bims-prodis Biomed News
on Proteomics in disease
Issue of 2018–12–09
forty-nine papers selected by
Nancy Gough, Bioserendipity
  1. Novel and conventional approaches for the analysis of quantitative proteomic data are complementary towards the identification of seminal plasma alterations in infertile patients.
  2. Targeted Feature Extraction in MALDI Mass Spectrometry Imaging to Discriminate Proteomic Profiles of Breast and Ovarian Cancer.
  3. Proteomic Landscape of Cholangiocarcinomas Reveals 3 Different Subgroups According to their Localization and the Aspect of Non-Tumor Liver.
  4. Needle lost in the haystack: multiple reaction monitoring fails to detect Treponema pallidum candidate protein biomarkers in plasma and urine samples from individuals with syphilis.
  5. Trypanosoma cruzi immunoproteome: Calpain-like CAP5.5 differentially detected throughout distinct stages of human Chagas disease cardiomyopathy.
  6. Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival.
  7. A two-step strategy for identification of plasma protein biomarkers for endometrial and ovarian cancer.
  8. Oncolytic adenovirus Delta-24-RGD induces a widespread glioma proteotype remodeling during autophagy.
  9. Candidate early predictive plasma protein markers of doxorubicin-induced chronic cardiotoxicity in B6C3F1 mice.
  10. Proteomic profiling reveals key cancer progression modulators in shed microvesicles released from isogenic human primary and metastatic colorectal cancer cell lines.
  11. A high throughput bead-based affinity assay enables analysis of genital protein signatures in women at risk of HIV infection.
  12. Olfactory cleft proteome does not reflect olfactory performance in patients with idiopathic and postinfectious olfactory disorder: A pilot study.
  13. Proteomics of Uterosacral Ligament Connective Tissue from Women With and Without Pelvic Organ Prolapse.
  14. Urine proteomic profiling in patients with nephrolithiasis and cystinuria.
  15. Prenatal retinoic acid exposure reveals candidate genes for craniofacial disorders.
  16. Quantitative proteomics using SILAC-MS identifies N-acetylcysteine-solution-triggered reversal response of renal cell carcinoma cell lines.
  17. High-density and targeted glycoproteomic profiling of serum proteins in pancreatic cancer and intraductal papillary mucinous neoplasm.
  18. Multi-Study Proteomic and Bioinformatic Identification of Molecular Overlap between Amyotrophic Lateral Sclerosis (ALS) and Spinal Muscular Atrophy (SMA).
  19. Contribution of Plasmodium immunomics: potential impact for serological testing and surveillance of malaria.
  20. Quantitative assessment of serum heat shock protein 27 for the diagnosis of epithelial ovarian cancer using targeted proteomics coupled with immunoaffinity enrichment.
  21. Quantitative proteomics reveals distinct composition of amyloid plaques in Alzheimer's disease.
  22. Clinical Proteomics in Colorectal Cancer, a Promising Tool for Improving Personalised Medicine.
  23. iTRAQ-based quantitative proteomics reveals the neuroprotection of rhubarb in experimental intracerebral hemorrhage.
  24. Urinary proteome analysis of acute hypercoagulable state in rat model induced by ε-aminocaproic acid.
  25. Adipose tissue exosomal proteomic profile reveals a role on placenta glucose metabolism in gestational diabetes mellitus.
  26. In vitro and in vivo Proteomic Comparison of Human Neural Progenitor Cell-Induced Photoreceptor Survival.
  27. STON2 negatively modulates stem-like properties in ovarian cancer cells via DNMT1/MUC1 pathway.
  28. Salivaomics in oral cancer.
  29. Implementation of clinical proteomics: A step closer to personalised medicine?
  30. Mass spectrometric imaging of cysteine rich proteins in human skin.
  31. A Double-Edged Sword:Complement Component 3 in Toxoplasma gondii Infection.
  32. The temporal pattern of immune and inflammatory proteins prior to a recurrent coronary event in post-acute coronary syndrome patients.
  33. Altered levels of focal adhesion and extracellular matrix-receptor interacting proteins were identified in Hailey-Hailey disease by quantitative iTRAQ proteome analysis.
  34. Application of iTRAQ proteomics in identification of the differentially expressed proteins of placenta of pregnancy with preeclampsia.
  35. Styryl-Cinnamate Hybrid Inhibits Glioma by Alleviating Translation, Bioenergetics and Other Key Cellular Responses Leading to Apoptosis.
  36. Bioassay of saliva proteins: The best alternative for conventional methods in non-invasive diagnosis of cancer.
  37. Characterization of the Blister Fluid Proteome for Pediatric Burn Classification.
  38. Antigen Specificity and Clinical Significance of IgG and IgA Autoantibodies Produced in situ by Tumor-Infiltrating B Cells in Breast Cancer.
  39. Archaea Symbiont of T. cruzi Infection May Explain Heart Failure in Chagas Disease.
  40. Systems Analysis of Transcriptomic and Proteomic Profiles Identifies Novel Regulation of Fibrotic Programs by miRNAs in Pulmonary Fibrosis Fibroblasts.
  41. Cooperative effect of oncogenic MET and PIK3CA in an HGF-dominant environment in breast cancer.
  42. Bacterial sepsis triggers an antiviral response that causes translation shutdown.
  43. A SUMOylation dependent switch of Rab7 governs intracellular life and pathogenesis of Salmonella Typhimurium.
  44. IgE-mediated allergic responses associated to Ailanthus altissima pollen using an animal model.
  45. Identification of Integrin β1 as a Novel PAG1-Interacting Protein Involved in the Inherent Radioresistance of Human Laryngeal Carcinoma.
  46. Identification of evolutionarily conserved gene networks mediating neurodegenerative dementia.
  47. Exosomes and chronic rhinosinusitis.
  48. Characterization of metalloproteases and serine proteases of Toxoplasma gondii tachyzoites and their effect on epithelial cells.
  49. Single-Cell Imaging of Metastatic Potential of Cancer Cells.
  1. Mol Cell Proteomics. 2018 Dec 05. pii: mcp.RA118.001248. [Epub ahead of print]
    Novel and conventional approaches for the analysis of quantitative proteomic data are complementary towards the identification of seminal plasma alterations in infertile patients.
    Ferran Barrachina, Meritxell Jodar, David Delgado-Dueñas, Ada Soler-Ventura, Josep Maria Estanyol, Carme Mallofré, Jose Luis Ballesca, Rafael Oliva.
      Our aim was to define seminal plasma proteome signatures of infertile patients categorized according to their seminal parameters using TMT-LC-MS/MS. To that extent, quantitative proteomic data was analyzed following two complementary strategies: (i) the conventional approach based on standard statistical analyses of relative protein quantification values; and (ii) a novel strategy focused on establishing stable-protein pairs. By conventional analyses, the abundance of some seminal plasma proteins was found to be positively correlated with sperm concentration. However, this correlation was not found for all the peptides within a specific protein, bringing to light the high heterogeneity existing in the seminal plasma proteome due to both the proteolytic fragments and/or the post-translational modifications. This issue was overcome by conducting the novel stable-protein pairs analysis proposed herein. A total of 182 correlations comprising 24 different proteins were identified in the normozoospermic-control population, while this proportion was drastically reduced in infertile patients with altered seminal parameters (18 in patients with reduced sperm motility, 0 in patients with low sperm concentration and 3 in patients with no sperm in the ejaculate). These results suggest the existence of multiple etiologies causing the same alteration in seminal parameters. Additionally, the repetition of the stable-protein pair analysis in the control group by adding the data from a single patient at a time enabled to identify alterations in the stable-protein pairs profile of individual patients with altered seminal parameters. These results suggest potential underlying pathogenic mechanisms in individual infertile patients, and might open up a window to its application in the personalized diagnostic of male infertility.
    Keywords:  Biomarker: Diagnostic; Clinical proteomics; High Throughput Screening; Male infertility; Mass Spectrometry; Quantification; Quantitative proteomics; Seminal parameters; Seminal plasma; Stable-protein pairs
    DOI:  https://doi.org/10.1074/mcp.RA118.001248
  2. Proteomics Clin Appl. 2018 Dec 06. e1700168
    Targeted Feature Extraction in MALDI Mass Spectrometry Imaging to Discriminate Proteomic Profiles of Breast and Ovarian Cancer.
    Yovany Cordero Hernandez, Tobias Boskamp, Rita Casadonte, Lena Hauberg-Lotte, Janina Oetjen, Delf Lachmund, Annette Peter, Dennis Trede, Katharina Kriegsmann, Mark Kriegsmann, Jörg Kriegsmann, Peter Maass.
       PURPOSE: To develop a mass spectrometry imaging (MSI) based workflow for extracting m/z values related to putative protein biomarkers and using these for reliable tumor classification.
    EXPERIMENTAL DESIGN: Given a list of putative breast and ovarian cancer biomarker proteins, we extracted a set of related m/z values from heterogeneous MSI datasets derived from formalin-fixed paraffin-embedded tissue material. Based on these features, a linear discriminant analysis classification model was trained to discriminate the two tumor types.
    RESULTS: We show that the discriminative power of classification models based on the extracted features is increased compared to the automatic training approach, especially when classifiers are applied to spectral data acquired under different conditions (instrument, preparation, laboratory).
    CONCLUSIONS AND CLINICAL RELEVANCE: We obtained robust classification models not confounded by technical variation between MSI measurements. This supports the assumption that the classification of the respective tumor types is based on biological rather than technical differences, and that the selected features are related to the proteomic profiles of the tumor types under consideration. This article is protected by copyright. All rights reserved.
    Keywords:  MALDI MSI; biomarker proteins; feature extraction; tissue classification; tumor typing
    DOI:  https://doi.org/10.1002/prca.201700168
  3. Proteomics Clin Appl. 2018 Dec 06. e1800128
    Proteomic Landscape of Cholangiocarcinomas Reveals 3 Different Subgroups According to their Localization and the Aspect of Non-Tumor Liver.
    Julie Le Faouder, Elia Gigante, Thibaut Léger, Miguel Albuquerque, Aurélie Beaufrère, Olivier Soubrane, Safi Dokmak, Jean Michel Camadro, Jérôme Cros, Valérie Paradis.
       PURPOSE: Cholangiocarcinomas (CC), tumors derived from epithelial biliary cells, define a heterogeneous entity based upon their anatomic localization (intra- versus extrahepatic) and, for those developing in the liver, depending on the aspect of non-tumor liver (normal versus cirrhosis). The aim of the study was to characterize the molecular heterogeneity of the different types of CC by a global proteomic approach.
    EXPERIMENTAL DESIGN: Thirty-three tumor samples from 17 intrahepatic CC (iCC) including 9 and 8 developed on normal (iCCN ) and cirrhotic liver (iCCC ), respectively; 5 hilar CC (CCH ), 5 CC developed in the pancreatic portion of the bile duct (CCP ) and 6 hepatocellular carcinoma (HCC), were submitted to label-free quantitative proteomic analysis. Differentially expressed proteins were further analyzed by immunohistochemistry in a validation set of 30 CC.
    RESULTS: In the overall series, 4590 proteins were quantified. Unsupervised analysis revealed two main clusters: cluster 1 contained most the iCCC while cluster 2 was divided in 2 subgroups, one containing most of the iCCN and the other regrouping CCH and CCP . Compared to iCCN , iCCC displayed upregulation of molecules involved in cell adhesion and motility and in angiogenesis. Epithelial markers associated with secretory pathway (mucins and AGR2) as well as fibroblast markers (S100A4) were overexpressed in CCH compared to iCCN .
    CONCLUSION AND CLINICAL RELEVANCE: This study demonstrated that among iCC, iCCC is a specific entity, suggesting a major impact of the underlying liver condition on the tumor biology, and confirmed that extrahepatic CCs, including CCP and CCH, define an homogeneous subgroup. This article is protected by copyright. All rights reserved.
    Keywords:  cholangiocarcinoma; cirrhosis; label-free quantitative proteomics; tissue; tumor heterogeneity
    DOI:  https://doi.org/10.1002/prca.201800128
  4. F1000Res. 2018 ;7 336
    Needle lost in the haystack: multiple reaction monitoring fails to detect Treponema pallidum candidate protein biomarkers in plasma and urine samples from individuals with syphilis.
    Geert A Van Raemdonck, Kara K Osbak, Xaveer Van Ostade, Chris R Kenyon.
      Background: Current syphilis diagnostic strategies are lacking a sensitive manner of directly detecting Treponema pallidum antigens. A diagnostic test that could directly detect T. pallidum antigens in individuals with syphilis would be of considerable clinical utility, especially for the diagnosis of reinfections and for post-treatment serological follow-up. Methods: In this study, 11 candidate T. pallidum biomarker proteins were chosen according to their physiochemical characteristics, T. pallidum specificity and predicted abundance. Thirty isotopically labelled proteotypic surrogate peptides (hPTPs) were synthesized and incorporated into a scheduled multiple reaction monitoring assay. Protein extracts from undepleted/unenriched plasma (N = 18) and urine (N = 4) samples from 18 individuals with syphilis in various clinical stages were tryptically digested, spiked with the hPTP mixture and analysed with a triple quadruple mass spectrometer. Results: No endogenous PTPs corresponding to the eleven candidate biomarkers were detected in any samples analysed. To estimate the Limit of Detection (LOD) of a comparably sensitive mass spectrometer (LTQ-Orbitrap), two dilution series of rabbit cultured purified T. pallidum were prepared in PBS. Polyclonal anti- T. pallidum antibodies coupled to magnetic Dynabeads were used to enrich one sample series; no LOD improvement was found compared to the unenriched series. The estimated LOD of MS instruments is 300 T. pallidum/ml in PBS. Conclusions: Biomarker protein detection likely failed due to the low (femtomoles/liter) predicted concentration of T. pallidum proteins. Alternative sample preparation strategies may improve the detectability of T. pallidum proteins in biofluids.
    Keywords:  MRM; Multiple Reaction Monitoring; Treponema pallidum; antigen test; biomarker discovery; plasma; syphilis; targeted proteomics
    DOI:  https://doi.org/10.12688/f1000research.13964.1
  5. J Proteomics. 2018 Nov 29. pii: S1874-3919(18)30417-2. [Epub ahead of print]
    Trypanosoma cruzi immunoproteome: Calpain-like CAP5.5 differentially detected throughout distinct stages of human Chagas disease cardiomyopathy.
    Marcelle A Caminha, Virginia Maria B de Lorena, Wilson de Oliveira Júnior, Jonas Perales, Paulo C Carvalho, Diogo B Lima, Maria da Glória A M Cavalcanti, Sílvia M Martins, Richard H Valente, Rubem F S Menna-Barreto.
      Chagas disease, caused by the protozoan Trypanosoma cruzi, affects millions of people worldwide, especially in Latin America. Approximately 30% of the cases evolve to the chronic symptomatic stage due to cardiac and/or digestive damage, generally accompanied by nervous system impairment. Given the higher frequency and severity of clinical manifestations related to cardiac tissue lesion, the goal of this study was the identification of proteins associated with the disease progression towards its cardiac form. Thus, T. cruzi bloodstream trypomastigotes proteins were submitted to immunoprecipitation using antibodies from patients with the asymptomatic or cardiac (stages B1 and C) forms of the disease and from healthy donors as control. Immunoreactive proteins were identified and quantified based on mass spectrometry analysis and shifts in the recognition profile were further evaluated. Compared to asymptomatic samples, IgG from stage C patients predominantly detected the I/6 autoantigen, whereas IgG from B1 patients resulted in higher yield of dihydrolipoamide acetyltransferase precursor, calpain cysteine peptidase, and two variants of CAP5.5. In this work, CAP5.5 recognition by serum immunoglobulin from patients with early cardiomyopathy generated a 23-fold abundance variation when compared to samples from asymptomatic patients, highlighting the participation of this protein in cardiac form progression of the disease. SIGNIFICANCE: While T. cruzi has become the major cause of infectious cardiomyopathy in Latin America, research groups have been struggling to find alternative treatment, vaccine candidates, and improved diagnostic tests. In addition, the absence of adequate biomarkers to assess cure and progression of disease is a major setback for clinical trials and patients monitoring. Therefore, our findings may contribute to a better understanding of T. cruzi pathogenesis and evaluation of suitable candidates for vaccine and diagnostic tests, besides the clinical applicability of the potential biomarkers for patient follow-up and prognosis. Finally, the identification of T. cruzi proteins recognized by IgG from healthy donors may contribute for the understanding and discovery of epitope conservation among a broad range of pathogens.
    Keywords:  Biomarkers; CAP5.5; Cardiomyopathy; Chagas disease; Mass spectrometry; Trypanosoma cruzi
    DOI:  https://doi.org/10.1016/j.jprot.2018.11.019
  6. Genome Med. 2018 Dec 03. 10(1): 94
    Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival.
    Wei Tang, Ming Zhou, Tiffany H Dorsey, DaRue A Prieto, Xin W Wang, Eytan Ruppin, Timothy D Veenstra, Stefan Ambs.
       BACKGROUND: Transcriptome analysis of breast cancer discovered distinct disease subtypes of clinical significance. However, it remains a challenge to define disease biology solely based on gene expression because tumor biology is often the result of protein function. Here, we measured global proteome and transcriptome expression in human breast tumors and adjacent non-cancerous tissue and performed an integrated proteotranscriptomic analysis.
    METHODS: We applied a quantitative liquid chromatography/mass spectrometry-based proteome analysis using an untargeted approach and analyzed protein extracts from 65 breast tumors and 53 adjacent non-cancerous tissues. Additional gene expression data from Affymetrix Gene Chip Human Gene ST Arrays were available for 59 tumors and 38 non-cancerous tissues in our study. We then applied an integrated analysis of the proteomic and transcriptomic data to examine relationships between them, disease characteristics, and patient survival. Findings were validated in a second dataset using proteome and transcriptome data from "The Cancer Genome Atlas" and the Clinical Proteomic Tumor Analysis Consortium.
    RESULTS: We found that the proteome describes differences between cancerous and non-cancerous tissues that are not revealed by the transcriptome. The proteome, but not the transcriptome, revealed an activation of infection-related signal pathways in basal-like and triple-negative tumors. We also observed that proteins rather than mRNAs are increased in tumors and show that this observation could be related to shortening of the 3' untranslated region of mRNAs in tumors. The integrated analysis of the two technologies further revealed a global increase in protein-mRNA concordance in tumors. Highly correlated protein-gene pairs were enriched in protein processing and disease metabolic pathways. The increased concordance between transcript and protein levels was additionally associated with aggressive disease, including basal-like/triple-negative tumors, and decreased patient survival. We also uncovered a strong positive association between protein-mRNA concordance and proliferation of tumors. Finally, we observed that protein expression profiles co-segregate with a Myc activation signature and separate breast tumors into two subgroups with different survival outcomes.
    CONCLUSIONS: Our study provides new insights into the relationship between protein and mRNA expression in breast cancer and shows that an integrated analysis of the proteome and transcriptome has the potential of uncovering novel disease characteristics.
    Keywords:  African-American; Breast cancer; Gene expression profiling; Proteomics; Survival; Systems analysis; Transcription
    DOI:  https://doi.org/10.1186/s13073-018-0602-x
  7. Clin Proteomics. 2018 ;15 38
    A two-step strategy for identification of plasma protein biomarkers for endometrial and ovarian cancer.
    Stefan Enroth, Malin Berggrund, Maria Lycke, Martin Lundberg, Erika Assarsson, Matts Olovsson, Karin Stålberg, Karin Sundfeldt, Ulf Gyllensten.
       Background: Over 500,000 women worldwide are diagnosed with ovarian or endometrial cancer each year. We have used a two-step strategy to identify plasma proteins that could be used to improve the diagnosis of women with an indication of gynecologic tumor and in population screening.
    Methods: In the discovery step we screened 441 proteins in plasma using the proximity extension assay (PEA) and five Olink Multiplex assays (CVD II, CVD III, INF I, ONC II, NEU I) in women with ovarian cancer (n = 106), endometrial cancer (n = 74), benign ovarian tumors (n = 150) and healthy population controls (n = 399). Based on the discovery analyses a set of 27 proteins were selected and two focused multiplex PEA assays were developed. In a replication step the focused assays were used to study an independent set of cases with ovarian cancer (n = 280), endometrial cancer (n = 228), women with benign ovarian tumors (n = 76) and healthy controls (n = 57).
    Results: In the discovery step, 27 proteins that showed an association to cancer status were identified. In the replication analyses, the focused assays distinguished benign tumors from ovarian cancer stage III-IV with a sensitivity of 0.88 and specificity of 0.92 (AUC = 0.92). The assays had a significantly higher AUC for distinguishing benign tumors from late stage ovarian cancer than using CA125 and HE4 (p = 9.56e-22). Also, population controls could be distinguished from ovarian cancer stage III-IV with a sensitivity of 0.85 and a specificity of 0.92 (AUC = 0.89).
    Conclusion: The PEA assays represent useful tools for identification of new biomarkers for gynecologic cancers. The selected protein assays could be used to distinguish benign tumors from ovarian and endometrial cancer in women diagnosed with an unknown suspicious pelvic mass. The panels could also be used in population screening, for identification of women in need of specialized gynecologic transvaginal ultrasound examination.
    Funding: The Swedish Cancer Foundation, Vinnova (SWELIFE), The Foundation for Strategic Research (SSF), Assar Gabrielsson Foundation.
    Keywords:  Diagnostics; Endometrial cancer; Ovarian cancer; Proximity extension assay (PEA); Sensitivity; Specificity
    DOI:  https://doi.org/10.1186/s12014-018-9216-y
  8. J Proteomics. 2018 Nov 29. pii: S1874-3919(18)30418-4. [Epub ahead of print]
    Oncolytic adenovirus Delta-24-RGD induces a widespread glioma proteotype remodeling during autophagy.
    Andrea González-Morales, Aintzane Zabaleta, Marc García-Moure, Marta M Alonso, Joaquín Fernández-Irigoyen, Enrique Santamaría.
      Adenovirus Delta-24-RGD has shown a remarkable efficacy in a phase I clinical trial for glioblastoma. Delta-24-RGD induces autophagy in glioma cells, however, the molecular derangements associated with Delta-24-RGD infection remains poorly understood. Here, proteomics was applied to characterize the glioma metabolic disturbances soon after Delta-24-RGD internalization and late in infection. Minutes post-infection, a rapid survival reprogramming of glioma cells was evidenced by an early c-Jun activation and a time-dependent dephosphorylation of multiple survival kinases. At 48 h post-infection (hpi), a severe intracellular proteostasis impairment was characterized, detecting differentially expressed proteins related to mRNA splicing, cytoskeletal organization, oxidative response, and inflammation. Specific kinase-regulated protein interactomes for Delta-24-RGD-modulated proteome revealed interferences with the activation dynamics of protein kinases C and A (PKC, PKA), tyrosine-protein kinase Src (c-Src), glycogen synthase kinase-3 (GSK-3) as well as serine/threonine-protein phosphatases 1 and 2A (PP1, PP2A) at 48hpi, in parallel with adenoviral protein overproduction. Moreover, the late activation of the nuclear factor kappa B (NF-κB) correlates with the extracellular increment of specific cytokines involved in migration, and activation of different inflammatory cells. Taken together, our integrative analysis provides further insights into the effects triggered by Delta-24-RGD in the modulation of tumor suppression and immune response against glioma. SIGNIFICANCE: The current study provides new insights regarding the molecular mechanisms governing the glioma metabolism during Delta-24-RGD oncolytic adenoviral therapy. The compilation and analysis of intracellular and extracellular proteomics have led us to characterize: i) the cell survival reprogramming during Delta-24-RGD internalization, ii) the proteostatic disarrangement induced by Delta-24-RGD during the autophagic stage, iii) the protein interactomes for Delta-24-RGD-modulated proteome, iv) the regulatory effects on kinase dynamics induced by Delta-24-RGD late in infection, and v) the overproduction of multitasking cytokines upon Delta-24-RGD treatment. We consider that the quantitative molecular maps generated in this study may establish the foundations for the development of complementary adenoviral based-vectors to increase the potency against glioma.
    Keywords:  Adenovirus; Delta-24RGD infection; Glioma; Networks; Proteomics; Signaling
    DOI:  https://doi.org/10.1016/j.jprot.2018.11.020
  9. Toxicol Appl Pharmacol. 2018 Dec 02. pii: S0041-008X(18)30536-2. [Epub ahead of print]
    Candidate early predictive plasma protein markers of doxorubicin-induced chronic cardiotoxicity in B6C3F1 mice.
    Varsha G Desai, Taewon Lee, Carrie L Moland, Vikrant Vijay, Tao Han, Sherry M Lewis, Eugene H Herman, James C Fuscoe.
      Cardiotoxicity is a serious adverse effect of doxorubicin (DOX) treatment in cancer patients. Currently, there is a lack of sensitive biomarkers to predict the risk of DOX-induced cardiotoxicity. Using SOMAmer-based proteomic technology, 1129 proteins were profiled to identify potential early biomarkers of cardiotoxicity in plasma from male B6C3F1 mice given a weekly intravenous dose of 3 mg/kg DOX or saline (SAL) for 2, 3, 4, 6, or 8 weeks (6, 9, 12, 18, or 24 mg/kg cumulative DOX doses, respectively). Also, a group of mice received the cardio-protectant, dexrazoxane (DXZ; 60 mg/kg; intraperitoneal) 30 min before a weekly DOX or SAL dose. Proteomic analysis in plasma collected a week after the last dose showed a significant ≥1.2-fold change in plasma level of 18 proteins in DOX-treated mice compared to SAL-treated counterparts during 8-week exposure. Of these, neurogenic locus notch homolog protein 1 (NOTCH1), von Willebrand factor (vWF), mitochondrial glutamate carrier 2, Wnt inhibitory factor 1, legumain, and mannan-binding lectin serine protease 1 were increased in plasma at 6 mg/kg cumulative dose, prior to the release of myocardial injury marker, cardiac troponin I at 12 mg/kg and higher cumulative doses. These six proteins also remained significantly elevated following myocardial injury or pathology at 24 mg/kg. Pretreatment of mice with DXZ significantly attenuated DOX-induced elevated levels of only NOTCH1 and vWF with mitigation of cardiotoxicity. This suggests NOTCH1 and vWF as candidate early biomarkers of DOX cardiotoxicity, which may help in addressing a clinically important question of identifying cancer patients at risk for cardiotoxicity.
    Keywords:  Biomarkers; Cardiotoxicity; Dexrazoxane; Doxorubicin; Mouse Plasma; SOMAscan™ Proteomic Assay
    DOI:  https://doi.org/10.1016/j.taap.2018.11.016
  10. Biochim Biophys Acta Proteins Proteom. 2018 Nov 28. pii: S1570-9639(18)30206-1. [Epub ahead of print]
    Proteomic profiling reveals key cancer progression modulators in shed microvesicles released from isogenic human primary and metastatic colorectal cancer cell lines.
    Wittaya Suwakulsiri, Alin Rai, Rong Xu, Maoshan Chen, David W Greening, Richard J Simpson.
      Extracellular vesicles can be classified into two main classes - exosomes and shed microvesicles (sMVs). Whilst much is known about exosome cargo and functionality, sMVs are poorly understood. Here, we describe the large-scale purification of sMVs released from primary (SW480) and metastatic (SW620) human isogenic colorectal cancer (CRC) cell lines using a combination of differential ultracentrifugation and isopycnic iodixanol density centrifugation. The yield of SW480-sMVs and SW620-sMVs was 0.75 mg and 0.80 mg, respectively. Both SW480-/SW620-sMVs are heterogeneous in size (100-600 nm diameter) and exhibit identical buoyant densities (1.10 g/mL). In contrast to exosomes, sMVs are ALIX-, TSG101-, CD63- and CD9-. Quantitative mass spectrometry identified 1295 and 1300 proteins in SW480-sMVs and SW620-sMVs, respectively. Gene Ontology enrichment analysis identified 'cell adhesion' (CDH1, OCLN, CTN families), 'signalling pathway' (KRAS, NRAS, MAPK1, MAP2K1), and 'translation/RNA related' processes (EIF, RPL, HNRNP families) in both sMV types. Strikingly, SW480- and SW620-sMVs exhibit distinct protein signatures - SW480-sMVs enriched in ITGA/B, ANXA1, CLDN7, CD44 and EGFR/NOTCH signalling networks, while SW620-sMVs are enriched in PRKCA, MACC1, and FGFR4/MTOR/ MARCKS signalling networks. Both SW480- and SW620-sMVs are taken up by NIH3T3 fibroblasts, demonstrating similar cell invasion capability. This study provides, for the first time, molecular insights into sMVs and CRC biology.
    Keywords:  Colon cancer; Extracellular vesicles; Metastasis; Proteomics; Shed microvesicles
    DOI:  https://doi.org/10.1016/j.bbapap.2018.11.008
  11. Mol Cell Proteomics. 2018 Nov 30. pii: mcp.RA118.000757. [Epub ahead of print]
    A high throughput bead-based affinity assay enables analysis of genital protein signatures in women at risk of HIV infection.
    Anna Månberg, Frideborg Bradley, Ulrika Qundos, Brandon L Guthrie, Kenzie Birse, Laura Noël-Romas, Cecilia Lindskog, Rose Bosire, James Kiarie, Carey Farquhar, Adam D Burgener, Peter Nilsson, Kristina Broliden.
      Women at high risk of HIV infection, including sex workers and those with active genital inflammation, have molecular signatures of immune activation and epithelial barrier remodeling in samples of their genital mucosa. These alterations in the local immunological milieu are likely to impact HIV susceptibility. We here analyze host genital protein signatures in HIV uninfected women, with high frequency of condom use, living in HIV-serodiscordant relationships. Cervicovaginal secretions from women living in HIV-serodiscordant relationships (n=62) were collected at three time points over 12 months. Women living in HIV-negative seroconcordant relationships (controls, n=25) were sampled at one time point. All study subjects were examined for demographic parameters associated with susceptibility to HIV infection. The cervicovaginal samples were analyzed using a high throughput bead-based affinity assay. Proteins involved in epithelial barrier function and inflammation were increased in HIV-serodiscordant women. By combining several methods of analysis, a total of five proteins (CAPG, KLK10, SPRR3, elafin/PI3, CSTB) were consistently associated with this study group. Proteins analyzed using the affinity set-up were further validated by label-free tandem mass spectrometry in a partially overlapping cohort with concordant results. Women living in HIV-serodiscordant relationships thus had elevated levels of proteins involved in epithelial barrier function and inflammation despite low prevalence of sexually transmitted infections and a high frequency of safe sex practices. The identified proteins are important markers to follow during assessment of mucosal HIV susceptibility factors and a high throughput bead-based affinity set-up could be a suitable method for such evaluation.
    Keywords:  Affinity proteomics; HIV; HIV-serodiscordant; Immunology*; Inflammation; Tandem Mass Spectrometry; cervix; female reproductive tract; reproductive immunology; vagina
    DOI:  https://doi.org/10.1074/mcp.RA118.000757
  12. Sci Rep. 2018 Dec 03. 8(1): 17554
    Olfactory cleft proteome does not reflect olfactory performance in patients with idiopathic and postinfectious olfactory disorder: A pilot study.
    Axel Wolf, Laura Liesinger, Stefan Spoerk, Matthias Schittmayer, Doris Lang-Loidolt, Ruth Birner-Gruenberger, Peter V Tomazic.
      Technical advances including liquid chromatography-tandem mass spectrometry and its data analysis enable detailed proteomic analysis of the nasal mucus. Alterations of the nasal mucus proteome may provoke substantial changes of the nasal physiology and have already been associated with rhinologic diseases such as allergic rhinitis. This study was conducted as a pilot study to map the olfactory cleft proteome using current techniques for proteomic analysis. Furthermore, we aimed to investigate proteomic changes as potential biomarkers in patients suffering from idiopathic and postinfectious olfactory disorders compared to healthy controls. Seven patients with idiopathic hyposmia and anosmia, seven patients with postinfectious hyposmia and anosmia and seven healthy controls were included in this study. In total, 1117 different proteins were detected in at least five patients in at least one group. Results of this study did not reveal significant differences regarding the proteomic composition of the olfactory cleft mucus between patients versus healthy controls. Among proteins involved in olfactory perception the G protein family was detected but also found unchanged between groups. Investigation of protein composition by liquid chromatography-tandem mass spectrometry enabled us to perform an in-depth analysis of the olfactory cleft mucus proteome regarding the diversity of different proteins in individual patients. However untargeted proteomics of the olfactory cleft mucus may not be an applicable approach to develop biomarkers for olfactory disorders. Targeted analyses of distinct proteins known to be involved in olfactory perception but not detected by our approach, e.g. odorant binding proteins, may provide more information regarding pathophysiology of olfactory diseases.
    DOI:  https://doi.org/10.1038/s41598-018-35776-8
  13. Proteomics Clin Appl. 2018 Dec 05. e1800086
    Proteomics of Uterosacral Ligament Connective Tissue from Women With and Without Pelvic Organ Prolapse.
    Xiang-Juan Li, Hai-Tao Pan, Juan-Juan Chen, Yi-Bin Fu, Min Fang, Guo-Hua He, Tao Zhang, Hai-Gang Ding, Bin Yu, Yi Cheng, Ya-Jing Tan, Fa-Lin Zhao, Abraham N Morse, He-Feng Huang.
       PURPOSE: Damage to the uterosacral ligaments is an important contributor to uterine and vaginal prolapse. The aim of this study was to identify differentially expressed proteins in the uterosacral ligaments of women with and without pelvic organ prolapse and analyze their relationships to cellular mechanisms involved in the pathogenesis of pelvic organ prolapse.
    EXPERIMENTAL DESIGN: Uterosacral ligament connective tissue from four patients with pelvic organ prolapse and four control women underwent iTRAQ analysis followed by Ingenuity Pathway Analysis of differentially expressed proteins. Differentially expressed proteins were validated using western blot analysis.
    RESULTS: A total of 1789 unique protein sequences were identified in the uterosacral ligament connective tissues. The expression levels of 88 proteins were significantly different between prolapse and control groups (≥1.2-fold, p<0.05). Ingenuity pathway analysis demonstrated the association of 14 differentially expressed proteins with "Connective Tissue Function". Among them, fibromodulin (FMOD), Collagen alpha-1 (XIV) chain (COL14A1), Calponin-1 (CNN-1), Tenascin (TNC), and Galectin-1 (LGALS1) appeared most likely to play a role in the etiology of pelvic organ prolapse. Data are available via ProteomeXchange with identifier PXD011467.
    CONCLUSIONS AND CLINICAL RELEVENCE: We identified at least 6 proteins not previously associated with the pathogenesis of pelvic organ prolapse with biologic functions that suggest a plausible relationship to the disorder. These results may be helpful for furthering our understanding of the pathophysiological mechanisms of pelvic organ prolapse. This article is protected by copyright. All rights reserved.
    Keywords:  iTRAQ analysis; ingenuity pathway analysis; molecular pathogenesis; musculoskeletal system; pelvic organ prolapse; reproductive system; uterosacral ligament
    DOI:  https://doi.org/10.1002/prca.201800086
  14. Int Urol Nephrol. 2018 Dec 05.
    Urine proteomic profiling in patients with nephrolithiasis and cystinuria.
    Larisa Kovacevic, Joseph A Caruso, Hong Lu, Natalija Kovacevic, Yegappan Lakshmanan, Nicholas J Carruthers, David S Goldfarb.
       PURPOSE: The purpose of the study was to assess the differences in the concentration and function of urinary proteins between patients with cystine stones (CYS) and healthy controls (HC). We postulated that CYS and HC groups would demonstrate different proteomic profiles.
    METHODS: A pilot study was performed comparing urinary proteomes of 10 patients with CYS and 10 age- and gender-matched HC, using liquid chromatography-mass spectrometry. Proteins which met the selection criteria (i) ≥ 2 unique peptide identifications; (ii) ≥ twofold difference in protein abundance; and (iii) ≤ 0.05 p value for the Fisher's Exact Test were analyzed using Gene Ontology classifications.
    RESULTS: Of the 2097 proteins identified by proteomic analysis, 398 proteins were significantly different between CYS and HC. Of those, 191 were involved in transport processes and 61 in inflammatory responses. The majority were vesicle-mediated transport proteins (78.5%), and 1/3 of them were down-regulated; of those, 12 proteins were involved in endosomal transport (including 6 charged multivesicular body proteins (CHMP) and 3 vacuolar sorting-associated proteins) and 9 in transmembrane transport. Myosin-2 and two actin-related proteins were significantly up-regulated in the vesicle-mediated transport group.
    CONCLUSION: We provide proteomic evidence of impaired endocytosis, dysregulation of actin and myosin cytoskeleton, and inflammation in CYS. Endosomal transport proteins were down-regulated mainly through defective CHMP. These findings may contribute to further understanding of the pathogenesis of CYS, potentially affecting its management.
    Keywords:  Cystinuria; Nephrolithiasis; Proteomics; Urine
    DOI:  https://doi.org/10.1007/s11255-018-2044-1
  15. Sci Rep. 2018 Nov 30. 8(1): 17492
    Prenatal retinoic acid exposure reveals candidate genes for craniofacial disorders.
    Marie Berenguer, Muriel Darnaudery, Stéphane Claverol, Marc Bonneu, Didier Lacombe, Caroline Rooryck.
      Syndromes that display craniofacial anomalies comprise a major class of birth defects. Both genetic and environmental factors, including prenatal retinoic acid (RA) exposure, have been associated with these syndromes. While next generation sequencing has allowed the discovery of new genes implicated in these syndromes, some are still poorly characterized such as Oculo-Auriculo-Vertebral Spectrum (OAVS). Due to the lack of clear diagnosis for patients, developing new strategies to identify novel genes involved in these syndromes is warranted. Thus, our study aimed to explore the link between genetic and environmental factors. Owing to a similar phenotype of OAVS reported after gestational RA exposures in humans and animals, we explored RA targets in a craniofacial developmental context to reveal new candidate genes for these related disorders. Using a proteomics approach, we detected 553 dysregulated proteins in the head region of mouse embryos following their exposure to prenatal RA treatment. This novel proteomic approach implicates changes in proteins that are critical for cell survival/apoptosis and cellular metabolism which could ultimately lead to the observed phenotype. We also identified potential molecular links between three major environmental factors known to contribute to craniofacial defects including maternal diabetes, prenatal hypoxia and RA exposure. Understanding these links could help reveal common key pathogenic mechanisms leading to craniofacial disorders. Using both in vitro and in vivo approaches, this work identified two new RA targets, Gnai3 and Eftud2, proteins known to be involved in craniofacial disorders, highlighting the power of this proteomic approach to uncover new genes whose dysregulation leads to craniofacial defects.
    DOI:  https://doi.org/10.1038/s41598-018-35681-0
  16. J Cell Biochem. 2018 Dec 05.
    Quantitative proteomics using SILAC-MS identifies N-acetylcysteine-solution-triggered reversal response of renal cell carcinoma cell lines.
    Cuihong Zhao, Jianhua Chen, Yong Ling, Shenghai Wang.
      N-acetylcysteine (NAC), a precursor for glutathione (GSH), causes permeable antioxidation protecting normal cells and disrupting cancer cells. In the present study, we found that a NAC-based medium can trigger a reversal response of human clear cell renal cell carcinoma (ccRCC). To further investigate the action of a NAC-based solution in ccRCC cell lines, 786-O and SN12C were incubated in a serum-free acid medium (low pH) in the presence of 2 mM NAC for 24 hours or in a serum-free medium (normal pH) as the control, and then a phenotypic and proteomic analyses were performed. To determine the reversal occurrence, we tested the phenotypic features associated with cancer cells. Under this premise, a systematic and in-depth analysis of NAC-solution-triggered protein alterations was carried out by quantitative proteomics in both cell lines. Among the paramount protein signature, we identified a large number of proteins associated with cancer features were downregulated, but other proteins in the KEGG pathways associated with recovery of the missing tumorigenicity, such as the p53 pathway and repair pathway, were significantly upregulated. Quantification of notable proteins was validated by messenger RNA (mRNA) and protein levels in the ccRCC cell line. Collectively, our data indicate that the NAC-based solution inhibits human ccRCC cell growth by decreasing cell proliferation and inducing apoptosis, limiting their migration by limiting cell motility and completely changing their metabolic mode. Thus, NAC-based solutions could be used for the prevention or treatment of ccRCC.
    Keywords:  N-acetylcysteine; antioxidation; clear cell renal cell carcinoma; quantitative proteomics; reversal response
    DOI:  https://doi.org/10.1002/jcb.28226
  17. Scand J Gastroenterol. 2018 Dec 03. 1-7
    High-density and targeted glycoproteomic profiling of serum proteins in pancreatic cancer and intraductal papillary mucinous neoplasm.
    Linus Aronsson, Roland Andersson, Monika Bauden, Bodil Andersson, Thomas Bygott, Daniel Ansari.
       OBJECTIVE: Glycoproteomics is an emerging subfield of proteomics. Tumor-specific variations in protein glycosylation might be potential targets for the development of new cancer diagnostics. Here, we performed high-throughput screening and targeted verification of glycome alterations in serum samples from patients with pancreatic cancer and the precancerous lesion intraductal papillary mucinous neoplasm (IPMN).
    MATERIAL AND METHODS: The glycosylation profile of 1000 proteins was mapped in a discovery cohort comprising serum samples from 16 individuals, including 8 patients with pancreatic cancer and 8 healthy controls. The top 10 glycoprotein biomarker candidates with the highest signal intensity difference in glycosylation levels were evaluated in a cohort consisting of 109 serum samples, including 49 patients with resectable pancreatic cancer, 13 patients with resectable noninvasive IPMN and 47 healthy controls, using a targeted assay.
    RESULTS: Multivariable analysis defined sets of panels comprising CA19-9 and distinctively glycosylated proteins for discrimination between pancreatic cancer, IPMN and healthy controls. A panel including CA 19-9, IL.17E, B7.1 and DR6 gave an AUC of 0.988 at 100% sensitivity at 90% specificity for the discrimination of stage 1 pancreatic cancer and healthy controls. B7.1 was found to be a valuable biomarker for differentiating between IPMN and healthy controls, with better performance alone than CA 19-9.
    CONCLUSIONS: Measurement of protein glycosylation profiles in serum may aid in the early detection of pancreatic cancer and precursor lesions.
    Keywords:  Glycoproteomics; biomarker; early diagnosis; intraductal papillary mucinous neoplasm; pancreatic cancer; serum
    DOI:  https://doi.org/10.1080/00365521.2018.1532020
  18. Brain Sci. 2018 Dec 04. pii: E212. [Epub ahead of print]8(12):
    Multi-Study Proteomic and Bioinformatic Identification of Molecular Overlap between Amyotrophic Lateral Sclerosis (ALS) and Spinal Muscular Atrophy (SMA).
    Darija Šoltić, Melissa Bowerman, Joanne Stock, Hannah K Shorrock, Thomas H Gillingwater, Heidi R Fuller.
      Unravelling the complex molecular pathways responsible for motor neuron degeneration in amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA) remains a persistent challenge. Interest is growing in the potential molecular similarities between these two diseases, with the hope of better understanding disease pathology for the guidance of therapeutic development. The aim of this study was to conduct a comparative analysis of published proteomic studies of ALS and SMA, seeking commonly dysregulated molecules to be prioritized as future therapeutic targets. Fifteen proteins were found to be differentially expressed in two or more proteomic studies of both ALS and SMA, and bioinformatics analysis identified over-representation of proteins known to associate in vesicles and molecular pathways, including metabolism of proteins and vesicle-mediated transport-both of which converge on endoplasmic reticulum (ER)-Golgi trafficking processes. Calreticulin, a calcium-binding chaperone found in the ER, was associated with both pathways and we independently confirm that its expression was decreased in spinal cords from SMA and increased in spinal cords from ALS mice. Together, these findings offer significant insights into potential common targets that may help to guide the development of new therapies for both diseases.
    Keywords:  ER-Golgi trafficking; amyotrophic lateral sclerosis (ALS); bioinformatics; calcium; calreticulin (CALR); endoplasmic reticulum; endoplasmic reticulum-Golgi trafficking; proteomics; spinal muscular atrophy (SMA)
    DOI:  https://doi.org/10.3390/brainsci8120212
  19. Expert Rev Proteomics. 2018 Dec 04.
    Contribution of Plasmodium immunomics: potential impact for serological testing and surveillance of malaria.
    Kokouvi Kassegne, Eniola Michael Abe, Yan-Bin Cui, Shen-Bo Chen, Bin Xu, Wang-Ping Deng, Hai-Mo Shen, Yue Wang, Jun-Hu Chen, Xiao-Nong Zhou.
       INTRODUCTION: Plasmodium vivax and P. knowlesi account together for a considerable share of the global burden of malaria, along with P. falciparum. However, inaccurate diagnosis and undetectable asymptomatic/submicroscopic malaria infections remain very challenging. Blood-stage antigens involved in either invasion of red blood cells or sequestration/cytoadherence of parasitized erythrocytes have been immunomics-characterized, and are vital for the detection of malaria incidence. Areas covered: We review the recent advances in Plasmodium immunomics to discuss serological markers with potential for specific and sensitive diagnosis of malaria. Insights on alternative use of immunomics to assess malaria prevalence are also highlighted. Finally, we provide practical applications of serological markers as diagnostics, with an emphasis on dot immunogold filtration assay which holds promise for malaria diagnosis and epidemiological surveys. Expert commentary: The approach largely contributes to P. falciparum and P. vivax research in identifying promising non-orthologous antigens able to detect malaria incidence and to differentiate between past and recent infections. However, further studies to profiling naturally acquired immune responses are expected in order to help discover/validate serological markers of no cross-seroreactivity and guide control interventions. More so, the application of immunomics to knowlesi infections would help validate the recently identified antigens and contribute to the discovery of additional biomarkers of exposure, immunity, or both.
    Keywords:  Malaria; Plasmodium; dot immunogold filtration assay; immunomics; serodiagnosis and surveillance; serological markers
    DOI:  https://doi.org/10.1080/14789450.2019.1554441
  20. Clin Chim Acta. 2018 Nov 28. pii: S0009-8981(18)30613-2. [Epub ahead of print]
    Quantitative assessment of serum heat shock protein 27 for the diagnosis of epithelial ovarian cancer using targeted proteomics coupled with immunoaffinity enrichment.
    Ting Yang, Pengfei Xu, Lize Gu, Zhiyuan Xu, Weihong Ge, Qing Li, Feifei Xu.
       BACKGROUND: Heat shock protein 27 (HSP27) may take part in the epithelial ovarian cancer (EOC) malignant process because it is elevated in the serum of EOC patients, suggesting that HSP27 may serve as an EOC biomarker to complement the standard serum carbohydrate antigen 125 (CA125) test. Thus, accurate quantification of serum HSP27 would assist the diagnosis of EOC.
    METHODS: Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based targeted proteomics coupled with an immunoaffinity enrichment assay was developed and validated to monitor HSP27 concentrations in serum.
    RESULTS: Tryptic peptide 80QLSSGVSEIR89 was selected as a surrogate analyte for quantification, and an immuno-depleted serum extract was used as a surrogate matrix. Immunoaffinity enrichment was effective for protein enrichment and sensitivity enhancement, and the resulting LOQ was 500 pg/ml (>10-fold increase). Then, serum HSP27 concentrations in EOC patients, benign ovarian tumors patients and healthy volunteers were accurately determined to be 4.95 ± 0.37 ng/ml, 2.98 ± 0.16 ng/ml and 2.82 ± 0.15 ng/ml, respectively, suggesting that the EOC samples had significantly higher concentrations of HSP27 than a sample from benign ovarian tumor patients. The experimental values for the samples were compared with those obtained from enzyme-linked immune sorbent assays (ELISAs). The ROC curve analysis showed that the combined area under the curve (AUC) for CA125 and HSP27 was 0.88, which is significantly superior to that of CA125 alone.
    CONCLUSIONS: Targeted proteomics coupled with immunoaffinity enrichment may provide more accurate quantification of low-abundant proteins.
    Keywords:  Epithelial ovarian cancer; Heat shock protein 27; Immunoaffinity; Liquid chromatography-tandem mass spectrometry; Targeted proteomics
    DOI:  https://doi.org/10.1016/j.cca.2018.11.032
  21. Alzheimers Dement. 2018 Nov 28. pii: S1552-5260(18)33580-5. [Epub ahead of print]
    Quantitative proteomics reveals distinct composition of amyloid plaques in Alzheimer's disease.
    Feng Xiong, Wei Ge, Chao Ma.
       INTRODUCTION: We investigated the proteomic profiles of amyloid plaques (APs) from Alzheimer's disease (AD) and age-matched non-AD brains and APP/PS1 transgenic model mice.
    METHODS: APs and adjacent control regions were collected from fresh-frozen brain sections using laser capture dissection. Proteins were quantitated using tag-labeling coupled high-throughput mass spectra.
    RESULTS: Over 4000 proteins were accurately quantified, and more than 40 were identified as highly enriched in both AD and non-AD APs, including APOE, midkine, VGFR1, and complement C4. Intriguingly, proteins including synaptic structural proteins and complement C1r, C5, and C9 were found to be upregulated in AD APs but not non-AD APs. Moreover, the proteomic pattern of AD APs was distinct from APP/PS1 APs and exhibited some correlation with aging hippocampus.
    DISCUSSION: Our results provide new insight into AP composition. We demonstrate unexpected differences between AD, non-AD, and APP/PS1 mouse APs, which may relate to different pathological processes.
    Keywords:  Alzheimer's disease; Amyloid plaque; Laser dissection; Proteomics
    DOI:  https://doi.org/10.1016/j.jalz.2018.10.006
  22. Proteomes. 2018 Dec 02. pii: E49. [Epub ahead of print]6(4):
    Clinical Proteomics in Colorectal Cancer, a Promising Tool for Improving Personalised Medicine.
    Anaïs Chauvin, François-Michel Boisvert.
      Colorectal cancer is the third most common and the fourth most lethal cancer worldwide. In most of cases, patients are diagnosed at an advanced or even metastatic stage, thus explaining the high mortality. The lack of proper clinical tests and the complicated procedures currently used for detecting this cancer, as well as for predicting the response to treatment and the outcome of a patient's resistance in guiding clinical practice, are key elements driving the search for biomarkers. In the present overview, the different biomarkers (diagnostic, prognostic, treatment resistance) discovered through proteomics studies in various colorectal cancer study models (blood, stool, biopsies), including the different proteomic techniques used for the discovery of these biomarkers, are reviewed, as well as the various tests used in clinical practice and those currently in clinical phase. These studies define the limits and perspectives related to proteomic biomarker research for personalised medicine in colorectal cancer.
    Keywords:  biomarkers; clinical proteomics; colorectal cancer; personalised medicine; predictive biomarkers
    DOI:  https://doi.org/10.3390/proteomes6040049
  23. J Ethnopharmacol. 2018 Nov 28. pii: S0378-8741(18)30616-0. [Epub ahead of print]
    iTRAQ-based quantitative proteomics reveals the neuroprotection of rhubarb in experimental intracerebral hemorrhage.
    Tao Liu, Jing Zhou, Hanjin Cui, Pengfei Li, Jiekun Luo, Yang Wang, Tao Tang.
       ETHNOPHARMACOLOGICAL RELEVANCE: Rhubarb is a traditional Chinese medicine(TCM), that possesses neuroprotective, anti-inflammatory, antibacterial, antioxidative, purgative and anticancer properties, and has been used to treat intracerebral hemorrhage (ICH) and many other diseases.
    AIMS OF THE STUDY: This study aimed to investigate the changes of brain protein in ICH rats treated with rhubarb and to explore the multi-target mechanism of rhubarb in the treatment of ICH via bioinformatics analysis of differentially expressed proteins (DEPs).
    MATERIALS AND METHODS: Rats were subjected to collagenase-induced ICH and then treated orally with 3 or 12g/kg rhubarb daily for 2 days following ICH. After sacrifice, total protein of brain tissue was extracted, and isobaric tag for relative and absolute quantification (iTRAQ)-based liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis was employed to quantitatively identify of the DEPs in two treatment groups compared with the vehicle group. The DEPs were analyzed by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and STRING databases. Bioinformatics Analysis Tool for Molecular mechanism of TCM (BATMAN-TCM) was used to predict the target of rhubarb and western blotting was used for verification.
    RESULTS: In total, 1356 proteins were identified with a 1% false discovery rate (FDR). Among them, 55 DEPs were significantly altered in the sham, vehicle, low dose rhubarb group (LDR, 3g/kg), and high dose rhubarb group (HDR, 12g/kg). Enrichment analysis of GO annotations indicated that rhubarb mainly regulated expression of some neuron projection proteins involved in the response to drug and nervous system development. The dopaminergic synapse pathway was found to be the most significant DEP in the combined analysis of the KEGG and BATMAN-TCM databases. Based on the results of the STRING analysis, oxidative stress (OS), calcium binding protein regulation, vascularization, and energy metabolism were important in the rhubarb therapeutic process.
    CONCLUSION: Rhubarb achieves its effects mainly through the dopaminergic synapse pathway in ICH treatment. The ICH-treating mechanisms of rhubarb may also involve anti-OS, calcium binding protein regulation, angiogenic regulation, and energy metabolism improvement. This study adds new evidence to clinical applications of rhubarb for ICH.
    DOI:  https://doi.org/10.1016/j.jep.2018.11.032
  24. Biomed Pharmacother. 2018 Dec 01. pii: S0753-3322(18)35235-1. [Epub ahead of print]110 275-284
    Urinary proteome analysis of acute hypercoagulable state in rat model induced by ε-aminocaproic acid.
    Jian Jing, Zhenhuan Du, Songyang Ji, Keqiang Han.
      The hypercoagulable state occurs in a group of prothrombotic disorders associated with an increased risk for thromboembolic events, but it is difficult to diagnose due to the lack of available biomarkers. This study aimed to investigate systematic changes of urinary proteome in acute hypercoagulable state induced by certain antifibrinolytics. To reduce the effects of both genetic and environmental factors on the urinary proteome, we used a rat model of acute hypercoagulable state induced by an antifibrinolytic agent ε-aminocaproic acid, resembling human hypercoagulable state. Urine samples were collected during acute hypercoagulable state for analysis by liquid chromatography-tandem mass spectrometry (LCMS/MS). Of 65 significantly changed proteins in acute hypercoagulable state, 38 proteins had human orthologs, and 18 proteins were identified as stable in normal human urine. None of the identified proteins have been found to be clotting factors, but 4 proteins are known to be involved in the regulation of blood coagulation factors. Two proteins were verified as the markers associated with acute hypercoagulable state by Western blot analysis. In addition, four common differential urinary proteins have been found in acute hypercoagulable state induced by another antifibrinolytics tranexamic acid. These four proteins are potential biomarkers for early diagnosis of hypercoagulable state to prevent the development of thrombotic diseases.
    Keywords:  Animal model; Biomarker; Hypercoagulable state; Urinary proteome; ε-Aminocaproic acid
    DOI:  https://doi.org/10.1016/j.biopha.2018.11.148
  25. J Clin Endocrinol Metab. 2018 Dec 03.
    Adipose tissue exosomal proteomic profile reveals a role on placenta glucose metabolism in gestational diabetes mellitus.
    Nanthini Jayabalan, Andrew Lai, Valeska Ormazabal, Stefanie Adam, Dominic Guanzon, Carlos Palma, Katherin Scholz-Romero, Ratana Lim, Thomas Jansson, Harold David McIntyre, Martha Lappas, Carlos Salomon.
       Context: Molecules produced by adipose tissue (AT) function as an endocrine link between maternal AT and fetal growth by regulating placental function in normal and gestational diabetes mellitus (GDM).
    Objective: We hypothesised that AT-derived exosomes from women with GDM carry a specific set of proteins that influences glucose metabolism in placenta.
    Design: Exosomes were isolated from omental AT-conditioned media from pregnant women with normal glucose tolerance (exo-NGT, n=65) and women with GDM (exo-GDM, n=82). SWATH mass spectrometry (MS) was used to construct a small ion library from AT and exosomal proteins followed by ingenuity pathway analysis (IPA) to determine canonical pathways and biofunctions. The effect of exosomes on human placental cells was determined using a Human Glucose Metabolism RT2 Profiler PCR Array.
    Results: The number of exosomes (vesicles/μg-tissue/24h) was significantly (1.7-fold) higher in GDM compared to NGT, and the number of exosomes positively correlated with birthweight Z score. IPA of the exosomal proteins revealed differential expression of the proteins targeting sirtuin (sirt) signalling pathway, oxidative phosphorylation (OXPHOS) and mechanistic target of rapamycin (mTOR) signalling pathways in GDM compared to NGT. Exo-GDM increased the expression of genes associated with glycolysis and gluconeogenesis in placental cells compared to the effect of exo-NGT.
    Conclusions: Our findings are consistent with the possibility that AT exosomes play an important role in mediating the changes in placental function in GDM, which may be responsible for some of the adverse consequences in this pregnancy complication, such as fetal overgrowth.
    DOI:  https://doi.org/10.1210/jc.2018-01599
  26. Proteomics. 2018 Dec 04. e1800213
    In vitro and in vivo Proteomic Comparison of Human Neural Progenitor Cell-Induced Photoreceptor Survival.
    Melissa K Jones, Bin Lu, Dawn Z Chen, Weston R Spivia, August Mercedo, Alexander V Ljubimov, Clive N Svendsen, Jennifer E Van Eyk, Shaomei Wang.
      Retinal degenerative diseases are some of the leading causes of blindness with few treatments. Various cell-based therapies have aimed to slow the progression of vision loss by preserving light-sensing photoreceptor cells. A subretinal injection of human neural progenitor cells (hNPCs) into the Royal College of Surgeons (RCS) rat model of retinal degeneration has aided in photoreceptor survival, though the mechanisms are mainly unknown. Identifying the retinal proteomic changes that occur following hNPC treatment will lead to better understanding of neuroprotection. To mimic the retinal environment following hNPC injection, a co-culture system of retinas and hNPCs was developed. Less cell death occurred in RCS retinal tissue co-cultured with hNPCs than in retinas cultured alone, suggesting that hNPCs provide retinal protection in vitro. Comparison of ex vivo and in vivo retinas identified NRF2-mediated oxidative response signaling as an hNPC-induced pathway. This is the first study to compare proteomic changes following treatment with hNPCs in both an ex vivo and in vivo environment, further allowing the use of ex vivo modeling for mechanisms of retinal preservation. Elucidation of the protein changes in the retina following hNPC treatment may lead to the discovery of mechanisms of photoreceptor survival and its therapeutic for clinical applications. This article is protected by copyright. All rights reserved.
    Keywords:  Human neural progenitor cells; neuroprotection; retinal degeneration; stem cells; transplantation
    DOI:  https://doi.org/10.1002/pmic.201800213
  27. J Exp Clin Cancer Res. 2018 Dec 05. 37(1): 305
    STON2 negatively modulates stem-like properties in ovarian cancer cells via DNMT1/MUC1 pathway.
    Shanshan Xu, Yongfang Yue, Songfa Zhang, Caiyun Zhou, Xiaodong Cheng, Xing Xie, Xinyu Wang, Weiguo Lu.
       BACKGROUND: Cancer stem cells (CSCs) possess abilities of self-renewal and differentiation, have oncogenic potential and are regarded to be the source of cancer recurrence. However, the mechanism by which CSCs maintain their stemness remains largely unclear.
    METHODS: In this study, the cell line-derived ovarian CSCs (OCSCs), 3AO and Caov3, were enriched in serum-free medium (SFM). Differentially expressed proteins were compared between the OCSC subpopulation and parental cells using liquid chromatography (LC)-mass spectrometry (MS)/MS label-free quantitative proteomics. Sphere-forming ability assays, flow cytometry, quantitative real-time polymerase chain reaction (qPCR), western blotting, and in vivo xenograft experiments were performed to evaluate stemness. RNA-sequencing (RNA-seq) and pyrosequencing were used to reveal the mechanism by which STON2 negatively modulates the stem-like properties of ovarian cancer cells.
    RESULTS: Among the 74 most differentially expressed proteins, stonin 2 (STON2) was confirmed to be down-regulated in the OCSC subpopulation. We show that STON2 negatively modulates the stem-like properties of ovarian cancer cells, which are characterized by sphere formation, a CD44+CD24- ratio, and by CSC- and epithelial mesenchymal transition (EMT)-related markers. STON2 knockdown also accelerated tumorigenesis in NOD/SCID mice. Further investigation revealed a downstream target, mucin 1 (MUC1), as up-regulated upon the down regulation of STON2. A decrease in both DNA methyltransferase 1 (DNMT1) expression and methylation in the promoter region of MUC1 was associated with subsequently elevated MUC1 expression, as detected in STON2 knockdown in 3AO and Caov3 cells. Direct DNMT1 knockdown simultaneously elevated MUC1 expression. The functional significance of this STON2-DNMT1/MUC1 pathway is supported by the observation that STON2 overexpression suppresses MUC1-induced sphere formation of OCSCs. The paired expression of STON2 and MUC1 in ovarian cancer specimens was also detected revealing the prognostic value of STON2 expression to be highly dependent on MUC1 expression.
    CONCLUSIONS: Our results imply that STON2 may negatively regulate stemness in ovarian cancer cells via DNMT1-MUC1 mediated epigenetic modification. STON2 is therefore involved in OCSC biology and may represent a therapeutic target for innovative treatments aimed at ovarian cancer eradication.
    Keywords:  Cancer stem cell; DNMT1; MUC1; Ovarian cancer; STON2
    DOI:  https://doi.org/10.1186/s13046-018-0977-y
  28. Curr Opin Otolaryngol Head Neck Surg. 2018 Nov 30.
    Salivaomics in oral cancer.
    Katri Aro, Karolina Kaczor-Urbanowicz, Carmen Martín Carreras-Presas.
       PURPOSE OF REVIEW: The goal of cancer screening is to detect tumor at an early stage, and early cancer detection is the hallmark of successful treatment. In addition to traditional tissue biopsy-based diagnostics, more reliable, inexpensive, and noninvasive methods are required for early diagnosis of cancer. In this review, we highlight some of the recent advancements in the field of salivary diagnostics in oral cancer.
    RECENT FINDINGS: 'Salivaomics' is a broad collection of technologies used to explore different types of molecules contained in saliva. Although many protein and mRNA salivary biomarkers have been identified that can detect oral squamous cell carcinoma (OSCC), none have so far been validated for current clinical use. As the heterogeneity in carcinogenesis and multifactorial cause for OSCC, the most reliable results are gathered with the use of multiple biomarker candidates to improve accuracy and sensitivity of the test used. This further requires sensitive technology to detect salivary biomarkers in low quantities.
    SUMMARY: Large scale studies that incorporate proteomic, transcriptomic, and additional 'omics,' need to be initiated to bring technology to clinical point-of-care applications.
    DOI:  https://doi.org/10.1097/MOO.0000000000000502
  29. Proteomics Clin Appl. 2018 Dec 06. e1800088
    Implementation of clinical proteomics: A step closer to personalised medicine?
    Antonia Vlahou.
      The success of clinical proteomics, per definition, is ultimately defined by the clinical implementation of proteomics findings. Extensive research activity in the field, targeting especially biomarker discovery, has been conducted the past decades, with several studies suggesting a benefit from proteome based application in patient management. This viewpoint article discusses the current status in clinical proteomics with respect to implementation, (as evidenced by use of protein findings in drug labeling and patient stratification), and proposes specific action points for accelerating the biomarker validation process, placing special emphasis on the importance of data and resource sharing. This article is protected by copyright. All rights reserved.
    DOI:  https://doi.org/10.1002/prca.201800088
  30. Int J Biol Macromol. 2018 Dec 02. pii: S0141-8130(18)35624-1. [Epub ahead of print]
    Mass spectrometric imaging of cysteine rich proteins in human skin.
    Lucie Vanickova, Roman Guran, Sándor Kollár, Gabriella Emri, Sona Krizkova, Tomas Do, Zbynek Heger, Ondrej Zitka, Vojtech Adam.
      Looking insight pathological processes, metallothioneins (MTs) are considered to be potential biomarkers for monitoring of a development of various types of malignant disease, such as cancer. The early identification of the MT biomarkers in biological tissues could be important tool for the estimation of appropriate clinical therapy. Therefore here we investigated the application of matrix assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) together with immunohistochemical analyses (IHC) using MT-1/2 antibody for MT detection in formalin-fixed paraffin-embedded (FFPE) biopsy specimens of human skin. Principal component analyses revealed differences in the peptide/protein profiles separating healthy skin from the carcinoma specimens. Statistically significant ion peaks at m/z 6038, 6300, 6676, and 7026 were more frequently detected in squamous cell carcinoma (SCC), basal cell carcinoma (BCC) and melanoma. Using IHC, we found that MT-1/2 was significantly higher in SCC and melanoma compared to healthy skin. Surprisingly, significantly low levels of MT-1/2 were found in BCC. On one side, the results indicate important role of MTs in melanoma occurrence and progression, as on the second side, there are hidden processes associated with MTs based on differences of the occurrence of the MS peaks, which could be associated with cycling of MTs isoforms.
    Keywords:  Immunohistochemistry; MALDI MSI; Melanoma; Metallothionein; Squamous cell carcinoma
    DOI:  https://doi.org/10.1016/j.ijbiomac.2018.11.272
  31. Proteomics. 2018 Dec 04. e1800271
    A Double-Edged Sword:Complement Component 3 in Toxoplasma gondii Infection.
    Wan-Yi Huang, Ya-Pei Wang, Yasser S Mahmmod, Jun-Jie Wang, Tang-Hui Liu, Yu-Xiang Zheng, Xue Zhou, Xiu-Xiang Zhang, Zi-Guo Yuan.
      We artificially infected Sprague Dawley (SD) rats and Kunming (KM) mice with type II Toxoplasma gondii (T. gondii) strain Prugniaud (Pru) to generate toxoplasmosis, which is a fatal disease mediated by T. gondii invasion of the central nervous system (CNS) by unknown mechanisms. We aimed to explore the mechanism of differential susceptibility of mice and rats to T. gondii infection. Therefore, we established a strategy of isobaric tags for relative and absolute quantitation (iTRAQ) to identify differentially expressed proteins (DEPs) in the rats' and the mice's brains compared to the healthy groups. In KM mice, which is susceptible to T. gondii infection, complement component 3 (C3) was upregulated and the tight junction (TJ) pathway showed a disorder. We presumed that T. gondii-stimulated C3 disrupts the TJ of the blood-brain barrier (BBB) in the CNS. This effect allows more T. gondii passing to the brain through the intercellular space. This article is protected by copyright. All rights reserved.
    Keywords:  Toxoplasma gondii; blood-brain barrier; central nervous system; complement component 3; paracellular entry mechanism
    DOI:  https://doi.org/10.1002/pmic.201800271
  32. Biomarkers. 2018 Dec 04. 1-7
    The temporal pattern of immune and inflammatory proteins prior to a recurrent coronary event in post-acute coronary syndrome patients.
    Maxime M Vroegindewey, Rohit M Oemrawsingh, Isabella Kardys, Folkert W Asselbergs, Pim van der Harst, Anton J Oude Ophuis, G Etienne Cramer, Arthur Maas, S Hong Kie The, Alexander J Wardeh, Henk Mouthaan, Eric Boersma, K Martijn Akkerhuis.
       PURPOSE: We assessed the temporal pattern of 29 immune and inflammatory proteins in post-acute coronary syndrome (ACS) patients, prior to the development of recurrent ACS.
    METHODS: High-frequency blood sampling was performed in 844 patients admitted for ACS during one-year follow-up. We conducted a case-control study on the 45 patients who experienced reACS (cases) and two matched event-free patients (controls) per case. Olink Proteomics' immunoassay was used to obtain serum levels of the 29 proteins, expressed in an arbitrary unit on the log2-scale (Normalized Protein eXpression, NPX). Linear mixed-effects models were applied to examine the temporal pattern of the proteins, and to illustrate differences between cases and controls.
    RESULTS: Mean age was 66 ± 12 years and 80% were men. Cases and controls had similar baseline clinical characteristics. During the first 30 days, and after multiple testing correction, cases had significantly higher serum levels of CXCL1 (difference of 1.00 NPX, p = 0.002), CD84 (difference of 0.64 NPX, p = 0.002) and TNFRSF10A (difference of 0.41 NPX, p < 0.001) than controls. After 30 days, serum levels of all 29 proteins were similar in cases and controls. In particular, no increase was observed prior to reACS.
    CONCLUSIONS: Among 29 immune and inflammatory proteins, CXCL1, CD84 and TNFRSF10A were associated with early reACS after initial ACS-admission.
    Keywords:  Acute coronary syndrome; biomarkers; immune and inflammatory system; proteins; proteomics; temporal pattern
    DOI:  https://doi.org/10.1080/1354750X.2018.1539768
  33. J Cell Biochem. 2018 Dec 03.
    Altered levels of focal adhesion and extracellular matrix-receptor interacting proteins were identified in Hailey-Hailey disease by quantitative iTRAQ proteome analysis.
    Dingwei Zhang, Jia Huo, Ruilian Li, Yanfei Zhang, Zhenghui Wang, Xiaoli Li.
      Benign chronic familial pemphigus or Hailey-Hailey disease (HHD, OMIM 169600) is a rare, autosomal dominant blistering skin disorder characterized by suprabasal cell separation (acantholysis) of the epidermis. To date, the proteomic changes in skin lesions from HHD patients has not been reported yet. In this study, a sample of skin lesions from HHD patients was collected for isobaric tags for relative and absolute quantitation to analyze proteome changes compared with unaffected individuals. The 134 differentially expressed proteins were assigned to at least one Gene Ontology term, and 123 annotated proteins with significant matches were assigned to 187 known metabolic or signaling pathways listed in the Kyoto Encyclopedia of Genes and Genomes. Most of the altered proteins in skin lesions of HHD patients were enriched in pathways involved in the PI3K-Akt signaling, focal adhesion, extracellular matrix (ECM)-receptor interaction, and protein digestion and absorption, such as collagen family members, microfibril-associated glycoprotein 4 and plakophilin. The changes of proteins related to cell adhesion, ECM-receptor interaction, and protein folding and glycosylation suggested that strategy targeted to alter cell junction and extracellular microenvironment might provide a potential treatment for HHD.
    Keywords:  Gene Ontology; Hailey-Hailey disease; KEGG; iTRAQ; proteome
    DOI:  https://doi.org/10.1002/jcb.27662
  34. J Cell Biochem. 2018 Dec 03.
    Application of iTRAQ proteomics in identification of the differentially expressed proteins of placenta of pregnancy with preeclampsia.
    Yaling Feng, Yue He, Jianxia Wang, Hua Yuan, Jinfang Zou, Lan Yang, Jianjuan Xu.
       OBJECTIVE: To explore the differential protein profile of preeclampsia and identify its potential biomarker.
    METHODS: Around 20 pregnant women with preeclampsia (preeclampsia group) and 20 normal-term pregnancy (normal group) were collected from 2017 to 2018 in the study. Total protein of placenta tissues was extracted, denaturized, deoxidized, and enzymolyzed. The sample was labeled with isobaric tags for relative and absolute quantitation (iTRAQ) and analyzed with mass spectrum to identify differentially expressed proteins.
    RESULTS: There were 37 proteins, which were differentially expressed with significance (P < 0.05). Among them, 17 proteins were upregulated and 20 proteins were downregulated with significance in the placenta of preeclampsia group compared with control group, those proteins may have an induction or protection function during the development of preeclampsia.
    CONCLUSION: iTRAQ technology can effectively screen the differentially expressed proteins in the placenta, which can effectively diagnose the preeclampsia during pregnancy.
    Keywords:  iTRAQ; preeclampsia; pregnancy
    DOI:  https://doi.org/10.1002/jcb.27819
  35. Exp Cell Res. 2018 Dec 01. pii: S0014-4827(18)31141-8. [Epub ahead of print]
    Styryl-Cinnamate Hybrid Inhibits Glioma by Alleviating Translation, Bioenergetics and Other Key Cellular Responses Leading to Apoptosis.
    Kiran Rawat, Amit Shard, Manali Jadhav, Mayuri Gandhi, Prince Anand, Rituraj Purohit, Yogendra Padwad, Arun K Sinha.
      Gliomas are lethal and aggressive form of brain tumors with resistance to conventional radiation and cytotoxic chemotherapies; inviting continuous efforts for drug discovery and drug delivery. Interestingly, small molecule hybrids are one such pharmacophore that continues to capture interest owing to their pluripotent medicinal effects. Accordingly, we earlier reported synthesis of potent Styryl-cinnamate hybrids (analogues of Salvianolic acid F) along with its plausible mode of action (MOA). We explored iTRAQ-LC/MS-MS technique to deduce differentially expressed landscape of native & phospho-proteins in treated glioma cells. Based on this, Protein-Protein Interactome (PPI) was looked into by employing computational tools and further validated in vitro. We hereby report that the Styryl-cinnamate hybrid, an analogue of natural Salvianolic acid F, alters key regulatory proteins involved in translation, cytoskeleton development, bioenergetics, DNA repair, angiogenesis and ubiquitination. Cell cycle analysis dictates arrest at G0/G1 stage along with reduced levels of cyclin D; involved in G1 progression. We discovered that Styryl-cinnamate hybrid targets glioma by intrinsically triggering metabolite-mediated stress. Various oncological circuits alleviated by the potential drug candidate strongly supports the role of such pharmacophores as anticancer drugs. Although, further analysis of SC hybrid in treating xenografts or solid tumors is yet to be explored but their candidature has gained huge impetus through this study. This study equips us better in understanding the shift in proteomic landscape after treating glioma cells with SC hybrid. It also allows us to elicit molecular targets of this potential drug before progressing to preclinical studies.
    Keywords:  Anti-cancer; G0/G1 arrest; Glioma; Protein-Protein interaction; Salvianolic acid F analogues; Stryl-cinnamate hybrids
    DOI:  https://doi.org/10.1016/j.yexcr.2018.11.015
  36. Int J Biol Macromol. 2018 Dec 01. pii: S0141-8130(18)35937-3. [Epub ahead of print]
    Bioassay of saliva proteins: The best alternative for conventional methods in non-invasive diagnosis of cancer.
    Aziz Eftekhari, Mohammad Hasanzadeh, Simin Sharifi, Solmaz Maleki Dizaj, Rovshan Khalilov, Elham Ahmadian.
      Non-invasive diagnosis of cancer is often the key to effective treatment and patient survival. Saliva as a multi-constituent oral fluid comprises various disease signaling biomarkers, holds great potential for early-stage cancer diagnostics with cost-effective and easy collection, storage, transport and processing. Therefore, detection of biomarkers and proteins in the saliva samples is highly demand. The current review was performed using reliable internet database (mainly PubMed) to provide an overview of the most recent developments on non-invasive diagnosis of cancers in saliva and highlights main challenges and future prospects in sensing of the salivary biomarkers. The conventional detection methods of cancer biomarkers in saliva is discussed in the paper, however, the main focus is on non-invasive diagnosis of cancers in saliva using immunosensing (electrochemical, optical, piezoelectric), DNA based sensors, aptasensors and peptide based bio-assays The reviewed literature revealed that non-invasive cancer detection methods using the mentioned biosensors and without any processing of saliva sample offers a quick, sensitive, specific and cost effective analytical tool. Besides, salivary based detection methods can be used for simultaneous detection of panels of disease specific biomarkers in a real time manner or as home testing kits in near future.
    Keywords:  Biomarkers; Biomedical analysis; Cancer; Non-invasive diagnosis; Protein; Saliva
    DOI:  https://doi.org/10.1016/j.ijbiomac.2018.11.277
  37. J Proteome Res. 2018 Dec 06.
    Characterization of the Blister Fluid Proteome for Pediatric Burn Classification.
    Tuo Zang, Leila Cuttle, Daniel A Broszczak, James A Broadbent, Catherine Tanzer, Tony J Parker.
      Blister fluid (BF) is a novel and viable research matrix for burn injury study, which can reflect both systemic and local micro-environmental responses. The protein abundance in BF from different burn severities were initially observed using a 2D SDS-PAGE approach. Subsequently, a quantitative data independent acquisition (DIA) method - SWATHTM was employed to characterize the proteome of pediatric burn blister fluid. More than 600 proteins were quantitatively profiled in 87 BF samples from different pediatric burn patients. These data were correlated with clinically assessed burn depth and time until complete wound re-epithelialization through several different statistical analyses. Several proteins from these analyses exhibited significant abundance change between different burn depth or re-epithelialization groups, and can be considered as potential biomarker candidates. Further gene ontology (GO) enrichment analysis of the significant proteins revealed the most significant burn related biological processes (BP) that are altered with burn depth including homeostasis and oxygen transport. However, for wounds with re-epithelialization times more or less than 21 days, the significant GO annotations were related to enzyme activity. This quantitative proteomics investigation of burn BF may enable objective classification of burn wound severity and assist with clinical decision-making. Data are available via ProteomeXchange with identifier PXD011102.
    DOI:  https://doi.org/10.1021/acs.jproteome.8b00355
  38. Front Immunol. 2018 ;9 2660
    Antigen Specificity and Clinical Significance of IgG and IgA Autoantibodies Produced in situ by Tumor-Infiltrating B Cells in Breast Cancer.
    Soizic Garaud, Pawel Zayakin, Laurence Buisseret, Undine Rulle, Karina Silina, Alexandre de Wind, Gert Van den Eyden, Denis Larsimont, Karen Willard-Gallo, Aija Linē.
      An important role for tumor infiltrating B lymphocytes (TIL-B) in the immune response to cancer is emerging; however, very little is known about the antigen specificity of antibodies produced in situ. The presence of IgA antibodies in the tumor microenvironment has been noted although their biological functions and clinical significance are unknown. This study used a 91-antigen microarray to examine the IgG and IgA autoantibody repertoires in breast cancer (BC). Tumor and adjacent breast tissue supernatants and plasma from BC patients together with normal breast tissue supernatants and plasma from healthy controls (patients undergoing mammary reduction and healthy blood donors) were analyzed to investigate relationships between autoantibodies and the clinical, histological and immunological features of tumors. Our data show that >84% of the BC samples tested contain autoantibodies to one or more antigens on the array, with ANKRD30BL, COPS4, and CTAG1B being most frequently reactive. Ex vivo TIL-B responses were uncoupled from systemic humoral responses in the majority of cases. A comparison of autoantibody frequencies in supernatants and plasma from patients and controls identified eight antigens that elicit BC-associated autoantibody responses. The overall prevalence of IgG and IgA autoantibodies was similar and while IgG and IgA responses were not linked they did correlate with distinct clinical, pathological and immunological features. Higher levels of ex vivo IgG responses to BC-associated antigens were associated with shorter recurrence-free survival (RFS), HER2 overexpression and lower tumor-infiltrating CD8+ T cell counts. Higher IgA levels were associated with estrogen and progesterone receptor-negative cancers but were not significantly associated with RFS. Furthermore, ex vivo IgA but not IgG autoantibodies reactive to BC-associated antigens were linked with germinal center and early memory B cell maturation and the presence of tertiary lymphoid structures suggesting that these TIL-B are activated in the tumor microenvironment. Overall, our results extend the current understanding of the antigen specificity, the biological and the clinical significance of IgG and IgA autoantibodies produced by BC TIL-B in situ.
    Keywords:  IgA; IgG; autoantibodies; breast cancer; tertiary lymphoid structures; tumor-infiltrating B cells
    DOI:  https://doi.org/10.3389/fimmu.2018.02660
  39. Front Cell Infect Microbiol. 2018 ;8 412
    Archaea Symbiont of T. cruzi Infection May Explain Heart Failure in Chagas Disease.
    Maria de Lourdes Higuchi, Joyce T Kawakami, Renata N Ikegami, Marcia M Reis, Jaqueline de Jesus Pereira, Barbara M Ianni, Paula Buck, Luanda Mara da Silva Oliveira, Marilia H H Santos, Ludhmila A Hajjar, Edimar A Bocchi.
      Background: Archaeal genes present in Trypanosoma cruzi may represent symbionts that would explain development of heart failure in 30% of Chagas disease patients. Extracellular vesicles in peripheral blood, called exosomes (< 0.1 μm) or microvesicles (>0.1 μm), present in larger numbers in heart failure, were analyzed to determine whether they are derived from archaea in heart failure Chagas disease. Methods: Exosomes and microvesicles in serum supernatant from 3 groups were analyzed: heart failure Chagas disease (N = 26), asymptomatic indeterminate form (N = 21) and healthy non-chagasic control (N = 16). Samples were quantified with transmission electron microscopy, flow cytometer immunolabeled with anti-archaemetzincin-1 antibody (AMZ 1, archaea collagenase) and probe anti-archaeal DNA and zymography to determine AMZ1 (Archaeal metalloproteinase) activity. Results: Indeterminate form patients had higher median numbers of exosomes/case vs. heart failure patients (58.5 vs. 25.5, P < 0.001), higher exosome content of AMZ1 antigens (2.0 vs. 0.0; P < 0.001), and lower archaeal DNA content (0.2 vs. 1.5, P = 0.02). A positive correlation between exosomes and AMZ1 content was seen in indeterminate form (r = 0.5, P < 0.001), but not in heart failure patients (r = 0.002, P = 0.98). Higher free archaeal DNA (63.0 vs. 11.1, P < 0.001) in correlation with exosome numbers (r = 0.66, P = 0.01) was seen in heart failure but not in indeterminate form (r = 0.29, P = 0.10). Flow cytometer showed higher numbers of AMZ1 microvesicles in indeterminate form (64 vs. 36, P = 0.02) and higher archaeal DNA microvesicles in heart failure (8.1 vs. 0.9, P < 0.001). Zymography showed strong% collagenase activity in HF group, mild activity in IF compared to non-chagasic healthy group (121 ± 14, 106 ± 13 and 100; P < 0.001). Conclusions: Numerous exosomes, possibly removing and degrading abnormal AMZ1 collagenase, are associated with indeterminate form. Archaeal microvesicles and their exosomes, possibly associated with release of archaeal AMZ1 in heart failure, are future candidates of heart failure biomarkers if confirmed in larger series, and the therapeutic focus in the treatment of Chagas disease.
    Keywords:  Chagas disease; biomarkers; exosomes; heart failure; microvesicles
    DOI:  https://doi.org/10.3389/fcimb.2018.00412
  40. Genes (Basel). 2018 Nov 29. pii: E588. [Epub ahead of print]9(12):
    Systems Analysis of Transcriptomic and Proteomic Profiles Identifies Novel Regulation of Fibrotic Programs by miRNAs in Pulmonary Fibrosis Fibroblasts.
    Steven Mullenbrock, Fei Liu, Suzanne Szak, Xiaoping Hronowski, Benbo Gao, Peter Juhasz, Chao Sun, Mei Liu, Helen McLaughlin, Qiurong Xiao, Carol Feghali-Bostwick, Timothy S Zheng.
      Fibroblasts/myofibroblasts are the key effector cells responsible for excessive extracellular matrix (ECM) deposition and fibrosis progression in both idiopathic pulmonary fibrosis (IPF) and systemic sclerosis (SSc) patient lungs, thus it is critical to understand the transcriptomic and proteomic programs underlying their fibrogenic activity. We conducted the first integrative analysis of the fibrotic programming in these cells at the levels of gene and microRNA (miRNA) expression, as well as deposited ECM protein to gain insights into how fibrotic transcriptional programs culminate in aberrant ECM protein production/deposition. We identified messenger RNA (mRNA), miRNA, and deposited matrisome protein signatures for IPF and SSc fibroblasts obtained from lung transplants using next-generation sequencing and mass spectrometry. SSc and IPF fibroblast transcriptional signatures were remarkably similar, with enrichment of WNT, TGF-β, and ECM genes. miRNA-seq identified differentially regulated miRNAs, including downregulation of miR-29b-3p, miR-138-5p and miR-146b-5p in disease fibroblasts and transfection of their mimics decreased expression of distinct sets of fibrotic signature genes as assessed using a Nanostring fibrosis panel. Finally, proteomic analyses uncovered a distinct "fibrotic" matrisome profile deposited by IPF and SSc fibroblasts compared to controls that highlights the dysregulated ECM production underlying their fibrogenic activities. Our comprehensive analyses of mRNA, miRNA, and matrisome proteomic profiles in IPF and SSc lung fibroblasts revealed robust fibrotic signatures at both the gene and protein expression levels and identified novel fibrogenesis-associated miRNAs whose aberrant downregulation in disease fibroblasts likely contributes to their fibrotic and ECM gene expression.
    Keywords:  gene expression; idiopathic pulmonary fibrosis; interstitial lung disease; myofibroblast; proteomics; systemic sclerosis
    DOI:  https://doi.org/10.3390/genes9120588
  41. Mol Cancer Ther. 2018 Dec 05. pii: molcanther.0710.2018. [Epub ahead of print]
    Cooperative effect of oncogenic MET and PIK3CA in an HGF-dominant environment in breast cancer.
    Shuying Liu, Shunqiang Li, Bailiang Wang, Wenbin Liu, Mihai Gagea, Huiqin Chen, Joohyuk Sohn, Napa Parinyanitikul, Tina Primeau, Kim-Anh Do, George F Vande Woude, John Mendelsohn, Naoto T Ueno, Gordon B Mills, Debu Tripathy, Ana M Gonzalez-Angulo.
      There is compelling evidence that oncogenic MET and PIK3CA signaling pathways contribute to breast cancer. However, the activity of pharmacological targeting of either pathway is modest. Mechanisms of resistance to these monotherapies have not been clarified. Currently commonly used mouse models are inadequate for studying the HGF-MET axis because mouse HGF does not bind human MET. We established human HGF-MET paired mouse models. In this study, we evaluated the cooperative effects of MET and PIK3CA in an environment with involvement of human HGF in vivo. Oncogenic MET/PIK3CA synergistically induced aggressive behavior and resistance to each targeted therapy in an HGF-paracrine environment. Combined targeting of MET and PI3K abrogates resistance. Associated cell signaling changes were explored by functional proteomics. Consistently, combined targeting MET and PI3K inhibited activation of associated oncogenic pathways. We also evaluated the response of tumor cells to HGF-stimulation using breast cancer patient-derived xenografts (PDXs). HGF-stimulation induced significant phosphorylation of MET for all PDX lines detected to varying degrees. However, the levels of phosphorylated MET are not correlated with its expression, suggesting that MET expression level cannot be used as a sole criterion to recruit patients to clinical trials for MET-targeted therapy. All together, our data suggests that combined targeting of MET and PI3K could be a potential clinical strategy for breast cancer patients, where phosphorylated MET and PIK3CA mutation status would be biomarkers for selecting patients who are most likely to derive benefit from these co-targeted therapy.
    DOI:  https://doi.org/10.1158/1535-7163.MCT-18-0710
  42. J Clin Invest. 2018 Dec 03. pii: 123284. [Epub ahead of print]
    Bacterial sepsis triggers an antiviral response that causes translation shutdown.
    Takashi Hato, Bernhard Maier, Farooq Syed, Jered Myslinski, Amy Zollman, Zoya Plotkin, Michael T Eadon, Pierre C Dagher.
      In response to viral pathogens, the host upregulates antiviral genes that suppress translation of viral mRNAs. However, induction of such antiviral responses may not be exclusive to viruses, as the pathways lie at the intersection of broad inflammatory networks that can also be induced by bacterial pathogens. Using a model of Gram-negative sepsis, we show that propagation of kidney damage initiated by a bacterial origin ultimately involves antiviral responses that result in host translation shutdown. We determined that activation of the eukaryotic translation initiation factor 2-α kinase 2/eukaryotic translation initiation factor 2α (Eif2ak2/Eif2α) axis is the key mediator of translation initiation block in late-phase sepsis. Reversal of this axis mitigated kidney injury. Furthermore, temporal profiling of the kidney translatome revealed that multiple genes involved in formation of the initiation complex were translationally altered during bacterial sepsis. Collectively, our findings imply that translation shutdown is indifferent to the specific initiating pathogen and is an important determinant of tissue injury in sepsis.
    Keywords:  Inflammation; Nephrology; Proteomics; Translation
    DOI:  https://doi.org/10.1172/JCI123284
  43. J Cell Sci. 2018 Dec 03. pii: jcs.222612. [Epub ahead of print]
    A SUMOylation dependent switch of Rab7 governs intracellular life and pathogenesis of Salmonella Typhimurium.
    Gayatree Mohapatra, Preksha Gaur, M Prabhakar, Mukesh Singh, Sarika Rana, Shivendra Singh, Navneet Kaur, Smriti Verma, V Krishna, Nirpendra Singh, C V Srikanth.
      Salmonella Typhimurium (ST) is an intracellular pathogen that causes gastroenteritis in humans. Aided by a battery of effector proteins, ST resides intracellularly in a specialized vesicle, called Salmonella-containing vacuole (SCV) that utilizes the host endocytic vesicular-transport pathway (VTP). Here we probed the possible role of SUMOylation, a post-translation modification pathway, in SCV biology. Proteome analysis by complex mass-spectrometry (MS/MS) revealed a dramatically altered SUMO-proteome (SUMOylome) in ST infected cells. Rab7, a component of VTP, was key among several crucial proteins identified in our study. Detailed MS/MS along with in vitro SUMOylation assays and structural docking analysis revealed SUMOylation of Rab7 specifically at Lysine-175. A SUMOylation deficient Rab7 mutant (Rab7K175R) displayed longer half-life, was beneficial to SCV dynamics and functionally blemished. Collectively the data revealed that Rab7 SUMOylation blockade by ST ensures availability of long-lived but functionally compromised Rab7 which was beneficial to the pathogen. Overall this SUMOylation dependent switch of Rab7 controlled by ST is an unexpected mode of VTP pathway regulation, and unveils mechanism of broad interest well beyond Salmonella-host crosstalk.
    Keywords:  PTMs; Rab7; SUMOylation; Salmonella; Salmonella-containing vacuole; Vesicular-transport system
    DOI:  https://doi.org/10.1242/jcs.222612
  44. Allergol Immunopathol (Madr). 2018 Nov 27. pii: S0301-0546(18)30142-3. [Epub ahead of print]
    IgE-mediated allergic responses associated to Ailanthus altissima pollen using an animal model.
    F Mousavi, G A Kardar, Z Pourpak.
       BACKGROUND: Murine models have been widely used in the study of allergy as sensitized mice can produce IgE and/or IgG1in response after the injection of an antigen/adjuvant combination. Ailanthus altissima pollen (AAP) has been recently reported as an emerging aeroallergen in Iran. So far, several AAP candidate allergens by the screening of allergen-specific IgE in the sera from AAP sensitized patients in Iran.
    OBJECTIVE: The aim of the present study was to detect and compare the allergens eliciting an IgE response in a mouse model, and in human, using pollen extract of A. altissima and an immunoproteomics based approach.
    METHODS: The pollen proteins were extracted in phosphate-buffered saline (PBS). Thirty male BALB/c mice were randomly divided into two groups of AP extract sensitized and sham that respectively received AAP PBS extract and a PBS control by intraperitoneal injections at regular intervals. The optimized AAP protein extracts were analyzed using 2D-gel electrophoresis and were subsequently confronted to pooled sera of sensitized mice.
    RESULTS: Two-D gel electrophoresis of AAP extract allowed the separation of 125 protein spots distributed in a wide range of pI and molecular masses. Two-DE immunoblotting using pooled sera of sensitized mice led to the detection of 14 IgE reactive spots with molecular masses ranging from 12 to 40-42kDa.
    CONCLUSION: The results do not correlate with our previous analyses using human AAP-sensitized sera. These findings reflect some differences in the sIgE reactivity to allergenic proteins in animal models.
    Keywords:  2-DE; Ailanthus; Allergy; BALB/C; IgE; Murine; Pollen
    DOI:  https://doi.org/10.1016/j.aller.2018.09.007
  45. J Cancer. 2018 ;9(22): 4128-4138
    Identification of Integrin β1 as a Novel PAG1-Interacting Protein Involved in the Inherent Radioresistance of Human Laryngeal Carcinoma.
    Xiaoxia Dong, Zhiguo Luo, Tiantian Liu, Jingjing Chai, Qing Ke, Li Shen.
      Inherent radioresistance plays a crucial role in the failure of radiotherapy. Using the inherent radioresistant (Hep-2max) and radiosensitive (Hep-2min) cell lines established from the parental cell line Hep-2, we previously reported that phosphoprotein associated with glycosphingolipid-enriched microdomains 1(PAG1) overexpression in laryngeal carcinoma cells was correlated with inherent radioresistant phenotypes. However, the underlying mechanisms of this effect remain unknown. In the present study, we performed a proteomic screen to investigate the interactome of PAG1 in Hep-2max cells resulting in the identification of several interaction partners. Bioinformatic analysis and immunofluorescence experiments indicated the integrin β1 to be a crucial interaction partner of PAG1. PAG1 was also highly expressed in laryngeal carcinoma radioresistant tissues and showed co-localization with integrin β1. In addition, we demonstrated that integrin β1's binding to PAG1 could be interrupted by MβCD, an inhibitor of lipid rafts formation. Moreover, knockdown of integrin β1 by RNA interference sensitized radioresistant cells to irradiation. Importantly, we identified 2 potential interaction sites (Pro216-Arg232 and Asn356-Gly377) in the cytoplasmic domain of PAG1 using high throughput peptide arrays. Taken together, these results suggest that the binding of PAG1 to integrin β1 in lipid rafts is essential for inherent radioresistance of human laryngeal carcinoma.
    Keywords:  PAG1; inherent radioresistance; integrin β1; interaction partner; laryngeal carcinoma
    DOI:  https://doi.org/10.7150/jca.26885
  46. Nat Med. 2018 Dec 03.
    Identification of evolutionarily conserved gene networks mediating neurodegenerative dementia.
    International Frontotemporal Dementia Genomics Consortium
      Identifying the mechanisms through which genetic risk causes dementia is an imperative for new therapeutic development. Here, we apply a multistage, systems biology approach to elucidate the disease mechanisms in frontotemporal dementia. We identify two gene coexpression modules that are preserved in mice harboring mutations in MAPT, GRN and other dementia mutations on diverse genetic backgrounds. We bridge the species divide via integration with proteomic and transcriptomic data from the human brain to identify evolutionarily conserved, disease-relevant networks. We find that overexpression of miR-203, a hub of a putative regulatory microRNA (miRNA) module, recapitulates mRNA coexpression patterns associated with disease state and induces neuronal cell death, establishing this miRNA as a regulator of neurodegeneration. Using a database of drug-mediated gene expression changes, we identify small molecules that can normalize the disease-associated modules and validate this experimentally. Our results highlight the utility of an integrative, cross-species network approach to drug discovery.
    DOI:  https://doi.org/10.1038/s41591-018-0223-3
  47. World J Otorhinolaryngol Head Neck Surg. 2018 Sep;4(3): 175-178
    Exosomes and chronic rhinosinusitis.
    Sarina K Mueller.
      The objective of this manuscripts to review current knowledge regarding exosomes as they relate to the physiology and pathology of the human nose as well as their role as biomarkers of chronic rhinosinusitis with nasal polyps (CRSwNP). Exosomes are 30-150 nm membrane-bound vesicles secreted by virtually all cell types. Exosomes contribute to the rapid inter-epithelial transfer of proteins and mediate innate immunosurveillance and defense mechanisms in the human nasal cavity. Exosomes also protect their cell specific cargo from degradation by nucleases and proteases and mirrorCRS related tissue protein perturbations more effectively than whole mucus. Thus, exosomal isolation and analysis may be used to non-invasively monitor disease severity, prognosis, and potentially even treatment response. Recent studies of exosomes in CRS suggest they can be used to study the immunopathology of chronic sinonasal inflammation. Furthermore, their relative accessibility suggests that exosomal proteomescan be used as non-invasive, serial, and quantitative biosignatures for rhinosinusitis that can be sampled in clinic in order to predict disease severity, prognosis, and treatment response. Exosomal research has also led to important revelations regarding their physiologic function as they seem to play an important role in innate immunosurveillance and defense. However, exosomal research is still nascent and cost-effectiveness as well as feasibility of implementation in the routine workup for CRS have to be further explored.
    DOI:  https://doi.org/10.1016/j.wjorl.2018.07.005
  48. Parasitol Res. 2018 Dec 01.
    Characterization of metalloproteases and serine proteases of Toxoplasma gondii tachyzoites and their effect on epithelial cells.
    Carlos J Ramírez-Flores, Rosalba Cruz-Mirón, Rossana Arroyo, Mónica E Mondragón-Castelán, Tais Nopal-Guerrero, Sirenia González-Pozos, Emmanuel Ríos-Castro, Ricardo Mondragón-Flores.
      Toxoplasma gondii can infect all nucleated cells from warm-blooded organisms. After infection, Toxoplasma spreads throughout the body and migrates across biological barriers, such as the intestinal and blood-brain barriers, as well as the placenta in pregnant women. The mechanisms for parasite dissemination are still unknown; however, proteases could play a role as a virulence factor. The aim of this study was to detect and to characterize proteases in whole-cell extracts and in excretion/secretion products from tachyzoites of the RH strain isolated from infected mice. Both fractions were analyzed by gelatin and casein zymography and by azocasein degradation. The biochemical characterization of proteases included standardization of optimal conditions for their activation, such as pH, the presence of cofactors, and a reducing agent. In both fractions, we detected at least nine gelatin-degrading metalloproteases in the range of 50 to 290 kDa. The proteases present in the excretion/secretion products were found as soluble proteins and not associated with exosome-like vesicles or other secretory vesicles. Moreover, by using casein zymography, it was possible to detect three serine proteases. Exposure of MDCK cells to excretion/secretion products modified the organization of the cell monolayer, and this effect was reverted after washing thoroughly with PBS and inhibition by metalloprotease and serine protease inhibitors. Proteomic analysis of excretion/secretion products identified 19 proteases. These findings suggest that tachyzoites of a highly virulent strain of Toxoplasma use a battery of proteases to modify the epithelium, probably as a strategy to facilitate their tissue dissemination.
    Keywords:  Epithelial alteration; Excretion/secretion products; Exosome-like vesicles; Proteases; Toxoplasma gondii; Zymography
    DOI:  https://doi.org/10.1007/s00436-018-6163-5
  49. iScience. 2018 Nov 15. pii: S2589-0042(18)30212-8. [Epub ahead of print]10 53-65
    Single-Cell Imaging of Metastatic Potential of Cancer Cells.
    Krishna Midde, Nina Sun, Cristina Rohena, Linda Joosen, Harsharan Dhillon, Pradipta Ghosh.
      Molecular imaging of metastatic "potential" is an unvanquished challenge. To engineer biosensors that can detect and measure the metastatic "potential" of single living cancer cells, we carried out a comprehensive analysis of the pan-cancer phosphoproteome to search for actin remodelers required for cell migration, which are enriched in cancers but excluded in normal cells. Only one phosphoprotein emerged, tyr-phosphorylated CCDC88A (GIV/Girdin), a bona fide metastasis-related protein across a variety of solid tumors. We designed multi-modular biosensors that are partly derived from GIV, and because GIV integrates prometastatic signaling by multiple oncogenic receptors, we named them "'integrators of metastatic potential (IMP)." IMPs captured the heterogeneity of metastatic potential within primary lung and breast tumors at steady state, detected those few cells that have acquired the highest metastatic potential, and tracked their enrichment during metastasis. These findings provide proof of concept that IMPs can measure the diversity and plasticity of metastatic potential of tumor cells in a sensitive and unbiased way.
    Keywords:  Cancer; Optical Imaging; Protein Physics
    DOI:  https://doi.org/10.1016/j.isci.2018.11.022
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