers exposed to methylbenzene and healthy individuals].

R M Miao, X T Yu, G L Qian.

  Objective: This study focused on the proteomicchanges between workers exposed to methylbenzene (WMB) and healthy individuals (HI) . Methods: The serum of WMB and HI was collected and the unmarked label free mass spectrometry was utilized for protein identification and quantitative comparison. The differentlyexpressed proteins in WMB and the HI were screened, followed by the analysis of protein and biological functions by bioinformatics tools. Results: Thirty nine proteins were differently expressed between WMB and HI. Compared with HI, 24 proteins were up regulated and 15 proteins were down regulated over 2 fold change in WMB. Theseproteins were mainly involved in signal transduction, serine endopeptidase activity, inflammatory response, protein modification, stress reaction, coagulation reaction and so on. Conclusion: The differently expressed proteins provide a potential protein marker for the health assessment of WMB and early diagnosis of methylbenzene poisioning and expand our understanding of the molecular mechanism of methylbenzene intoxication.

Keywords:  Methylbenzene; Occupational diseases; Poisoning; Proteomics

DOI:  https://doi.org/10.3760/cma.j.issn.1001-9391.2018.11.006
J Biol Regul Homeost Agents. 2018 Nov-Dec;32(6 Suppl. 1):32(6 Suppl. 1): 9-13

Multi-omics analysis of synovial fluid: a promising approach in the study of osteoarthritis.

G Vicenti, D Bizzoca, M Carrozzo, G Solarino, B Moretti.

Osteoarthritis (OA), affecting 250 million individuals worldwide, is a significant social health problem. Therefore, the search for synovial fluid (SF) biomarkers that could anticipate the diagnosis of OA is gaining increasing importance in orthopaedics. This review summarizes the recent progresses preformed in the multi-omics approach to OA, mainly focusing on proteome and metabolome analysis of SF. Proteomics of the SF has shown the up-regulation of several components of the classic complement pathway in OA samples, including C1, C2, C3, C4A, C4B, C5 and C4 C4BPA, thus depicting that complement is involved in the pathogenesis of OA. Moreover, proteomics has displayed that some pro-inflammatory cytokines, namely IL-6, IL-8 and IL-18, have a role in OA. The metabolomic profiling of the SF in OA has identified some metabolites as potential biomarkers of OA and has shown the existence of metabolically different OA subgroups. However, further studies with larger samples sizes and matched-control groups are needed to identify SF biomarkers that could be useful in the diagnosis, treatment and follow-up of OA.
Cancer Cell. 2019 Jan 14. pii: S1535-6108(18)30574-9. [Epub ahead of print]35(1): 111-124.e10

Proteogenomic Characterization of Human Early-Onset Gastric Cancer.

Dong-Gi Mun, Jinhyuk Bhin, Sangok Kim, Hyunwoo Kim, Jae Hun Jung, Yeonjoo Jung, Ye Eun Jang, Jong Moon Park, Hokeun Kim, Yeonhwa Jung, Hangyeore Lee, Jingi Bae, Seunghoon Back, Su-Jin Kim, Jieun Kim, Heejin Park, Honglan Li, Kyu-Baek Hwang, Young Soo Park, Jeong Hwan Yook, Byung Sik Kim, Sun Young Kwon, Seung Wan Ryu, Do Youn Park, Tae Yong Jeon, Dae Hwan Kim, Jae-Hyuck Lee, Sang-Uk Han, Kyu Sang Song, Dongmin Park, Jun Won Park, Henry Rodriguez, Jaesang Kim, Hookeun Lee, Kwang Pyo Kim, Eun Gyeong Yang, Hark Kyun Kim, Eunok Paek, Sanghyuk Lee, Sang-Won Lee, Daehee Hwang.

  We report proteogenomic analysis of diffuse gastric cancers (GCs) in young populations. Phosphoproteome data elucidated signaling pathways associated with somatic mutations based on mutation-phosphorylation correlations. Moreover, correlations between mRNA and protein abundances provided potential oncogenes and tumor suppressors associated with patient survival. Furthermore, integrated clustering of mRNA, protein, phosphorylation, and N-glycosylation data identified four subtypes of diffuse GCs. Distinguishing these subtypes was possible by proteomic data. Four subtypes were associated with proliferation, immune response, metabolism, and invasion, respectively; and associations of the subtypes with immune- and invasion-related pathways were identified mainly by phosphorylation and N-glycosylation data. Therefore, our proteogenomic analysis provides additional information beyond genomic analyses, which can improve understanding of cancer biology and patient stratification in diffuse GCs.

Keywords:  cancer subtypes; correlation between mRNA and protein abundance changes; correlation between mutation and phosphorylation; diffuse gastric cancer; proteogenomics; somatic nonsynonymous mutations

DOI:  https://doi.org/10.1016/j.ccell.2018.12.003
Respir Res. 2019 Jan 18. 20(1): 14

Modulation of blood inflammatory markers by benralizumab in patients with eosinophilic airway diseases.

Sriram Sridhar, Hao Liu, Tuyet-Hang Pham, Gautam Damera, Paul Newbold.

   BACKGROUND: Benralizumab, a humanized, afucosylated, monoclonal antibody that targets interleukin-5 receptor α, depletes eosinophils and basophils by enhanced antibody-dependent cell-mediated cytotoxicity. It demonstrated efficacy for patients with moderate to severe asthma and, in a Phase IIa trial, for chronic obstructive pulmonary disease (COPD) with eosinophilic inflammation. We investigated effects of benralizumab 100 mg every 8 weeks (first three doses every 4 weeks) subcutaneous on blood inflammatory markers through proteomic and gene-expression analyses collected during two Phase II studies of patients with eosinophilic asthma and eosinophilic COPD.
METHODS: Serum samples for proteomic analysis and whole blood for gene expression analysis were collected at baseline and 52 weeks (asthma study) or 32 weeks (COPD study) post-treatment. Proteomic analyses were conducted on a custom set of 90 and 147 Rules-Based Medicine analytes for asthma and COPD, respectively. Gene expression was profiled by Affymetrix Human Genome U133 plus 2 arrays (~ 54 K probes). Gene set variation analysis (GSVA) was used to determine transcriptomic activity of immune signatures. Treatment-related differences between analytes, genes, and gene signatures were analyzed for the overall population and for patient subgroups stratified by baseline blood eosinophil count (eosinophil-high [≥300 cells/μL] and eosinophil-low [< 300 cells/μL]) via t-test and repeated measures analysis of variance.
RESULTS: Eosinophil chemokines eotaxin-1 and eotaxin-2 were significantly upregulated (false discovery rate [FDR] < 0.05) by approximately 2.1- and 1.4-fold in the asthma study and by 2.3- and 1.7-fold in the COPD study following benralizumab treatment. Magnitude of upregulation of these two chemokines was greater for eosinophil-high patients than eosinophil-low patients in both studies. Benralizumab was associated with significant reductions (FDR < 0.05) in expression of genes associated with eosinophils and basophils, such as CLC, IL-5Rα, and PRSS33; immune-signaling complex genes (FCER1A); G-protein-coupled receptor genes (HRH4, ADORA3, P2RY14); and further immune-related genes (ALOX15 and OLIG2). The magnitude of downregulation of gene expression was greater for eosinophil-high than eosinophil-low patients. GSVA on immune signatures indicated significant treatment reductions (FDR < 0.05) in eosinophil-associated signatures.
CONCLUSIONS: Benralizumab is highly selective, modulating blood proteins or genes associated with eosinophils or basophils. Modulated protein and gene expression patterns are most prominently altered in eosinophil-high vs. eosinophil-low patients.
TRIAL REGISTRATION: NCT01227278 and NCT01238861 .

Keywords:  Asthma; Basophils; Benralizumab; Blood; Chronic obstructive pulmonary disease; Eosinophils; Gene expression; Gene set variation analysis; Inflammatory markers; Proteomics

DOI:  https://doi.org/10.1186/s12931-018-0968-8
Eur J Immunol. 2019 Jan 17.

The end of omics? High dimensional single cell analysis in precision medicine.

Edoardo Galli, Ekaterina Friebel, Florian Ingelfinger, Susanne Unger, Nicolás Gonzalo Núñez, Burkhard Becher.

  High-dimensional single-cell (HDcyto) technologies, such as mass cytometry (CyTOF) and flow cytometry, are the key techniques that hold a great promise for deciphering complex biological processes. During the last decade, we witnessed an exponential increase of novel HDcyto technologies that are able to deliver an in-depth profiling in different settings, such as various autoimmune diseases and cancer. The concurrent advance of custom data-mining algorithms has provided a rich substrate for the development of novel tools in translational medicine research. HDcyto technologies have been successfully used to investigate cellular cues driving pathophysiological conditions, and to identify disease-specific signatures that may serve as diagnostic biomarkers or therapeutic targets. These technologies now also offer the possibility to describe a complete cellular environment, providing unanticipated insights into human biology. In this review, we present an update on the current cutting-edge HDcyto technologies and their applications, which are going to be fundamental in providing further insights into human immunology and pathophysiology of various diseases. Importantly, we further provide an overview of the main algorithms currently available for data mining, together with the conceptual workflow for high-dimensional cytometric data handling and analysis. Overall, this review aims to be a handy overview for immunologists on how to design, develop and read HDcyto data. This article is protected by copyright. All rights reserved.

Keywords:  bioinformatic tools; diagnostic biomarkers; flow cytometry; mass cytometry (CyTOF); single cell analysis

DOI:  https://doi.org/10.1002/eji.201847758
Expert Rev Proteomics. 2019 Jan 18.

From Omics Technologies to Personalized Transfusion Medicine.

Angelo D'Alessandro.

   INTRODUCTION: Blood transfusion is the single most frequent in-hospital medical procedure, a life-saving intervention for millions of recipients worldwide every year. Storage in the blood bank is an enabling strategy for this critical procedure, as it logistically solves the issue of making ~110 million units available for transfusion every year. Unfortunately, storage in the blood bank promotes a series of biochemical and morphological changes to the red blood cell that compromise the integrity and functionality of the erythrocyte in vitro and in animal models, and could negatively impact transfusion outcomes in the recipient. Areas covered: While commenting on the clinical relevance of the storage lesion is beyond the scope of this manuscript, here we will review recent advancements in our understanding of the storage lesion as gleaned through omics technologies. We will focus on how the omics-scale appreciation of the biological variability at the donor and recipient level is impacting our understanding of red blood cell storage biology. Expert commentary: Omics technologies are paving the way for personalized transfusion medicine, a discipline that promises to revolutionize a critical field in medical practice. The era of recipient-tailored additives, processing and storage strategies may not be too far distant in the future.

Keywords:  band 3; metabolomics; oxidation; proteomics; red blood cell

DOI:  https://doi.org/10.1080/14789450.2019.1571917
Antiinflamm Antiallergy Agents Med Chem. 2019 Jan 14.

Differences in serum biomarkers between combined glucosamine and chondroitin versus celecoxib in a randomized, double-blind trial in osteoarthritis patients.

Sandi L Navarro, Marta Herrero, Helena Martinez, Yuzheng Zhang, Jon Ladd, Edward Lo, David Shelley, Timothy W Randolph, Johanna W Lampe, Paul D Lampe.

   BACKGROUND: Non-steroidal anti-inflammatory drugs, e.g., celecoxib, are commonly used for inflammatory conditions, but can be associated with adverse effects. Combined glucosamine hydrochloride plus chondroitin sulfate (GH+CS) are commonly used for joint pain and have no known adverse effects. Evidence from in vitro, animal and human studies suggests that GH+CS have anti-inflammatory activity, among other mechanisms of action.
OBJECTIVE: We evaluated the effects of GH+CS versus celecoxib on a panel of 20 serum proteins involved in inflammation and other metabolic pathways.
METHODS: Samples were from a randomized, parallel, double-blind trial of pharmaceutical grade 1500 mg GH + 1200 mg CS (n=96) versus 200 mg celecoxib daily (n=93) for 6-months in knee osteoarthritis (OA) patients. Linear mixed models adjusted for age, sex, body mass index, baseline serum protein values, and rescue medicine use assessed the intervention effects of each treatment arm adjusting for multiple testing.
RESULTS: All serum proteins except WNT16 were lower after treatment with GH+CS, while about half increased after celecoxib. Serum IL-6 was significantly reduced (by 9%, P=0.001) after GH+CS, and satisfied the FDR<0.05 threshold. CCL20, CSF3, and WNT16 increased after celecoxib (by 7%, 9% and 9%, respectively, P<0.05), but these serum proteins were no longer statistically significant after controlling for multiple testing.
CONCLUSION: The results of this study using samples from a previously conducted trial in OA patients, demonstrate that GH+CS reduces circulating IL-6, an inflammatory cytokine, but is otherwise comparable to celecoxib with regard to effects on other circulating protein biomarkers.

Keywords:  celecoxib; chondroitin; glucosamine; inflammation; knee osteoarthritis; randomized trial

DOI:  https://doi.org/10.2174/1871523018666190115094512
Evid Based Complement Alternat Med. 2018 ;2018 1293630

GZFLW Induces Apoptosis of Ectopic Endometrial Stromal Cells via Promoting VPS53 Protein Stability.

Ziyu Zhang, Faying Liu, YunYun Xu, Huang Huang, Yang Zou, Bicheng Yang, Yong Luo, Quan Zhang, Anwen Xiong, Liqun Wang, Ouping Huang.

Endometriosis is still a major problem in obstetrics and gynecology. While GZFLW (Gui Zhi Fu Ling Wan) has been originally used for treating gynecological diseases, however, the molecular mechanism that GZFLW acts on endometriosis is not clear. To investigate the molecular mechanism that GZFLW plays role on endometriosis, iTRAQ (isobaric tags for relative and absolute quantification) proteomics and human endometrial stromal cells (Y14) obtained from a patient with endometriosis were used in in vitro study. Our results demonstrated that GZFLW decreased Y14 cells proliferation while increased cells apoptosis. The differential expression protein VPS53 (Vacuolar protein sorting 53 homolog) was predicted by iTRAQ coupled LC-MS/MS and further identified by western blot. Besides, GZFLW induced VPS53 protein level by promoting its stabilization. Our findings highlight a novel role for VPS53 in gynecology and provide a potent therapeutic strategy against endometriosis.

DOI: https://doi.org/10.1155/2018/1293630
Invest Ophthalmol Vis Sci. 2019 Jan 02. 60(1): 282-293

VCAN Canonical Splice Site Mutation is Associated With Vitreoretinal Degeneration and Disrupts an MMP Proteolytic Site.

Peter H Tang, Gabriel Velez, Stephen H Tsang, Alexander G Bassuk, Vinit B Mahajan.

Purpose: To gain insight into the pathophysiology of vitreoretinal degeneration, the clinical course of three family members with Versican Vitreoretinopathy (VVR) is described, and a canonical splice site mutation in the gene encoding for versican (VCAN) protein was biochemically analyzed.
Methods: A retrospective chart review, human eye histopathology, Sanger DNA sequencing, protein structural modeling, and in vitro proteolysis assays were performed.
Results: The proband (II:1), mother (I:2), and younger sibling (II:2) suffered retinal degeneration with foveal sparing and retinal detachments with proliferative vitreoretinopathy, features that were confirmed on histopathologic analysis. All affected members carried a heterozygous adenine to guanine variant (c.4004-2A>G) predicted to result in exon 8 skipping or the deletion of 13 amino acids at the beginning of the GAGβ chain (VCAN p.1335-1347). This deleted region corresponded to a putative MMP cleavage site, validated using fluorescence resonance energy transfer (FRET)-based proteolysis assays. Proteomic network analysis identified 10 interacting partners in the human vitreous and retina linked to retinal detachment and degeneration.
Conclusions: VVR causes significant ocular disease, including retinal detachment and retinal dystrophy. The intronic VCAN mutation removes an MMP cleavage site, which alters versican structure and results in abnormal vitreous modeling. Disruption of a versican protein network may underlie clinicopathologic disease features and point to targeted therapies.

DOI: https://doi.org/10.1167/iovs.18-25624
Lab Invest. 2019 Jan 18.

Unlocking bone for proteomic analysis and FISH.

Claudius Mueller, Marco Gambarotti, Stefania Benini, Piero Picci, Alberto Righi, Monica Stevanin, Sabine Hombach-Klonisch, Dana Henderson, Lance Liotta, Virginia Espina.

Bone tissue is critically lagging behind soft tissues and biofluids in our effort to advance precision medicine. The main challenges have been accessibility and the requirement for deleterious decalcification processes that impact the fidelity of diagnostic histomorphology and hinder downstream analyses such as fluorescence in-situ hybridization (FISH). We have developed an alternative fixation chemistry that simultaneously fixes and decalcifies bone tissue. We compared tissue morphology, immunohistochemistry (IHC), cell signal phosphoprotein analysis, and FISH in 50 patient matched primary bone cancer cases that were either formalin fixed and decalcified, or theralin fixed with and without decalcification. Use of theralin improved tissue histomorphology, whereas overall IHC was comparable to formalin fixed, decalcified samples. Theralin-fixed samples showed a significant increase in protein and DNA extractability, supporting technologies such as laser-capture microdissection and reverse phase protein microarrays. Formalin-fixed bone samples suffered from a fixation artifact where protein quantification of β-actin directly correlated with fixation time. Theralin-fixed samples were not affected by this artifact. Moreover, theralin fixation enabled standard FISH staining in bone cancer samples, whereas no FISH staining was observed in formalin-fixed samples. We conclude that the use of theralin fixation unlocks the molecular archive within bone tissue allowing bone to enter the standard tissue analysis pipeline. This will have significant implications for bone cancer patients, in whom personalized medicine has yet to be implemented.

DOI: https://doi.org/10.1038/s41374-018-0168-7
EBioMedicine. 2019 Jan 14. pii: S2352-3964(19)30014-3. [Epub ahead of print]

Artificially intelligent proteomics improves cardiovascular risk assessment.

Siu Kwan Sze.

DOI: https://doi.org/10.1016/j.ebiom.2019.01.014
Nat Rev Gastroenterol Hepatol. 2019 Jan 18.

Big data in IBD: a look into the future.

Pablo Olivera, Silvio Danese, Nicolas Jay, Gioacchino Natoli, Laurent Peyrin-Biroulet.

Big data methodologies, made possible with the increasing generation and availability of digital data and enhanced analytical capabilities, have produced new insights to improve outcomes in many disciplines. Application of big data in the health-care sector is in its early stages, although the potential for leveraging underutilized data to gain a better understanding of disease and improve quality of care is enormous. Owing to the intrinsic characteristics of inflammatory bowel disease (IBD) and the management dilemmas that it imposes, the implementation of big data research strategies not only can complement current research efforts but also could represent the only way to disentangle the complexity of the disease. In this Review, we explore important potential applications of big data in IBD research, including predictive models of disease course and response to therapy, characterization of disease heterogeneity, drug safety and development, precision medicine and cost-effectiveness of care. We also discuss the strengths and limitations of potential data sources that big data analytics could draw from in the field of IBD, including electronic health records, clinical trial data, e-health applications and genomic, transcriptomic, proteomic, metabolomic and microbiomic data.

DOI: https://doi.org/10.1038/s41575-019-0102-5