bims-prodis 2019-02-24 papers

bims-prodis

Biomed News

on Proteomics in disease

Issue of 2019–02–24
thirty papers selected by
Nancy Gough, Bioserendipity

The Case for Proteomics and Phospho-Proteomics in Personalized Cancer Medicine.
Quantitative label-free mass spectrometry using contralateral and adjacent breast tissues reveal differentially expressed proteins and their predicted impacts on pathways and cellular functions in breast cancer.
Translating transcription: proteomics in chronic rhinosinusitis with nasal polyps reveals significant discordance with messenger RNA expression.
Quantitative proteomic characterization of lung tissue in idiopathic pulmonary fibrosis.
Two subgroups in systemic lupus erythematosus with features of antiphospholipid or Sjögren's syndrome differ in molecular signatures and treatment perspectives.
Proteomics characterisation of central nervous system metastasis biomarkers in triple negative breast cancer.
Proteomic analysis of synovial fluid: current and potential uses to improve clinical outcomes.
A comparative protein analysis of lung cancer, along with three controls using a multidimensional proteomic approach.
[Biomarkers screening for viral myocarditis through proteomics analysis of plasma exosomes].
Application of protein chip combined with SELDI-TOF-MS detection to investigate serum protein expression in patients with silicosis fibrosis.
Identification of CCDC180 and LRRC4 as Potential Immunohistochemical Markers for Liposarcoma Based on Proteomic Analysis Using Formalin-Fixed, Paraffin-Embedded Tissue.
Protein signatures linking history of miscarriages and metabolic syndrome: a proteomic study among North Indian women.
ENA-78 Is a Novel Predictor of Wound Healing in Patients with Diabetic Foot Ulcers.
Potential biomarkers for antidiastole of tuberculous and malignant pleural effusion by proteome analysis.
A plasma protein classifier for predicting amyloid burden for preclinical Alzheimer's disease.
SELDI-TOF MS Analysis of Hepatocellular Carcinoma in an Australian Cohort.
Application of Proteomics to Inflammatory Bowel Disease Research: Current Status and Future Perspectives.
Significance of the Differential Peptidome in Multidrug-Resistant Tuberculosis.
Saliva molecular inflammatory profiling in female migraine patients responsive to adjunctive cervical non-invasive vagus nerve stimulation: the MOXY Study.
Urinary proteome signature of Renal Cysts and Diabetes syndrome in children.
High-Throughput Profiling of Circulating Antibody Signatures for Stroke Diagnosis Using Small Volumes of Whole Blood.
BAP1 haploinsufficiency predicts a distinct immunogenic class of malignant peritoneal mesothelioma.
Comparison of protein expression between formalin-fixed core-cut biopsies and surgical excision specimens using a novel multiplex approach.
Development of a multiplexed assay for the detection of Leishmania donovani/Leishmania infantum protein biomarkers in the urine of patients with visceral leishmaniasis.
Systems proteogenomics for precision oncology.
Metabolic, anti-apoptotic and immune evasion strategies of primary human myeloma cells indicate adaptations to hypoxia.
Are there any theranostic biomarkers in small cell lung carcinoma?
Variation of Fetuin-A in maternal and fetal serum during human parturition.
Phosphoproteomic Analysis of Signaling Pathways in Lymphomas.
A case of spheroid-type localized lactoferrin amyloidosis in the bronchus.

Proteomics Clin Appl. 2019 Feb 20. e1800113

The Case for Proteomics and Phospho-Proteomics in Personalized Cancer Medicine.

Sophia Doll, Florian Gnad, Matthias Mann.

The concept of personalized medicine has predominantly been pursued through genomic and transcriptomic technologies, leading to the identification of multiple mutations in a large variety of cancers. However, it has proven challenging to distinguish driver and passenger mutations and to deal with tumor heterogeneity and resistant clonal populations. More generally, these heterogeneous mutation patterns do not in themselves predict the tumor phenotype. Analysis of the expressed proteins in a tumor and their modification states reveals if and how these mutations are translated to the functional level. It is already known that proteomic changes including posttranslational modifications are crucial drivers of oncogenesis, but proteomics technology has only recently become comparable in depth and accuracy to RNAseq. These advances also allow the rapid and highly sensitive analysis of formalin-fixed and paraffin-embedded biobank tissues, on both the proteome and phosphoproteome levels. In this perspective, we highlight pioneering mass spectrometry-based proteomic studies that pave the way towards clinical implementation. We argue that proteomics and phosphoproteomics could provide the missing link to make omics analysis actionable in the clinic. This article is protected by copyright. All rights reserved.

DOI: https://doi.org/10.1002/prca.201800113
J Proteomics. 2019 Feb 14. pii: S1874-3919(19)30050-8. [Epub ahead of print]

Quantitative label-free mass spectrometry using contralateral and adjacent breast tissues reveal differentially expressed proteins and their predicted impacts on pathways and cellular functions in breast cancer.

Talita Helen Bombardelli Gomig, Iglenir João Cavalli, Ricardo Lehtonen Rodrigues de Souza, Evelyn Vieira, Aline Castro Rodrigues Lucena, Michel Batista, Kelly Cavalcanti Machado, Fabricio Klerynton Marchini, Fabio Albuquerque Marchi, Rubens Silveira Lima, Cícero de Andrade Urban, Luciane Regina Cavalli, Enilze Maria de Souza Fonseca Ribeiro.

  Proteins play an essential role in the biological processes associated with cancer. Their altered expression levels can deregulate critical cellular pathways and interactive networks. In this study, the mass spectrometry-based label-free quantification followed by functional annotation was performed to investigate the most significant deregulated proteins among tissues of primary breast tumor (PT) and axillary metastatic lymph node (LN) and corresponding non-tumor tissues contralateral (NCT) and adjacent (ANT) from patients diagnosed with invasive ductal carcinoma. A total of 462 proteins was observed as differentially expressed (DEPs) among the groups analyzed. A high level of similarity was observed in the proteome profile of both non-tumor breast tissues and DEPs (n = 12) were mainly predicted in the RNA metabolism. The DEPs among the malignant and non-tumor breast tissues [n = 396 (PTxNCT) and n = 410 (LNxNCT)] were related to pathways of the LXR/RXR, NO, eNOS, eIF2 and sirtuins, tumor-related functions, fatty acid metabolism and oxidative stress. Remarkable similarity was observed between both malignant tissues, which the DEPs were related to metastatic capabilities. Altogether, our findings revealed differential proteomic profiles that affected cancer associated and interconnected signaling processes. Validation studies are recommended to demonstrate the potential of individual proteins and/or pathways as biological markers in breast cancer. SIGNIFICANCE: The proteomic analysis of this study revealed high similarity in the proteomic profile of the contralateral and adjacent non-tumor breast tissues. Significant differences were identified among the proteome of the malignant and non-tumor tissue groups of the same patients, providing relevant insights into the hallmarks, signaling pathways, biological functions, and interactive protein networks that act during tumorigenesis and breast cancer progression. These proteins are suggested as targets of relevant interest to be explored as potential biological markers related to tumor development and metastatic progression in the breast cancer disease.

Keywords:  Bioinformatics analysis; Breast cancer; Contralateral breast tissue; Label-free mass spectrometry; Proteomics

DOI:  https://doi.org/10.1016/j.jprot.2019.02.007
Int Forum Allergy Rhinol. 2019 Feb 18.

Translating transcription: proteomics in chronic rhinosinusitis with nasal polyps reveals significant discordance with messenger RNA expression.

Alan D Workman, Angela L Nocera, Sarina K Mueller, Hasan H Otu, Towia A Libermann, Benjamin S Bleier.

   BACKGROUND: Much of the literature examining chronic rhinosinusitis with nasal polyps (CRSwNP) immunopathology has been predicated on messenger RNA (mRNA) analysis with the assumption that transcriptional changes would reflect end-effector protein expression. The purpose of this study was to test this hypothesis using matched transcriptomic and proteomic data sets.
METHODS: Matched tissue proteomic and transcriptomic arrays were quantified in CRSwNP polyp tissue and control inferior turbinate tissue (n = 10/group). Mucus samples were additionally collected in 6 subjects from each group. Proteins were grouped into functional categories by bioinformatics and differential expression analyses. Log-log regression and Pearson correlations were performed to determine the level of agreement between data sets.
RESULTS: Of the 1310 proteins examined, 393 were significantly differentially expressed in CRSwNP. On regression analysis, differences in protein expression were poorly predicted by differences in mRNA expression (R2 = 0.020, p < 0.05). Several genes canonically thought to be overexpressed in CRSwNP, including IL-5, IL-13, TSLP, CCL13, and CCL26, showed substantial increases in mRNA transcription, but had minimally or unchanged protein expression. Others, including IgE, periostin, CCL18, and CST1/2, were increased at both the transcriptomic and proteomic levels. Among differentially regulated proteins, tissue and mucus protein levels showed weak correlation (r = 0.26, p < 0.0001).
CONCLUSION: Proteomic analysis in CRSwNP has revealed novel disease-associated proteins and pathways, yet correlates poorly with transcriptomic data. The increasing availability of proteomic arrays opens the door to new potential explanatory mechanisms in CRSwNP and suggests that mRNA based studies should be validated with protein analysis.

Keywords:  biomarker; chronic rhinosinusitis; chronic rhinosinusitis with nasal polyps; eosinophilic rhinitis; nasal polyposis; proteomics; transcriptomics

DOI:  https://doi.org/10.1002/alr.22315
Clin Proteomics. 2019 ;16 6

Quantitative proteomic characterization of lung tissue in idiopathic pulmonary fibrosis.

Yaqiong Tian, Hui Li, Yujuan Gao, Chuanmei Liu, Ting Qiu, Hongyan Wu, Mengshu Cao, Yingwei Zhang, Hui Ding, Jingyu Chen, Hourong Cai.

   Background: Idiopathic pulmonary fibrosis (IPF) is a progressive, eventually fatal disease. IPF is characterized by excessive accumulation of the extracellular matrix (ECM) in the alveolar parenchyma and progressive lung scarring. The pathogenesis of IPF and whether the ECM involved in the process remain unknown.
Methods: To identify potential treatment target and ECM associated proteins that may be involved in the development of IPF, we employed isobaric tag for relative and absolute quantitation (iTRAQ) combined liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach to examine protein expression in lung tissues from IPF patients.
Results: A total of 662 proteins with altered expression (455 upregulated proteins and 207 downregulated proteins) were identified in lung tissue of IPF patients compared with control. KEGG pathway enrichment analysis showed that the altered proteins in lung tissue mainly belonged to the PI3K-Akt signaling, focal adhesion, ECM-receptor interaction, and carbon metabolism pathways. According to the bioinformatic definition of the matrisome, 229 matrisome proteins were identified in lung tissue. These proteins comprised the ECM of lung, of which 104 were core matrisome proteins, and 125 were matrisome-associated proteins. Of the 229 ECM quantified proteins, 56 significantly differentially expressed proteins (19 upregulated proteins and 37 downregulated proteins) were detected in IPF lung tissue samples. In addition to proteins with well-known functions such as COL1A1, SCGB1A1, TAGLN, PSEN2, TSPAN1, CTSB, AGR2, CSPG2, and SERPINB3, we identified several novel ECM proteins with unknown function deposited in IPF lung tissue including LGALS7, ASPN, HSP90AA1 and HSP90AB1. Some of these differentially expressed proteins were further verified using Western blot analysis and immunohistochemical staining.
Conclusions: This study provides a list of proteomes that were detected in IPF lung tissue by iTRAQ technology combined with LC-MS/MS. The findings of this study will contribute better understanding to the pathogenesis of IPF and facilitate the development of therapeutic targets.

Keywords:  Extracellular matrix; Idiopathic pulmonary fibrosis; Isobaric tag for relative and absolute quantitation (iTRAQ); Proteomic

DOI:  https://doi.org/10.1186/s12014-019-9226-4
Arthritis Res Ther. 2019 Feb 18. 21(1): 62

Two subgroups in systemic lupus erythematosus with features of antiphospholipid or Sjögren's syndrome differ in molecular signatures and treatment perspectives.

Helena Idborg, Arash Zandian, Ann-Sofi Sandberg, Bo Nilsson, Kerstin Elvin, Lennart Truedsson, Azita Sohrabian, Johan Rönnelid, John Mo, Giorgia Grosso, Marika Kvarnström, Iva Gunnarsson, Janne Lehtiö, Peter Nilsson, Elisabet Svenungsson, Per-Johan Jakobsson.

   BACKGROUND: Previous studies and own clinical observations of patients with systemic lupus erythematosus (SLE) suggest that SLE harbors distinct immunophenotypes. This heterogeneity might result in differences in response to treatment in different subgroups and obstruct clinical trials. Our aim was to understand how SLE subgroups may differ regarding underlying pathophysiology and characteristic biomarkers.
METHODS: In a cross-sectional study, including 378 well-characterized SLE patients and 316 individually matched population controls, we defined subgroups based on the patients' autoantibody profile at inclusion. We selected a core of an antiphospholipid syndrome-like SLE (aPL+ group; positive in the lupus anticoagulant (LA) test and negative for all three of SSA (Ro52 and Ro60) and SSB antibodies) and a Sjögren's syndrome-like SLE (SSA/SSB+ group; positive for all three of SSA (Ro52 and Ro60) and SSB antibodies but negative in the LA test). We applied affinity-based proteomics, targeting 281 proteins, together with well-established clinical biomarkers and complementary immunoassays to explore the difference between the two predefined SLE subgroups.
RESULTS: The aPL+ group comprised 66 and the SSA/SSB+ group 63 patients. The protein with the highest prediction power (receiver operating characteristic (ROC) area under the curve = 0.89) for separating the aPL+ and SSA/SSB+ SLE subgroups was integrin beta-1 (ITGB1), with higher levels present in the SSA/SSB+ subgroup. Proteins with the lowest p values comparing the two SLE subgroups were ITGB1, SLC13A3, and CERS5. These three proteins, rheumatoid factor, and immunoglobulin G (IgG) were all increased in the SSA/SSB+ subgroup. This subgroup was also characterized by a possible activation of the interferon system as measured by high KRT7, TYK2, and ETV7 in plasma. In the aPL+ subgroup, complement activation was more pronounced together with several biomarkers associated with systemic inflammation (fibrinogen, α-1 antitrypsin, neutrophils, and triglycerides).
CONCLUSIONS: Our observations indicate underlying pathogenic differences between the SSA/SSB+ and the aPL+ SLE subgroups, suggesting that the SSA/SSB+ subgroup may benefit from IFN-blocking therapies while the aPL+ subgroup is more likely to have an effect from drugs targeting the complement system. Stratifying SLE patients based on an autoantibody profile could be a way forward to understand underlying pathophysiology and to improve selection of patients for clinical trials of targeted treatments.

Keywords:  Affinity-based proteomics; Antiphospholipid syndrome; Personalized medicine; Sjögren’s syndrome; Subgroups; Systemic lupus erythematosus

DOI:  https://doi.org/10.1186/s13075-019-1836-8
Ecancermedicalscience. 2019 ;13 891

Proteomics characterisation of central nervous system metastasis biomarkers in triple negative breast cancer.

Katerin Rojas L, Lucía Trilla-Fuertes, Angelo Gámez-Pozo, Cristina Chiva, Juan Sepúlveda, Luis Manso, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Rocío López-Vacas, María Ferrer-Gómez, César Mendiola, Enrique Espinosa, Eduard Sabidó, Eva Ciruelos, Juan Ángel Fresno Vara.

   Background: Breast cancer (BC) is the most frequent tumour in women. Triple negative tumours (TNBC)-which are associated with minor survival rates-lack markers predictive of response to anticancer drugs. Triple negative tumours frequently metastasise to the central nervous system (CNS).
Objective: The main objective of this study was to study differences in tumour protein expression between patients with CNS metastases and those without this kind of spread, and propose new biomarkers.
Methods: A retrospective study was performed. Targeted proteomics and statistical analyses were used to identify possible biomarkers.
Results: Proteins were quantified by a targeted proteomics approach and protein expression data were successfully obtained from 51 triple negative formalin-fixed paraffin-embedded samples. ISG15, THBS1 and AP1M1 were identified as possible biomarkers related with CNS metastasis development.
Conclusions: Three possible biomarkers associated with CNS metastases in TNBC tumours were identified: ISG15, THBS1 and AP1M1. They may become markers predicting the appearance of CNS infiltration in triple negative BC.

Keywords:  biomarkers; breast cancer; central nervous system metastases; personalised medicine; proteomics; triple negative

DOI:  https://doi.org/10.3332/ecancer.2019.891
Expert Rev Proteomics. 2019 Feb 22. 1-16

Proteomic analysis of synovial fluid: current and potential uses to improve clinical outcomes.

Mandy Jayne Peffers, Aibek Smagul, James Ross Anderson.

   INTRODUCTION: Synovial fluid (SF) is in close proximity to tissues which are primarily altered during articular disease and has significant potential to better understand the underlying disease pathogeneses of articular pathologies and biomarker discovery. Although development of mass spectrometry-based methods has allowed faster and higher sensitivity techniques, interrogation of the SF proteome has been hindered by its large protein concentration dynamic range, impeding quantification of lower abundant proteins. Areas covered: Recent advances have developed methodologies to reduce the large protein concentration dynamic range of SF and subsequently allow deeper exploration of the SF proteome. This review concentrates on methods to overcome biofluid complexity, mass spectrometry proteomics methodologies, extracellular vesicles proteomics and the application of advances within the field in clinical disease, including osteoarthritis, rheumatoid arthritis, spondyloarthritis and juvenile arthritis. A narrative review was conducted with articles searched using PubMed, 1991-2018. Expert opinion: The SF proteomics field faces various challenges, including the requirement for rigorous and standardised methods of sample collection/storage, the sensitivity and specificity of proteomic assays, techniques to combat the large protein concentration dynamic range and comprehensive data analysis to reduce falsely identified markers. Additionally, there are challenges in developing multi 'omic' integration techniques, with computational integration enhancing analysis.

Keywords:  mass spectrometry; proteomics; synovial fluid

DOI:  https://doi.org/10.1080/14789450.2019.1578214
Exp Biol Med (Maywood). 2019 Jan;244(1): 36-41

A comparative protein analysis of lung cancer, along with three controls using a multidimensional proteomic approach.

Mahwish Saleem, Syed K Raza, Syed G Musharraf.

   IMPACT STATEMENT: A multistep proteomics fractionation strategy was developed and validated for the discovery of proteomic biomarkers which could be used as potential diagnostic biomarkers for monitoring the progression of disease in smokers and COPD patients towards lung cancer.

Keywords:  Lung cancer; MALDI-TOF mass spectrometry; two-dimensional gel electrophoresis

DOI:  https://doi.org/10.1177/1535370219826525
Zhonghua Yi Xue Za Zhi. 2019 Jan 29. 99(5): 343-348

[Biomarkers screening for viral myocarditis through proteomics analysis of plasma exosomes].

Z L Zhao, S Du, S X Shen, P Luo, S K Ding, G G Wang, L X Wang.

  Objective: To compare and analyze the differentially expressed plasma exosomic proteome between healthy control group (Control group) and viral myocarditis group (VMC group) to search for biomarkers that maybe used for early diagnosis of VMC. Methods: Fifty plasma samples of Control group and VMC group were collected respectively from Henan Provincial People's Hospital (from January 2016 to December 2017), and then 5 samples (1 ml) of each group were selected randomly, after exosomes extraction with ultra-centrifugation, difference gel electrophoresis (DIGE) was used to isolate the total proteins, and then the protein spots with more than 2-fold changes between VMC and Control group were picked up after the software analysis, afterward, the varied proteins were identified by MALDI-TOF/TOF mass spectrometry. Finally, the specifically related protein was selected to be verified by ELISA with the plasma exosomic samples of Control (n=40) and VMC (n=40). Results: A total of 10 varied protein spots were found including 8 up-regulated proteins and 2 down-regulated proteins between VMC and Control group. After MS analysis, the up-regulated proteins in VMC group contained KRT2, KRT5, KRT9, KRT77, KRT78, AZGP1, HP and RBP4, whereas the down-regulated ones were CD5L and C1QB. RBP4 was selected to validate by ELISA analysis, and the corresponding results showed that RBP4 was increased specifically in plasma exosomes of VMC group (P<0.05) after comparing with Control group, which was consistent with DIGE. Conclusion: Ten proteins related to VMC are detected in total, and RBP4 might serve as a potential specific biomarker for early screening and diagnosis of VMC.

Keywords:  Biological markers; Exosome; Plasma; Proteomics; Viral myocarditis

DOI:  https://doi.org/10.3760/cma.j.issn.0376-2491.2019.05.005
Exp Ther Med. 2019 Mar;17(3): 2172-2184

Application of protein chip combined with SELDI-TOF-MS detection to investigate serum protein expression in patients with silicosis fibrosis.

Guitao Liu, Junfeng Yu, Cuidong Li, Xiaoyun Zhou, Liping Nie, Yanhua Wei, Wenyu Wang, Ying Zhang, Nuziguli Nusilaiti, Ping Hua, Xiaohua Wang, Wenlong Wei, Xinyan Li.

  The present study aimed to observe the identification of biomarkers of silicosis based on the differentially expressed serum proteins between normal healthy individuals and patients with silicosis fibrosis. A total number of 20 patients with clinically diagnosed silicosis were screened, which were designated as the foundation treatment group. In addition, 20 age-matched healthy patients attending a check-up at the physical examination department were selected. Serum samples were obtained and a combined protein chip with surface-enhanced laser desorption ionization flight mass spectrometry was applied to perform serum analysis. Data preprocessing, screening differences in peak, hierarchical cluster analysis, Principal Component Analysis, construction of a decision tree model, and prediction based on the differences between peaks corresponding to proteins were performed to analyze the data. The results revealed differences in the proteins in serum between the normal group and the group prior to foundation treatment prediction. The corresponding names of the protein peak, predicted protein, and gene name were as follows: M1948_00, complement c3 frag, C3; M2017_02, amyloid-βa4 protein, APP; and M2879_56, hepcidin, HAMP. Differentially expressed serum proteins in the normal group and the basis treatment group were predicted, including M2017_02, amyloid-βa4 protein, APP; M2879_56, hepcidin, HAMP; and M3224_97, fibrinogen-α chain frags, FGA. The differentially expressed serum proteins in the group prior to basis treatment and the group following basis treatment were predicted, including M2001_69, amyloid-βa4 protein, APP; M2017_02, amyloid-βa4 protein, APP, M4144_81, plasma protease c1 inhibitor frag, and SERPING1. In conclusion, there were differences in the proteins in serum between the patients with silicosis fibrosis and healthy individuals.

Keywords:  different protein in serum; silicosis fibrosis; surface-enhanced laser desorption ionization flight mass spectrometry

DOI:  https://doi.org/10.3892/etm.2019.7166
Am J Pathol. 2019 Feb 18. pii: S0002-9440(18)30625-4. [Epub ahead of print]

Identification of CCDC180 and LRRC4 as Potential Immunohistochemical Markers for Liposarcoma Based on Proteomic Analysis Using Formalin-Fixed, Paraffin-Embedded Tissue.

Tomoyuki Aoyama, Akira Takasawa, Kumi Takasawa, Yusuke Ono, Makoto Emori, Masaki Murata, Takahiro Hayasaka, Naoki Fujitani, Makoto Osanai, Toshihiko Yamashita, Tadashi Hasegawa, Norimasa Sawada.

Recent technical improvements in both mass spectrometry and protein extraction have made it possible to use formalin-fixed, paraffin-embedded (FFPE) tissues for proteome analysis. In this study, comparable proteome analysis of FFPE tissues revealed multiple candidate marker molecules for differentiating atypical lipomatous tumor/well-differentiated liposarcoma (ALT/WDL) from lipoma. One-hundred and eighty-one unique proteins were identified for ALT/WDL. Of the identified proteins, coiled-coil domain-containing protein 180 (CCDC180) and leucine-rich repeat-containing protein 4 (LRRC4) were studied as candidate markers of ALT/WDL. CCDC180 and LRRC4 immunohistochemistry clearly stained tumor cells of ALT/WDL and dedifferentiated liposarcoma and could differentiate them from lipoma with high accuracy. Cell biological methods were used to further examine the expression of the candidate marker molecules in liposarcoma cells. In liposarcoma cells, knockdown of CCDC180 and LRRC4 inhibited cell proliferation. CCDC180 inhibited cell migration, invasion, and apoptosis resistance in WDL cells. Adipogenic differentiation suppressed the expression of CCDC180 and LRRC4 in WDL cells. These results indicated that LRRC4 and CCDC180 are novel immunohistochemical markers for differentiating ALT/WDLS. Their expression was associated with adipocyte differentiation and contributed to malignant potentials of WDL cells. Proteome analysis using a standard stock of FFPE tissues can reveal novel biomarkers for various diseases, which contributes to the progress of molecular pathology.

DOI: https://doi.org/10.1016/j.ajpath.2019.01.013
PeerJ. 2019 ;7 e6321

Protein signatures linking history of miscarriages and metabolic syndrome: a proteomic study among North Indian women.

Saurabh Sharma, Suniti Yadav, Ketaki Chandiok, Radhey Shyam Sharma, Vandana Mishra, Kallur Nava Saraswathy.

   Background: Metabolic syndrome (MeS), a constellation of metabolic adversities, and history of miscarriage make women at a higher risk for cardiovascular diseases (CVDs). However, molecular evidence indicating a link between the two phenotypes (history of miscarriage and MeS) among women would offer an opportunity to predict the risk factor for CVDs at an early stage. Thus, the present retrospective study attempts to identify the proteins signatures (if any) to understand the connection between the history of miscarriage and MeS.
Methods: Age-matched 80 pre-menopausal women who were not on any medical intervention or drugs were recruited from a Mendelian population of the same gene pool. Recruited women were classified into four groups-(a) Group A-absolute cases with history of miscarriage and MeS, (b) Group B-absolute controls without any history of miscarriage and MeS, (c) Group C-cases with MeS but lack any history of miscarriage, (d) Group D-cases with history of miscarriage but lack MeS. Differentially expressed proteins in plasma samples of women from four groups were identified using 2-D gel electrophoresis and mass spectrometry.
Results: Three case groups (A, C, and D) showed 18 differentially expressed proteins. Nearly 60% of proteins (11/18) were commonly dysregulated in Group C (only with MeS) and Group D (only with miscarriage history). Nearly 40% of proteins (7/18) were commonly dysregulated in the three case groups (Groups A, C, and D), indicating a shared pathophysiology. Four proteins were exclusive but shared by case groups C and D indicating the independent routes for CVDs through MeS or miscarriages. In absolute cases, transthyretin (TTR) showed exclusive upregulation, which was further validated by Western blotting and ELISA. Networking analyses showed the strong association of TTR with haptoglobin, transferrin and ApoA1 hinting toward a cross-talk among these proteins which could be a cause or an effect of TTR upregulation.
Conclusion: The study provides evidence for molecular link between the history of miscarriage and MeS through a putative role of TTR. However, longitudinal follow-up studies with larger sample size would further help to demonstrate the significance of TTR and other targeted proteins in risk stratification and the onset of CVDs.

Keywords:  Adverse pregnancy outcome; Cardiovascular disease; History of miscarriage; Metabolic syndrome; Proteomics

DOI:  https://doi.org/10.7717/peerj.6321
J Diabetes Res. 2019 ;2019 2695436

ENA-78 Is a Novel Predictor of Wound Healing in Patients with Diabetic Foot Ulcers.

Ju-Yi Li, Zhong-Jing Wang, Ai-Ping Deng, Yu-Ming Li.

Objectives: Chronic foot ulceration is a severe complication of diabetes, driving morbidity and mortality. The aim of our study was to identify novel biomarkers of impaired wound healing in diabetic foot ulcers.
Methods: 109 patients with neuropathic diabetic foot ulcers and 30 burn victims otherwise healthy participated. Antibody-coated glass slide arrays were used to determine the levels of 80 human cytokines in pooled plasma or pooled wound exudate of diabetic foot ulcers with rapidly healing (RH, n = 12) and matched nonhealing (NH, n = 12) patients. Potential biomarkers were confirmed in an independent cohort by enzyme-linked immunosorbent assay (ELISA).
Results: Protein array profiling identified 27 proteins or 15 proteins significantly altered in protein profiling of pooled plasma or pooled wound exudate of 12 RH patients compared with 12 matched NH patients, respectively. In an independent cohort, quantitative ELISA validation confirmed a decrease in MCP-2 and ENA-78 levels in NH patients versus RH patients or burn victims. After adjusting for the traditional risk factors (sex, age, body mass index, fasting plasma glucose, ulcer area, HbA1C, diabetes duration, hyperlipidemia, and antibiotic therapy), only wound exudate level of ENA-78 remained having a significant association with an increased odds ratio (OR) for wound healing by binary logistic regression analysis (P < 0.05).
Conclusion: Decreased wound exudate ENA-78 was independently associated with wound healing of patients with diabetic foot. Exudate ENA-78 level is implicated as a novel predictor of wound healing in patients with diabetic foot ulcers.

DOI: https://doi.org/10.1155/2019/2695436
Biomark Med. 2019 Feb 22.

Potential biomarkers for antidiastole of tuberculous and malignant pleural effusion by proteome analysis.

Jing Shi, Pu Li, Lijin Zhou, Suwen Qi, Bo Wang, Dandan Li, Liang Duan, Wei Xian Chen, Jirong Xia, Lin Zou, Shuangshuang Yang.

   AIM: To investigate novel potential biomarkers for antidiastole of tuberculous pleural effusion (TPE) from malignant pleural effusion (MPE).
MATERIALS & METHODS: iTRAQTM-coupled LC-MS/MS were applied to analyze the proteome of TPE and MPE samples. The candidate proteins were verified by enzyme-linked immunosorbent assay.
RESULTS: A total of 432 differential proteins were identified. Enzyme-linked immunosorbent assay revealed significantly higher levels of fibronectin (FN) and cathepsin G (CTSG) in MPE than in TPE, but lower levels of leukotriene-A4 hydrolase (LTA4H). The receiver operator characteristic values were 0.285 for FN, 0.64 for LTA4H, 0.337 for CTSG and 0.793 for a combination of these candidate markers.
CONCLUSION: FN, LTA4H and CTSG were identified as potential biomarkers to differentiate TPE from MPE and their combination exhibited higher diagnostic capacity.

Keywords:  cathepsin G; fibronectin; iTRAQTM; leukotriene-A4 hydrolase; lung cancer; malignant pleural effusion; potential biomarkers; quantitative proteomic analyze; tuberculosis; tuberculous pleural effusion

DOI:  https://doi.org/10.2217/bmm-2018-0200
Sci Adv. 2019 Feb;5(2): eaau7220

A plasma protein classifier for predicting amyloid burden for preclinical Alzheimer's disease.

Nicholas J Ashton, Alejo J Nevado-Holgado, Imelda S Barber, Steven Lynham, Veer Gupta, Pratishtha Chatterjee, Kathryn Goozee, Eugene Hone, Steve Pedrini, Kaj Blennow, Michael Schöll, Henrik Zetterberg, Kathryn A Ellis, Ashley I Bush, Christopher C Rowe, Victor L Villemagne, David Ames, Colin L Masters, Dag Aarsland, John Powell, Simon Lovestone, Ralph Martins, Abdul Hye.

A blood-based assessment of preclinical disease would have huge potential in the enrichment of participants for Alzheimer's disease (AD) therapeutic trials. In this study, cognitively unimpaired individuals from the AIBL and KARVIAH cohorts were defined as Aβ negative or Aβ positive by positron emission tomography. Nontargeted proteomic analysis that incorporated peptide fractionation and high-resolution mass spectrometry quantified relative protein abundances in plasma samples from all participants. A protein classifier model was trained to predict Aβ-positive participants using feature selection and machine learning in AIBL and independently assessed in KARVIAH. A 12-feature model for predicting Aβ-positive participants was established and demonstrated high accuracy (testing area under the receiver operator characteristic curve = 0.891, sensitivity = 0.78, and specificity = 0.77). This extensive plasma proteomic study has unbiasedly highlighted putative and novel candidates for AD pathology that should be further validated with automated methodologies.

DOI: https://doi.org/10.1126/sciadv.aau7220
J Surg Res. 2019 Feb 13. pii: S0022-4804(19)30007-1. [Epub ahead of print]238 127-136

SELDI-TOF MS Analysis of Hepatocellular Carcinoma in an Australian Cohort.

Steven M Schlichtemeier, Christopher B Nahm, Aiqun Xue, Anthony J Gill, Ross C Smith, Thomas J Hugh.

   BACKGROUND: Hepatocellular carcinoma (HCC) is a common cause of cancer death worldwide. Resection offers the best chance of long-term survival, but a consistent adverse prognostic factor is the presence of microvascular invasion (MVI). In this study, surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS), a high throughput method of analyzing complex samples, was used to explore differentially expressed proteins between HCC and adjacent nontumour liver tissue (ANLT). These findings were correlated with clinical outcomes.
MATERIALS AND METHODS: From 2002 to 2011, tumor and ANLT were collected from patients who underwent liver resection and these samples were later prepared for SELDI-TOF MS. Output data were then used to identify proteins capable of discriminating HCC from ANLT. Proteins from the multivariate analysis were then analyzed to determine prognostic factors and the m/z ratios of these proteins were entered into the ExPASy database to infer potential candidates.
RESULTS: During the study period, 30 patients had SELDI-TOF MS performed on their HCC and ANLT samples. On multivariate analysis, a panel of four proteins-m/z 5840, m/z 8921, m/z 9961, and m/z 25,872-discriminated HCC from ANLT with an area under the ROC curve of 0.954 (P < 0.001). On prognostic factor assessment, decreased m/z 9961 was significantly associated with the presence of MVI (P = 0.025) and shorter disease-free survival (P = 0.045) in our patients. A potential candidate for this protein was coxsackievirus and adenovirus receptor, isoform 3 (CAR 3/7), which helps maintain tight junction integrity.
CONCLUSIONS: Using SELDI TOF-MS, we identified a panel of four proteins with excellent discriminative capacity between HCC and ANLT. Of these, m/z 9961 was the only protein significantly associated with a known poor prognostic factor (presence of MVI) and survival (shorter disease-free survival). While loss of CAR 3/7 could lead to MVI, further research is warranted to validate the identity of protein m/z 9961.

Keywords:  HCC; Hepatocellular carcinoma; Microvascular invasion; Proteomics; SELDI-TOF MS; m/z 9961

DOI:  https://doi.org/10.1016/j.jss.2019.01.008
Gastroenterol Res Pract. 2019 ;2019 1426954

Application of Proteomics to Inflammatory Bowel Disease Research: Current Status and Future Perspectives.

Arash Assadsangabi, Caroline A Evans, Bernard M Corfe, Alan Lobo.

Inflammatory bowel disease (IBD) is a chronic relapsing/remitting inflammatory illness of the gastrointestinal tract of unknown aetiology. Despite recent advances in decoding the pathophysiology of IBD, many questions regarding disease pathogenesis remain. Genome-wide association studies (GWAS) and knockout mouse models have significantly advanced our understanding of genetic susceptibility loci and inflammatory pathways involved in IBD pathogenesis. Despite their important contribution to a better delineation of the disease process in IBD, these genetic findings have had little clinical impact to date. This is because the presence of a given gene mutation does not automatically correspond to changes in its expression or final metabolic or structural effect(s). Furthermore, the existence of these gene susceptibility loci in the normal population suggests other driving prerequisites for the disease manifestation. Proteins can be considered the main functional units as almost all intracellular physiological functions as well as intercellular interactions are dependent on them. Proteomics provides methods for the large-scale study of the proteins encoded by the genome of an organism or a cell, to directly investigate the proteins and pathways involved. Understanding the proteome composition and alterations yields insights into IBD pathogenesis as well as identifying potential biomarkers of disease activity, mucosal healing, and cancer progression. This review describes the state of the art in the field with respect to the study of IBD and the potential for translation from biomarker discovery to clinical application.

DOI: https://doi.org/10.1155/2019/1426954
Biomed Res Int. 2019 ;2019 5653424

Significance of the Differential Peptidome in Multidrug-Resistant Tuberculosis.

Yan Yang, Jianqing Wu.

Most multidrug-resistant tuberculosis (MDR-TB) patients fail to receive a timely diagnosis and treatment. Therefore, we explored the differentially expressed peptides in MDR-TB compared with drug-susceptible tuberculosis (DS-TB) patients using LC-MS/MS and Ingenuity Pathway Analysis (IPA) to analyse the potential significance of these differentially expressed peptides. A total of 301 peptides were differentially expressed between MDR-TB and DS-TB groups. Of these, 24 and 16 peptides exhibited presented high (fold change ≥ 2.0, P < 0.05) and low (fold change ≤ -2.0, P < 0.05) levels in MDR-TB. Significant canonical pathways included the prothrombin activation system, coagulation system, and complement system. In the network of differentially expressed precursor proteins, lipopolysaccharide (LPS) regulates many precursor proteins, including four proteins correlated with organism survival. These four important differentially expressed proteins are prothrombin (F2), complement receptor type 2 (CR2), collagen alpha-2(V) chain (COL5A2), and inter-alpha-trypsin inhibitor heavy chain H4 (ITIH4). After addition of CR2 peptide, IL-6 mRNA expression in THP-1 cells decreased significantly in dose- and time-dependent manners. Cumulatively, our study proposes potential biomarkers for MDR-TB diagnosis and enables a better understanding of the pathogenesis of MDR-TB. The functions of differentially expressed peptides, especially CR2, in MDR-TB require further investigation.

DOI: https://doi.org/10.1155/2019/5653424
J Transl Med. 2019 Feb 22. 17(1): 53

Saliva molecular inflammatory profiling in female migraine patients responsive to adjunctive cervical non-invasive vagus nerve stimulation: the MOXY Study.

Azize Boström, Dirk Scheele, Birgit Stoffel-Wagner, Frigga Hönig, Shafqat R Chaudhry, Sajjad Muhammad, Rene Hurlemann, Joachim K Krauss, Ilana S Lendvai, Krishnan V Chakravarthy, Thomas M Kinfe.

   BACKGROUND: Rising evidence indicate that oxytocin and IL-1β impact trigemino-nociceptive signaling. Current perspectives on migraine physiopathology emphasize a cytokine bias towards a pro-inflammatory status. The anti-nociceptive impact of oxytocin has been reported in preclinical and human trials. Cervical non-invasive vagus nerve stimulation (nVNS) emerges as an add-on treatment for the preventive and abortive use in migraine. Less is known about its potential to modulate saliva inflammatory signaling in migraine patients. The rationale was to perform inter-ictal saliva measures of oxytocin and IL-1ß along with headache assessment in migraine patients with 10 weeks adjunctive nVNS compared to healthy controls.
METHODS: 12 migraineurs and 12 suitably matched healthy control were studied with inter-ictal saliva assay of pro- and anti-neuroinflammatory cytokines using enzyme-linked immuno assay techniques along with assessment of headache severity/frequency and associated functional capacity at baseline and after 10 weeks adjunctive cervical nVNS.
RESULTS: nVNS significantly reduced headache severity (VAS), frequency (headache days and total number of attacks) and significantly improved sleep quality compared to baseline (p < 0.01). Inter-ictal saliva oxytocin and IL-1β were significantly elevated pre- as well as post-nVNS compared to healthy controls (p < 0.01) and similarly showed changes that may reflect the observed clinical effects.
CONCLUSIONS: Our results add to accumulating evidence for a therapeutic efficacy of adjunct cervical non-invasive vagus nerve stimulation in migraine patients. This study failed to provide an evidence-derived conclusion addressed to the predictive value and usefulness of saliva assays due to its uncontrolled study design. However, saliva screening of mediators associated with trigemino-nociceptive traffic represents a novel approach, thus deserve future targeted headache research. Trial registration This study was indexed at the German Register for Clinical Trials (DRKS No. 00011089) registered on 21.09.2016.

Keywords:  Cervical non-invasive vagus nerve stimulation; MOXY pilot study; Migraine; Saliva oxytocin/IL-1β; Trigemino-nociceptive signaling

DOI:  https://doi.org/10.1186/s12967-019-1801-y
Sci Rep. 2019 Feb 18. 9(1): 2225

Urinary proteome signature of Renal Cysts and Diabetes syndrome in children.

Pierbruno Ricci, Pedro Magalhães, Magdalena Krochmal, Martin Pejchinovski, Erica Daina, Maria Rosa Caruso, Laura Goea, Iwona Belczacka, Giuseppe Remuzzi, Muriel Umbhauer, Jens Drube, Lars Pape, Harald Mischak, Stéphane Decramer, Franz Schaefer, Joost P Schanstra, Silvia Cereghini, Petra Zürbig.

Renal Cysts and Diabetes Syndrome (RCAD) is an autosomal dominant disorder caused by mutations in the HNF1B gene encoding for the transcriptional factor hepatocyte nuclear factor-1B. RCAD is characterized as a multi-organ disease, with a broad spectrum of symptoms including kidney abnormalities (renal cysts, renal hypodysplasia, single kidney, horseshoe kidneys, hydronephrosis), early-onset diabetes mellitus, abnormal liver function, pancreatic hypoplasia and genital tract malformations. In the present study, using capillary electrophoresis coupled to mass spectrometry (CE-MS), we investigated the urinary proteome of a pediatric cohort of RCAD patients and different controls to identify peptide biomarkers and obtain further insights into the pathophysiology of this disorder. As a result, 146 peptides were found to be associated with RCAD in 22 pediatric patients when compared to 22 healthy age-matched controls. A classifier based on these peptides was generated and further tested on an independent cohort, clearly discriminating RCAD patients from different groups of controls. This study demonstrates that the urinary proteome of pediatric RCAD patients differs from autosomal dominant polycystic kidney disease (PKD1, PKD2), congenital nephrotic syndrome (NPHS1, NPHS2, NPHS4, NPHS9) as well as from chronic kidney disease conditions, suggesting differences between the pathophysiology behind these disorders.

DOI: https://doi.org/10.1038/s41598-019-38713-5
Neurotherapeutics. 2019 Feb 19.

High-Throughput Profiling of Circulating Antibody Signatures for Stroke Diagnosis Using Small Volumes of Whole Blood.

Grant C O'Connell, Phillip Stafford, Kyle B Walsh, Opeolu Adeoye, Taura L Barr.

  Accurate stroke recognition during triage can streamline care and afford patients earlier access to life-saving interventions. However, the tools currently available to clinicians for prehospital and early in-hospital identification of stroke are limited. The peripheral immune system is intricately involved in stroke pathology and thus may be targetable for the development of immunodiagnostics. In this preliminary study, we sought to determine whether the circulating antibody pool is altered early in stroke, and whether such alterations could be leveraged for diagnosis. One hundred microliters of peripheral whole blood was sampled from 19 ischemic stroke patients, 17 hemorrhagic stroke patients, and 20 stroke mimics in the acute phase of care. A custom-fabricated high-density peptide array comprising 125,000 unique probes was used to assess the binding characteristics of blood-borne antibodies, and a random forest-based approach was used to select a parsimonious set of probes with an optimal ability to discriminate between groups. The coordinate antibody binding intensities of the top 17 probes identified in our analysis displayed an ability to differentiate the total pool of stroke patients from stroke mimics with 92% sensitivity and 90% specificity, as well as detect hemorrhage with 88% sensitivity and 87% specificity, as determined using a same-set cross-validation. These preliminary findings suggest that stroke-associated alterations in the circulating antibody pool may have clinical utility for diagnosis during triage, and that such a possibility warrants further investigation.

Keywords:  Biomarkers; immunology; machine-learning; molecular diagnostics; proteomics; triage

DOI:  https://doi.org/10.1007/s13311-019-00720-9
Genome Med. 2019 Feb 18. 11(1): 8

BAP1 haploinsufficiency predicts a distinct immunogenic class of malignant peritoneal mesothelioma.

Raunak Shrestha, Noushin Nabavi, Yen-Yi Lin, Fan Mo, Shawn Anderson, Stanislav Volik, Hans H Adomat, Dong Lin, Hui Xue, Xin Dong, Robert Shukin, Robert H Bell, Brian McConeghy, Anne Haegert, Sonal Brahmbhatt, Estelle Li, Htoo Zarni Oo, Antonio Hurtado-Coll, Ladan Fazli, Joshua Zhou, Yarrow McConnell, Andrea McCart, Andrew Lowy, Gregg B Morin, Tianhui Chen, Mads Daugaard, S Cenk Sahinalp, Faraz Hach, Stephane Le Bihan, Martin E Gleave, Yuzhuo Wang, Andrew Churg, Colin C Collins.

   BACKGROUND: Malignant peritoneal mesothelioma (PeM) is a rare and fatal cancer that originates from the peritoneal lining of the abdomen. Standard treatment of PeM is limited to cytoreductive surgery and/or chemotherapy, and no effective targeted therapies for PeM exist. Some immune checkpoint inhibitor studies of mesothelioma have found positivity to be associated with a worse prognosis.
METHODS: To search for novel therapeutic targets for PeM, we performed a comprehensive integrative multi-omics analysis of the genome, transcriptome, and proteome of 19 treatment-naïve PeM, and in particular, we examined BAP1 mutation and copy number status and its relationship to immune checkpoint inhibitor activation.
RESULTS: We found that PeM could be divided into tumors with an inflammatory tumor microenvironment and those without and that this distinction correlated with haploinsufficiency of BAP1. To further investigate the role of BAP1, we used our recently developed cancer driver gene prioritization algorithm, HIT'nDRIVE, and observed that PeM with BAP1 haploinsufficiency form a distinct molecular subtype characterized by distinct gene expression patterns of chromatin remodeling, DNA repair pathways, and immune checkpoint receptor activation. We demonstrate that this subtype is correlated with an inflammatory tumor microenvironment and thus is a candidate for immune checkpoint blockade therapies.
CONCLUSIONS: Our findings reveal BAP1 to be a potential, easily trackable prognostic and predictive biomarker for PeM immunotherapy that refines PeM disease classification. BAP1 stratification may improve drug response rates in ongoing phases I and II clinical trials exploring the use of immune checkpoint blockade therapies in PeM in which BAP1 status is not considered. This integrated molecular characterization provides a comprehensive foundation for improved management of a subset of PeM patients.

Keywords:  BAP1; Genomics; Peritoneal mesothelioma; Precision oncology; Tumor immunosurveillance

DOI:  https://doi.org/10.1186/s13073-019-0620-3
Breast Cancer Res Treat. 2019 Feb 22.

Comparison of protein expression between formalin-fixed core-cut biopsies and surgical excision specimens using a novel multiplex approach.

Mariana Ferreira Leal, Ben P Haynes, Fiona A MacNeill, Andrew Dodson, Mitch Dowsett.

   PURPOSE: We evaluated whether multiplex protein quantification using antibody bar-coding with photocleavable oligonucleotides (NanoString) can be applied to evaluate protein expression in breast cancer FFPE specimens. We also assessed whether diagnostic core-cuts fixed immediately at time of procedures and surgical excision sections from routinely fixed breast cancers are affected by the same fixation related differences noted using immunohistochemistry (IHC).
METHODS: The expression of 26 proteins was analysed using NanoString technology in 16 pairs of FFPE breast cancer core-cuts and surgical excisions. The measurements yielded were compared with those by IHC on Ki67, PgR and HER2 biomarkers and pAKT and pERK1/2 phosphorylated proteins.
RESULTS: When considered irrespective of sample type, expression measured by the two methods was strongly correlated for all markers (p < 0.001; ρ = 0.69-0.88). When core-cuts and excisions were evaluated separately, the correlations between NanoString and IHC were weaker but significant except for pAKT in excisions. Surgical excisions showed lower levels of 8/12 phosphoproteins and higher levels of 4/13 non-phosphorylated proteins in comparison to core-cuts (p < 0.01). Reduced p4EBP1, pAMPKa, pRPS6 and pRAF1 immunogenicity in excisions was correlated with tumour size and mastectomy specimens showed lower p4EBP1 and pRPS6 expression than lumpectomy (p < 0.05).
CONCLUSIONS: Our study supports the validity of the new multiplex approach to protein analysis but indicates that, as with IHC, caution is necessary for the analysis in excisions particularly of phosphoproteins. The specimen type, tumour size and surgery type may lead to biases in the quantitative analysis of many proteins of biologic and clinical interest in excision specimens.

Keywords:  Breast cancer; Immunohistochemistry; Multiplex protein analysis; NanoString technology; Phosphorylation; Tissue fixation

DOI:  https://doi.org/10.1007/s10549-019-05163-6
J Clin Microbiol. 2019 Feb 20. pii: JCM.02076-18. [Epub ahead of print]

Development of a multiplexed assay for the detection of Leishmania donovani/Leishmania infantum protein biomarkers in the urine of patients with visceral leishmaniasis.

Claudia Abeijon, Fabiana Alves, Severine Monnerat, Monique Wasunna, Jane Mbui, Agostinho G Viana, Lilian L Bueno, Williane F Siqueira, Silvio G Carvalho, Neha Agrawal, Ricardo Fujiwara, Shyam Sundar, Antonio Campos-Neto.

Visceral leishmaniasis (VL) is a serious and fatal disease caused by the parasites Leishmania infantum and Leishmania donovani The gold standard diagnostic test for VL is the demonstration of parasites or their DNA from spleen, lymph node or bone marrow aspirates. Serological tests exist but cannot distinguish active VL from either prior exposure to the parasites or subsequent to disease treatment. Using mass spectroscopy, we have previously identified three L. infantum protein biomarkers (Li-isd1, Li-txn1, and Li-ntf2) in urine of VL patients and developed a sensitive and specific urine-based antigen detection assay for diagnosis of VL that occurs in Brazil (where VL is caused by L. infantum). However, unpublished observations from our laboratory showed that these biomarkers were detected in only 55-60% of VL patients from India and Kenya, where the disease is caused by L. donovani Here, we report the discovery and characterization of two new biomarkers of L. donovani (Ld-mao1 and Ld-ppi1) present in the urine of VL patients from these two countries. Capture ELISAs using specific rabbit IgG and chicken IgY were developed and the assays had sensitivities of 44.4% and 28.8% to detect Ld-mao1 and Ld-ppi1 respectively. In contrast, a multiplexed assay designed to simultaneously detect all five leishmanial biomarkers markedly increased the assay sensitivity to 82.2%. These results validate the utility of leishmanial protein biomarkers found in urine of VL patients as powerful tools for the development of an accurate diagnostic tests for this disease.

DOI: https://doi.org/10.1128/JCM.02076-18
Oncotarget. 2019 Jan 22. 10(7): 692-693

Systems proteogenomics for precision oncology.

Frederick Klauschen.



Keywords:  genomics; precision oncology; proteomics; systems medicine; tumor profiling

DOI:  https://doi.org/10.18632/oncotarget.26601
Mol Cell Proteomics. 2019 Feb 21. pii: mcp.RA119.001390. [Epub ahead of print]

Metabolic, anti-apoptotic and immune evasion strategies of primary human myeloma cells indicate adaptations to hypoxia.

Lukas Janker, Rupert Laurenz Mayer, Andrea Bileck, Dominique Kreutz, Johanna C Mader, Kirsten Utpatel, Daniel Heudobler, Hermine Agis, Christopher Gerner, Astrid Slany.

  Multiple Myeloma (MM) is an incurable plasma cell malignancy primarily localized within the bone marrow (BM). It develops from a premalignant stage, monoclonal gammopathy of undetermined significance (MGUS), often via an intermediate stage, smoldering MM (SMM). The mechanisms of MM progression have not yet been fully understood, all the more because patients with MGUS and SMM already carry similar initial mutations as found in MM cells. Over the last years, increased importance has been attributed to the tumor microenvironment and its role in the pathophysiology of the disease. Adaptations of MM cells to hypoxic conditions in the BM have been shown to contribute significantly to MM progression, independently from the genetic predispositions of the tumor cells. Searching for consequences of hypoxia-induced adaptations in primary human MM cells, CD138-positive plasma cells freshly isolated from BM of patients with different disease stages, comprising MGUS, SMM, and MM, were analyzed by proteome profiling, which resulted in the identification of 6218 proteins. Results have been made fully accessible via ProteomeXchange with identifier PXD010600. Data previously obtained from normal primary B cells were included for comparative purposes. A principle component analysis revealed three clusters, differentiating B cells as well as MM cells corresponding to less and more advanced disease stages. Comparing these three clusters pointed to the alteration of pathways indicating adaptations to hypoxic stress in MM cells upon disease progression. Protein regulations indicating immune evasion strategies of MM cells were determined, supported by immunohistochemical stainings, as well as transcription factors involved in MM development and progression. Protein regulatory networks related to metabolic adaptations of the cells became apparent. Results were strengthened by targeted analyses of a selected panel of metabolites in MM cells and MM-associated fibroblasts. Based on our data, new opportunities may arise for developing therapeutic strategies targeting myeloma disease progression.

Keywords:  Cancer Biology*; Hypoxia; Immune evasion; Immunohistochemistry; Mass Spectrometry; Metabolic adaptations; Metabolomics; Multiple Myeloma; Primary human myeloma cells; Tandem Mass Spectrometry

DOI:  https://doi.org/10.1074/mcp.RA119.001390
J Thorac Dis. 2019 Jan;11(Suppl 1): S102-S112

Are there any theranostic biomarkers in small cell lung carcinoma?

Federica Pezzuto, Francesco Fortarezza, Francesca Lunardi, Fiorella Calabrese.

  Small cell lung cancer (SCLC), an aggressive lung tumour with a poor prognosis, has a high load of somatic mutations, mainly induced by tobacco carcinogens given the strong association with smoking. Advances in genomic, epigenetic and proteomic profiling have significantly improved our understanding of the molecular and cellular biology of SCLC. Given the high mutational burden of SCLC the immune microenvironment is another exciting area under investigation even if it seems to be quite distinct from that of other solid tumours. In this review we will outline the current progress in molecular etiology of SCLC mentioning some key markers considered promising theranostic biomarkers.

Keywords:  Small cell lung cancer (SCLC); biomarkers; theranostics

DOI:  https://doi.org/10.21037/jtd.2018.12.14
J Gynecol Obstet Hum Reprod. 2019 Feb 19. pii: S2468-7847(18)30536-1. [Epub ahead of print]

Variation of Fetuin-A in maternal and fetal serum during human parturition.

Miguel Albuquerque, Dominique Luton, Julie Le Faouder, Pierre Bedossa, Jean Guibourdenche, Pierre-François Ceccaldi.

   BACKGROUND: parturition involves multiple signalling pathways and most advances in research underline the importance of fetal development and maturation in the timing of labour, especially the fetal pituitary-adrenal axis. But, there is currently no consensual hypothesis on all the physiological processes responsible for human parturition.
METHODS: sixty low-risk pregnant women were enrolled in a prospective cohort. Maternal blood was sampled regularly during consultations each week in last trimester, at delivery and at postnatal consultation. Cord blood was collected at delivery. We used proteomic analysis to identify maternal blood biomarkers of potential interest, focusing on serum proteins from 39 W G in pregnancies to delivery and postpartum.
RESULTS: among 56 peaks we identified variation in the N-terminal part of fetuin-A in maternal serum. Fetuin-A is a natural antagonist of TGF-beta and is able to bind calcium. We found a significant decrease in maternal serum fetuin-A in the days preceding delivery, independently of the mode of delivery. Also, there does not appear to be significant influence of the different fetal parameters (sex, Z-score) on maternal serum variations at delivery.
CONCLUSION: fetuin-A is described by the literature as a potential biomarker for organ dysfunction and metabolic syndrome disorders. The protein mineral homeostasis would be an interesting pathway to explore during pregnancy and particularly parturition.

Keywords:  Fetuin-A; calcium; parturition

DOI:  https://doi.org/10.1016/j.jogoh.2019.02.003
Methods Mol Biol. 2019 ;1956 371-381

Phosphoproteomic Analysis of Signaling Pathways in Lymphomas.

Björn Häupl, Henning Urlaub, Thomas Oellerich.

  Cell fate decisions are controlled by complex signal transduction processes that transmit information via posttranslational protein modifications such as phosphorylation. In lymphoma, as in other cancer types, these signaling networks are often dysregulated and thus contribute to malignant transformation and tumor maintenance. For example, B-cell antigen receptor signals are rewired in certain lymphoma types, such as diffuse large B-cell lymphomas, to promote cell growth and survival of the malignant cell clones. Hence, global elucidation of such intricate signaling networks is important for an improved understanding of the biology of these tumors and the identification of target proteins for therapeutic purposes.We describe here a mass spectrometry-based phosphoproteomic approach for characterization of intracellular signaling events and their dynamics. This integrated phosphoproteomic technology combines phosphopeptide enrichment and fractionation with liquid-chromatography-coupled mass spectrometry for the site-specific mapping and quantification of thousands of phosphorylation events in a given cell type. Such global signaling analyses provide valuable insights into oncogenic signaling networks and can inform drug development efforts.

Keywords:  Antigen receptors; B-cell lymphomas; Mass spectrometry; Phosphoproteomics; Signaling

DOI:  https://doi.org/10.1007/978-1-4939-9151-8_19
Pathol Int. 2019 Feb 19.

A case of spheroid-type localized lactoferrin amyloidosis in the bronchus.

Shojiro Ichimata, Daiju Aoyagi, Tsuneaki Yoshinaga, Nagaaki Katoh, Fuyuki Kametani, Masahide Yazaki, Takeshi Uehara, Satoshi Shiozawa.

  We report a case of localized bronchial lactoferrin amyloidosis. A 47-year-old man presented with a complaint of persistent dry cough for two months. Chest computed-tomography revealed a calcification shadow of the right main bronchus; hence, a biopsy was performed, showing layered spheroid-type eosinophilic deposits in the bronchial wall. These deposits were positive for Congo red staining, exhibiting apple-green birefringence under polarized light. In addition, an electron microscopic examination demonstrated that this layered structure was formed by very thin cord-like amyloid deposits. By proteomics analysis using liquid chromatography-tandem mass spectrometry and immunohistochemistry, we confirmed that the deposited amyloid was composed of lactoferrin. While lactoferrin is known to be a precursor protein of localized corneal and seminal vesicle amyloidosis, localized lactoferrin amyloidosis of the bronchus has not been reported in the English literature. Our pathological findings suggested that localized lactoferrin amyloidosis may be caused by long-term tissue damage, and the characteristic spheroid-type appearance is thought to be associated with unique, thin cord-like amyloid deposits.

Keywords:  amyloidosis; bronchus; lactoferrin; liquid chromatography-tandem mass spectrometry (LC-MS/MS); spheroid structure

DOI:  https://doi.org/10.1111/pin.12774