bims-prodis 2019-05-19 papers

bims-prodis

Biomed News

on Proteomics in disease

Issue of 2019–05–19
twenty papers selected by
Nancy Gough, Bioserendipity

Quantitative proteomic analyses of CD4+ and CD8+ T cells reveal differentially expressed proteins in multiple sclerosis patients and healthy controls.
Proteomic Investigation of Malignant Major Salivary Gland Tumors.
Protein Fingerprinting of Seminal Plasma Reveals Dysregulation of Exosome-Associated Proteins in Infertile Men with Unilateral Varicocele.
Potential two-step proteomic signature for Parkinson's disease: Pilot analysis in the Harvard Biomarkers Study.
Comparative proteomics analysis of microvesicles in human serum for the evaluation of osteoporosis.
Reproducibility of biomarker identifications from mass spectrometry proteomic data in cancer studies.
A microfluidic chip enables isolation of exosomes and establishment of their protein profiles and associated signaling pathways in ovarian cancer.
Phosphoproteins Involved in the Inhibition of Apoptosis and in Cell Survival in the Leiomyoma.
CE-MS-based urinary biomarkers to distinguish non-significant from significant prostate cancer.
Comparative proteomic analysis between the gingival crevicular fluid and the corresponding periodontal pocket: a preliminary study.
Cashew Tree Pollen: An Unknown Source of IgE-Reactive Molecules.
Phase I/Ib study of olaparib and carboplatin in heavily pretreated recurrent high-grade serous ovarian cancer at low genetic risk.
Systems biology identifies cytosolic PLA2 as a target in vascular calcification treatment.
Albuminuria, the HDL (High-Density Lipoprotein) Proteome, and Coronary Artery Calcification in Type 1 Diabetes Mellitus.
Galectin-7 as a potential biomarker of Stevens-Johnson syndrome/ toxic epidermal necrolysis: Identification by targeted proteomics using causative drug-exposed peripheral blood cells.
Secretome profile selection of optimal IVF embryos by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.
Glycoproteogenomics: a frequent gene polymorphism affects the glycosylation pattern of the human serum fetuin/α-2-HS-glycoprotein.
The role of circulating extracellular vesicles in breast cancer classification and molecular subtyping.
Treatment of keratinocytes with 4-phenylbutyrate in epidermolysis bullosa: Lessons for therapies in keratin disorders.
Analysis of Retrieved Unicompartmental Knee Implants and Tissue: Third-Body Wear as a Potential Contributor to Progression of Arthritis to Adjacent Compartments.

Clin Proteomics. 2019 ;16 19

Quantitative proteomic analyses of CD4+ and CD8+ T cells reveal differentially expressed proteins in multiple sclerosis patients and healthy controls.

Tone Berge, Anna Eriksson, Ina Skaara Brorson, Einar August Høgestøl, Pål Berg-Hansen, Anne Døskeland, Olav Mjaavatten, Steffan Daniel Bos, Hanne F Harbo, Frode Berven.

   Background: Multiple sclerosis (MS) is an autoimmune, neuroinflammatory disease, with an unclear etiology. However, T cells play a central role in the pathogenesis by crossing the blood-brain-barrier, leading to inflammation of the central nervous system and demyelination of the protective sheath surrounding the nerve fibers. MS has a complex inheritance pattern, and several studies indicate that gene interactions with environmental factors contribute to disease onset.
Methods: In the current study, we evaluated T cell dysregulation at the protein level using electrospray liquid chromatography-tandem mass spectrometry to get novel insights into immune-cell processes in MS. We have analyzed the proteomic profiles of CD4+ and CD8+ T cells purified from whole blood from 13 newly diagnosed, treatment-naive female patients with relapsing-remitting MS and 14 age- and sex-matched healthy controls.
Results: An overall higher protein abundance was observed in both CD4+ and CD8+ T cells from MS patients when compared to healthy controls. The differentially expressed proteins were enriched for T-cell specific activation pathways, especially CTLA4 and CD28 signaling in CD4+ T cells. When selectively analyzing proteins expressed from the genes most proximal to > 200 non-HLA MS susceptibility polymorphisms, we observed differential expression of eight proteins in T cells between MS patients and healthy controls, and there was a correlation between the genotype at three MS genetic risk loci and protein expressed from proximal genes.
Conclusion: Our study provides evidence for proteomic differences in T cells from relapsing-remitting MS patients compared to healthy controls and also identifies dysregulation of proteins encoded from MS susceptibility genes.

Keywords:  Autoimmunity; Mass spectrometry; Multiple sclerosis; Proteomics; SNPs; T cells

DOI:  https://doi.org/10.1186/s12014-019-9241-5
Head Neck Pathol. 2019 May 16.

Proteomic Investigation of Malignant Major Salivary Gland Tumors.

Veronica Seccia, Elena Navari, Elena Donadio, Claudia Boldrini, Federica Ciregia, Maurizio Ronci, Antonio Aceto, Iacopo Dallan, Antonio Lucacchini, Augusto Pietro Casani, Maria Rosa Mazzoni, Laura Giusti.

  The purpose of this study was to define the proteome profile of fine needle aspiration (FNA) samples of malignant major salivary gland tumors (MSGT) compared to benign counterparts, and to evaluate potential clinical correlations and future applications. Patients affected by MSGT (n = 20), pleomorphic adenoma (PA) (n = 37) and Warthin's tumor (WT) (n = 14) were enrolled. Demographic, clinical and histopathological data were registered for all patients. FNA samples were processed to obtain the protein extracts. Protein separation was obtained by two-dimensional electrophoresis (2-DE) and proteins were identified by mass spectrometry. Western blot analysis was performed to validate the 2-DE results. Statistical differences between groups were calculated by the Mann-Whitney U test for non-normal data. Spearman's rank correlation coefficient was calculated to evaluate correlations among suggested protein biomarkers and clinical parameters. Twelve and 27 differentially expressed spots were found for MSGT versus PA and MSGT versus WT, respectively. Among these, annexin-5, cofilin-1, peptidyl-prolyl-cis-trans-isomerase-A and F-actin-capping-alpha-1 were able to differentiate MSGT from PA, WT, and healthy samples. Moreover, STRING analysis suggested cofilin-1 as a key node of protein interactions. Some of the overexpressed proteins are related to some clinical factors of our cohort, such as survival and outcome. Our results suggest potential protein biomarkers of MSGT, which could allow for more appropriate treatment plans, as well as shedding light on the molecular pathways involved.

Keywords:  Biomarkers; Major salivary glands; Parotid cancer; Proteomics; Two-dimensional electrophoresis (2-DE)

DOI:  https://doi.org/10.1007/s12105-019-01040-2
World J Mens Health. 2019 Apr 03.

Protein Fingerprinting of Seminal Plasma Reveals Dysregulation of Exosome-Associated Proteins in Infertile Men with Unilateral Varicocele.

Manesh Kumar Panner Selvam, Ashok Agarwal, Rakesh Sharma, Luna Samanta, Sajal Gupta, Tânia R Dias, Ana Dias Martins.

   PURPOSE: Aberrant expression of seminal plasma proteins are associated with altered homeostasis that may affect the fertilizing ability of spermatozoa. However, the precise roles of seminal exosomes on sperm function remain unclear. The objective of this study was to identify the differentially expressed proteins (DEPs) associated with varicocele-mediated infertility by comparing seminal plasma protein profile of unilateral varicocele patients with proven fertile donors.
MATERIALS AND METHODS: Semen samples were obtained from 10 proven fertile donors with normal semen parameters and 33 infertile patients with unilateral varicocele. For proteomic analysis, 5 samples from each group were pooled and run in triplicate. Key DEPs (ANXA2, TF, CD63, KIF5B, SEMG1) associated with the exosome function were selected by bioinformatic tools and validated using Western blotting.
RESULTS: A total of 47 seminal plasma proteins were differentially expressed in unilateral varicocele patients compared to fertile donors. Validation of exosome-associated DEPs in unilateral varicocele patients (n=7) and fertile donors (n=7) revealed significant upregulation of ANXA2 (p=0.0016) and downregulation of KIF5B (p=0.009). The main upstream regulators of the DEPs in seminal plasma of unilateral varicocele group were androgen receptor, YB1 and NRF2.
CONCLUSIONS: This is the first report to identify DEPs in seminal plasma of unilateral varicocele patients compared to fertile donors. Based on the detection of DEPs associated with exosomal function, Western blotting was used to validate the presence of defective exosome machinery in seminal plasma of unilateral varicocele patients. KIF5B and ANXA2 can be utilized as potential biomarkers of infertility in unilateral varicocele patients.

Keywords:  Exosomes; Male infertility; Proteomics; Seminal plasma; Varicocele

DOI:  https://doi.org/10.5534/wjmh.180108
Alzheimers Dement (Amst). 2019 Dec;11 374-382

Potential two-step proteomic signature for Parkinson's disease: Pilot analysis in the Harvard Biomarkers Study.

Sid E O'Bryant, Melissa Edwards, Fan Zhang, Leigh A Johnson, James Hall, Yuliya Kuras, Clemens R Scherzer.

   Introduction: We sought to determine if our previously validated proteomic profile for detecting Alzheimer's disease would detect Parkinson's disease (PD) and distinguish PD from other neurodegenerative diseases.
Methods: Plasma samples were assayed from 150 patients of the Harvard Biomarkers Study (PD, n = 50; other neurodegenerative diseases, n = 50; healthy controls, n = 50) using electrochemiluminescence and Simoa platforms.
Results: The first step proteomic profile distinguished neurodegenerative diseases from controls with a diagnostic accuracy of 0.94. The second step profile distinguished PD cases from other neurodegenerative diseases with a diagnostic accuracy of 0.98. The proteomic profile differed in step 1 versus step 2, suggesting that a multistep proteomic profile algorithm to detecting and distinguishing between neurodegenerative diseases may be optimal.
Discussion: These data provide evidence of the potential use of a multitiered blood-based proteomic screening method for detecting individuals with neurodegenerative disease and then distinguishing PD from other neurodegenerative diseases.

Keywords:  Blood biomarkers; Diagnostic accuracy; Parkinson's disease; Precision medicine; Proteomics

DOI:  https://doi.org/10.1016/j.dadm.2019.03.001
Electrophoresis. 2019 May 12.

Comparative proteomics analysis of microvesicles in human serum for the evaluation of osteoporosis.

Chunhui Huo, Yinghua Li, Zhi Qiao, Zhi Shang, Chengxi Cao, Yang Hong, Hua Xiao.

  Osteoporosis is an emerging health issue worldwide. Due to the decrease of bone mineral density and the deterioration of skeletal microarchitecture, osteoporosis could lead to increased bone fragility and higher fracture risk. Since lack of specific symptoms, novel serum proteomic indicators are urgently needed for the evaluation of osteoporosis. Microvesicles (MVs) are important messengers widely present in body fluids and have emerged as novel targets for the diagnosis of multiple diseases. In this study, MVs were successfully isolated from human serum and comprehensively characterized. Comparative proteomics analysis revealed differential MVs protein profiling in normal subjects, osteopenia patients, and osteoporosis patients. In total, about 200 proteins were identified and quantified from serum MVs, among which 19 proteins were upregulated (fold change > 2) and 5 proteins were downregulated (fold change < 0.5) in osteopenia group and osteoporosis group when compared to the normal group. Three protein candidates were selected for initial verification, including Vinculin, Filamin A, and Profilin 1. Profilin 1 was further pre-validated in an independent sample set, which could differentiate osteoporosis group from osteopenia group and normal group (p < 0.05). Our data collectively demonstrate that serum MVs proteome can be valuable indicators for the evaluation and diagnostics of bone loss disease. This article is protected by copyright. All rights reserved.

Keywords:  microvesicles; osteopenia; osteoporosis; proteomics; serum

DOI:  https://doi.org/10.1002/elps.201900130
Stat Appl Genet Mol Biol. 2019 May 11. pii: /j/sagmb.2019.18.issue-3/sagmb-2018-0039/sagmb-2018-0039.xml. [Epub ahead of print]18(3):

Reproducibility of biomarker identifications from mass spectrometry proteomic data in cancer studies.

Yulan Liang, Adam Kelemen, Arpad Kelemen.

  Reproducibility of disease signatures and clinical biomarkers in multi-omics disease analysis has been a key challenge due to a multitude of factors. The heterogeneity of the limited sample, various biological factors such as environmental confounders, and the inherent experimental and technical noises, compounded with the inadequacy of statistical tools, can lead to the misinterpretation of results, and subsequently very different biology. In this paper, we investigate the biomarker reproducibility issues, potentially caused by differences of statistical methods with varied distribution assumptions or marker selection criteria using Mass Spectrometry proteomic ovarian tumor data. We examine the relationship between effect sizes, p values, Cauchy p values, False Discovery Rate p values, and the rank fractions of identified proteins out of thousands in the limited heterogeneous sample. We compared the markers identified from statistical single features selection approaches with machine learning wrapper methods. The results reveal marked differences when selecting the protein markers from varied methods with potential selection biases and false discoveries, which may be due to the small effects, different distribution assumptions, and p value type criteria versus prediction accuracies. The alternative solutions and other related issues are discussed in supporting the reproducibility of findings for clinical actionable outcomes.

Keywords:  false discovery rate; mass spectrometry; ovarian cancer; p value; proteomics; reproducibility

DOI:  https://doi.org/10.1515/sagmb-2018-0039
Cancer Res. 2019 May 16. pii: canres.3538.2018. [Epub ahead of print]

A microfluidic chip enables isolation of exosomes and establishment of their protein profiles and associated signaling pathways in ovarian cancer.

Kalpana Deepa Priya Dorayappan, Miranda L Gardner, Colin L Hisey, Roman A Zingarelli, Brentley Q Smith, Michelle D S Lightfoot, Rajan Gogna, Meghan M Flannery, John Hays, Derek J Hansford, Michael A Freitas, Lianbo Yu, David E Cohn, Karuppaiyah Selvendiran.

Due to limits on specificity and purity to allow for in-depth protein profiling, a standardized method for exosome isolation has yet to be established. In this study, we describe a novel, in-house microfluidic-based device to isolate exosomes from culture media and patient samples. This technology overcomes contamination issues because sample separation is based on the expression of highly specific surface markers CD63 and EpCAM. Top exosome proteins were identified based on their fold change and statistical significance between groups. Mass spectrometry revealed over 25 exosome proteins that are differentially expressed in high-grade serous ovarian cancer (HGSOC) cell lines compared to normal cells - ovarian surface epithelia cells (OSE) and fallopian tube secretory epithelial cells (FTSEC). Ingenuity Pathway Analysis identified STAT3 and HGF as top regulator proteins. We further validated exosome proteins of interest (pSTAT3, HGF, and IL-6) in HGSOC samples of origin-based cell lines (OVCAR-8, FTSEC) and in early stage HGSOC patient serum exosome samples using LC-MS/MS and Proximity Extension Assay (PEA). Our microfluidic device will allow us to make new discoveries for exosome-based biomarkers for the early detection of HGSOC and contribute to the development of new targeted therapies based on signaling pathways that are unique to HGSOC, both of which could improve the outcome for women with HGSOC.

DOI: https://doi.org/10.1158/0008-5472.CAN-18-3538
J Clin Med. 2019 May 16. pii: E691. [Epub ahead of print]8(5):

Phosphoproteins Involved in the Inhibition of Apoptosis and in Cell Survival in the Leiomyoma.

Blendi Ura, Lorenzo Monasta, Giorgio Arrigoni, Ilaria Battisti, Danilo Licastro, Giovanni Di Lorenzo, Federico Romano, Michelangelo Aloisio, Isabel Peterlunger, Guglielmo Stabile, Federica Scrimin, Giuseppe Ricci.

  Uterine leiomyomas are benign smooth muscle cell tumors originating from the myometrium. In this study we focus on leiomyoma and normal myometrium phosphoproteome, to identify differentially phosphorylated proteins involved in tumorigenic signaling pathways, and in anti-apoptotic processes and cell survival. We obtained paired tissue samples of seven leiomyomas and adjacent myometria and analyzed the phosphoproteome by two-dimensional gel electrophoresis (2-DE) combined with immobilized metal affinity chromatography (IMAC) and Pro-Q Diamond phosphoprotein gel stain. We used mass spectrometry for protein identification and Western blotting for 2-DE data validation. Quantities of 33 proteins enriched by the IMAC approach were significantly different in the leiomyoma if compared to the myometrium. Bioinformatic analysis revealed ten tumorigenic signaling pathways and four phosphoproteins involved in both the inhibition of apoptosis and cell survival. Our study highlights the involvement of the phosphoproteome in leiomyoma growth. Further studies are needed to understand the role of phosphorylation in leiomyoma. Our data shed light on mechanisms that still need to be ascertained, but could open the path to a new class of drugs that not only can block the growth, but could also lead to a significant reduction in tumor size.

Keywords:  2-DE; leiomyoma; mass spectrometry; myometrium; phosphoproteomics

DOI:  https://doi.org/10.3390/jcm8050691
Br J Cancer. 2019 May 16.

CE-MS-based urinary biomarkers to distinguish non-significant from significant prostate cancer.

Maria Frantzi, Enrique Gomez Gomez, Ana Blanca Pedregosa, José Valero Rosa, Agnieszka Latosinska, Zoran Culig, Axel S Merseburger, Raul M Luque, María José Requena Tapia, Harald Mischak, Julia Carrasco Valiente.

BACKGROUND: Prostate cancer progresses slowly when present in low risk forms but can be lethal when it progresses to metastatic disease. A non-invasive test that can detect significant prostate cancer is needed to guide patient management.
METHODS: Capillary electrophoresis/mass spectrometry has been employed to identify urinary peptides that may accurately detect significant prostate cancer. Urine samples from 823 patients with PSA (<15 ng/ml) were collected prior to biopsy. A case-control comparison was performed in a training set of 543 patients (nSig = 98; nnon-Sig = 445) and a validation set of 280 patients (nSig = 48, nnon-Sig = 232). Totally, 19 significant peptides were subsequently combined by a support vector machine algorithm.
RESULTS: Independent validation of the 19-biomarker model in 280 patients resulted in a 90% sensitivity and 59% specificity, with an AUC of 0.81, outperforming PSA (AUC = 0.58) and the ERSPC-3/4 risk calculator (AUC = 0.69) in the validation set.
CONCLUSIONS: This multi-parametric model holds promise to improve the current diagnosis of significant prostate cancer. This test as a guide to biopsy could help to decrease the number of biopsies and guide intervention. Nevertheless, further prospective validation in an external clinical cohort is required to assess the exact performance characteristics.

DOI: https://doi.org/10.1038/s41416-019-0472-z
J Biol Regul Homeost Agents. 2019 May 15. 33(3):

Comparative proteomic analysis between the gingival crevicular fluid and the corresponding periodontal pocket: a preliminary study.

C Bertoldi, S Bergamini, M Ferrari, M Lalla, E Bellei, S Spinato, A Tomasi, E Monari.

Keywords: gingival crevicular fluid; inflammation; periodontal disease; periodontal poket tissue; proteomic
Int J Mol Sci. 2019 May 15. pii: E2397. [Epub ahead of print]20(10):

Cashew Tree Pollen: An Unknown Source of IgE-Reactive Molecules.

Daniele Danella Figo, Karine De Amicis, Denise Neiva Santos de Aquino, Fabiane Pomiecinski, Gabriele Gadermaier, Peter Briza, Clovis Eduardo Santos Galvão, Jônatas Bussador do Amaral, Carlo de Oliveira Martins, Fabio Fernandes Morato Castro, Jorge Kalil, Keity Souza Santos.

  Pollinosis is sub-diagnosed and rarely studied in tropical countries. Cashew tree pollen has been reported as an allergen source although the knowledge of its immunoglobulin E (IgE)-reactive molecules is lacking. Therefore, this work aimed to identify IgE-reactive molecules and provide a proteomic profile of this pollen. From the 830 proteins identified by shotgun analysis, 163 were annotated to gene ontology, and a list of 39 proteins filtered for high confidence was submitted to the Allfam database where nine were assigned to allergenic families. Thus, 12 patients from the northeast of Brazil with persistent allergic rhinitis and aggravation of symptoms during cashew flowering season were selected. Using a 2D-based approach, we identified 20 IgE-reactive proteins, four already recognized as allergens, including a homolog of the birch isoflavone-reductase (Bet v 6). IgE-reactivity against the extract in native form was confirmed for five patients in ELISA, with three being positive for Bet v 6. Herein, we present a group of patients with rhinitis exposed to cashew tree pollen with the first description of IgE-binding proteins and a proteomic profile of the whole pollen. Cashew tree pollen is considered an important trigger of rhinitis symptoms in clinical practice in the northeast of Brazil, and the elucidation of its allergenic molecules can improve the diagnostics and treatment for allergic patients.

Keywords:  Brazil; aeroallergens; novel allergens; pollinosis; proteome; shotgun analysis

DOI:  https://doi.org/10.3390/ijms20102397
Oncotarget. 2019 Apr 23. 10(30): 2855-2868

Phase I/Ib study of olaparib and carboplatin in heavily pretreated recurrent high-grade serous ovarian cancer at low genetic risk.

Erika J Lampert, John L Hays, Elise C Kohn, Christina M Annunziata, Lori Minasian, Minshu Yu, Nicolas Gordon, Tristan M Sissung, Victoria L Chiou, William D Figg, Nicole Houston, Jung-Min Lee.

  Purpose: To investigate maximum tolerated dose (MTD), activity and predictive biomarkers of olaparib with carboplatin in BRCA wild-type (BRCAwt) high grade serous ovarian carcinoma (HGSOC) patients. Methods: A 3+3 dose escalation study examined olaparib capsules (400 mg twice daily [BID], days 1-7) with carboplatin (AUC3-5 on day 1) every 21 days for 8 cycles, followed by olaparib 400 mg BID maintenance. Blood and tumor biopsy samples were collected pre- and on-treatment in the expansion cohort for PAR levels and proteomic endpoints. Results: 30 patients (median 7 prior regimens [2-12], 63% (19/30) platinum-resistant) were enrolled. Dose-limiting toxicity was thrombocytopenia/neutropenia, and infection with carboplatin AUC5 (2/6 patients). MTD was olaparib 400 mg BID + carboplatin AUC4. Grade 3/4 adverse events (>10%) included neutropenia (23%), thrombocytopenia (20%), and anemia (13%). Five of 25 (20%) evaluable patients had partial response (PR; median 4.5 months [3.3-9.5]). Clinical benefit rate (PR + stable disease ≥4 months) was 64% (16/25). A greater decrease in tissue PAR levels was seen in the clinical benefit group versus no benefit (median normalized linear change -1.84 [-3.39- -0.28] vs 0.51 [-0.27- 1.29], p = 0.001) and a DNA repair score by proteomics did not correlate with response. Conclusions: The olaparib and carboplatin combination is tolerable and has clinical benefit in subsets of heavily pretreated BRCAwt HGSOC, independent of platinum sensitivity.

Keywords:  BRCA wild type; carboplatin; high-grade serous ovarian cancer; olaparib

DOI:  https://doi.org/10.18632/oncotarget.26869
JCI Insight. 2019 May 16. pii: 125638. [Epub ahead of print]4(10):

Systems biology identifies cytosolic PLA2 as a target in vascular calcification treatment.

Joost P Schanstra, Trang Td Luong, Manousos Makridakis, Sophie Van Linthout, Vasiliki Lygirou, Agnieszka Latosisnska, Ioana Alesutan, Beate Boehme, Nadeshda Schelski, Dirk Von Lewinski, William Mullen, Stuart Nicklin, Christian Delles, Guylène Feuillet, Colette Denis, Florian Lang, Burkert Pieske, Jean-Loup Bascands, Harald Mischak, Jean-Sebastien Saulnier-Blache, Jakob Voelkl, Antonia Vlahou, Julie Klein.

  Although cardiovascular disease (CVD) is the leading cause of morbimortality worldwide, promising new drug candidates are lacking. We compared the arterial high-resolution proteome of patients with advanced versus early-stage CVD to predict, from a library of small bioactive molecules, drug candidates able to reverse this disease signature. Of the approximately 4000 identified proteins, 100 proteins were upregulated and 52 were downregulated in advanced-stage CVD. Arachidonyl trifluoromethyl ketone (AACOCF3), a cytosolic phospholipase A2 (cPLA2) inhibitor was predicted as the top drug able to reverse the advanced-stage CVD signature. Vascular cPLA2 expression was increased in patients with advanced-stage CVD. Treatment with AACOCF3 significantly reduced vascular calcification in a cholecalciferol-overload mouse model and inhibited osteoinductive signaling in vivo and in vitro in human aortic smooth muscle cells. In conclusion, using a systems biology approach, we have identified a potentially new compound that prevented typical vascular calcification in CVD in vivo. Apart from the clear effect of this approach in CVD, such strategy should also be able to generate novel drug candidates in other complex diseases.

Keywords:  Atherosclerosis; Cardiovascular disease; Vascular Biology

DOI:  https://doi.org/10.1172/jci.insight.125638
Arterioscler Thromb Vasc Biol. 2019 May 16. ATVBAHA119312556

Albuminuria, the HDL (High-Density Lipoprotein) Proteome, and Coronary Artery Calcification in Type 1 Diabetes Mellitus.

DCCT/EDIC Research Group

  Objective- Albuminuria is an important risk factor for cardiovascular disease in diabetes mellitus. We determined whether albuminuria associates with alterations in the proteome of HDL (high-density lipoprotein) of subjects with type 1 diabetes mellitus and whether those alterations associated with coronary artery calcification. Approach and Results- In a cross-sectional study of 191 subjects enrolled in the DCCT (Diabetes Control and Complications Trial)/EDIC study (Epidemiology of Diabetes Interventions and Complications), we used isotope dilution tandem mass spectrometry to quantify 46 proteins in HDL. Stringent statistical analysis demonstrated that 8 proteins associated with albuminuria. Two of those proteins, AMBP (α1-microglobulin/bikunin precursor) and PTGDS (prostaglandin-H2 D-isomerase), strongly and positively associated with the albumin excretion rate ( P<10-6). Furthermore, PON (paraoxonase) 1 and PON3 levels in HDL strongly and negatively associated with the presence of coronary artery calcium, with odds ratios per 1-SD difference of 0.63 (95% CI, 0.43-0.92; P=0.018) for PON1 and 0.59 (95% CI, 0.40-0.87; P=0.0079) for PON3. Only 1 protein, PON1, associated with both albumin excretion rate and coronary artery calcification. Conclusions- Our observations indicate that the HDL proteome is remodeled in type 1 diabetes mellitus subjects with albuminuria. Moreover, low concentrations of the antiatherosclerotic protein PON1 in HDL associated with both albuminuria and coronary artery calcification, raising the possibility that alterations in HDL protein cargo mediate, in part, the known association of albuminuria with cardiovascular risk in type 1 diabetes mellitus (Graphic Abstract).

Keywords:  albuminuria; isotopes; kidney diseases; odds ratio; triglycerides

DOI:  https://doi.org/10.1161/ATVBAHA.119.312556
J Allergy Clin Immunol Pract. 2019 May 14. pii: S2213-2198(19)30449-0. [Epub ahead of print]

Galectin-7 as a potential biomarker of Stevens-Johnson syndrome/ toxic epidermal necrolysis: Identification by targeted proteomics using causative drug-exposed peripheral blood cells.

Natsumi Hama, Keiko Nishimura, Akito Hasegawa, Akihiko Yuki, Hideaki Kume, Jun Adachi, Manao Kinoshita, Youichi Ogawa, Saeko Nakajima, Takashi Nomura, Hideaki Watanabe, Yoshiko Mizukawa, Takeshi Tomonaga, Hiroshi Shimizu, Riichiro Abe.

DOI: https://doi.org/10.1016/j.jaip.2019.05.002
J Assist Reprod Genet. 2019 May 15.

Secretome profile selection of optimal IVF embryos by matrix-assisted laser desorption ionization time-of-flight mass spectrometry.

Ray K Iles, Fady I Sharara, Raminta Zmuidinaite, Galal Abdo, Sholeh Keshavarz, Stephen A Butler.

   PURPOSE: Selecting an embryo at the transfer stage with the best chance of a successful pregnancy is still largely dependent on preceding subjective evaluation of morphokinetics. Expensive prenatal genomic profiling has been so far proved ineffective. Proteomics and metabolomics are promising new approaches to assess embryo viability, but methodologies are often complex and do not lend themselves to rapid analysis in the critical time between blastocyst formation and embryo transfer. Here, we used matrix-assisted laser desorption ionization time-of-flight (MALDI ToF) mass spectrometry to assess the secretome of blastocysts in the minutes prior to embryo transfer and correlated spectral features with pregnancy outcome.
METHODS: Four hundred one samples of spent blastocyst culture media were collected from embryo cultures at the time of embryo transfer, of which 136 were used to construct the predictive model. The media samples were frozen at - 20 °C and stored for analysis. Sample analysis was conducted in batches using 1 μl of spent embryo in direct MALDI ToF mass spectral analysis. Quantitative characteristics within this mass range (2000-17,000 m/z) were used to generate a score for selected mass regions (bins) in order to predict pregnancy outcome for each sample.
RESULTS: With a simple algorithm based on nine mass bins within the 2000-10,000 m/z region, it was possible to identify samples with the best chance of becoming an ongoing pregnancy (positive predictive value of 82.9%, p = 0.0018).
CONCLUSION: A simple, direct and rapid analysis of spent culture fluid from blastocysts at the point of embryo transfer can quickly identify optimal embryos with the best chance of achieving ongoing pregnancy. Methods like this, which take less than 20 min to perform, could dramatically improve the approach to embryo selection and live births.

Keywords:  Blastocyst; Culture media; Mass spectrometry; Non-invasive; Proteomics; Secretome

DOI:  https://doi.org/10.1007/s10815-019-01444-7
Mol Cell Proteomics. 2019 May 16. pii: mcp.RA119.001411. [Epub ahead of print]

Glycoproteogenomics: a frequent gene polymorphism affects the glycosylation pattern of the human serum fetuin/α-2-HS-glycoprotein.

Yu-Hsien Lin, Jing Zhu, Alexander B Meijer, Franc Vojtech, Albert J R Heck.

  Fetuin, also known as α-2-HS-glycoprotein (gene name: AHSG), is one of the more abundant glycoproteins secreted into the bloodstream. There are two frequently occurring alleles of human AHSG, resulting in three genotypes (AHSG*1, AHSG*2, and heterozygous AHSG1/2). The backbone amino acid sequences of fetuin coded by the AHSG*1 and AHSG*2 genes differ in two amino acids including one known O-glycosylation site (aa position 256). Although fetuin levels have been extensively studied, the originating genotype is often ignored in such analysis. As fetuin has been suggested repeatedly as a potential biomarker for several disorders, the question whether the gene polymorphism affects the fetuin profile is of great interest. In this work, we describe detailed proteoform profiles of fetuin, isolated from serum of 10 healthy and 10 septic patient individuals and investigate potential glycoproteogenomics correlations, e.g. how gene polymorphisms affect glycosylation. We established an efficient method for fetuin purification from individuals' serum using ion-exchange chromatography. Subsequently, we performed hybrid mass spectrometric approaches integrating data from native mass spectra and peptide-centric MS analysis. Our data reveal a crucial effect of the gene polymorphism on the glycosylation pattern of fetuin. Moreover, we clearly observed increased fucosylation in the samples derived from the septic patients. Our serum proteoform analysis, targeted at one protein obtained from 20 individuals, exposes the wide variability in proteoform profiles, which should be taken into consideration when using fetuin as biomarker. Importantly, focusing on a single or few proteins, the quantitative proteoform profiles can provide, as shown here, already ample data to classify individuals by genotype and disease state.

Keywords:  Glycoproteins*; Glycoproteomics; Plasma or serum analysis; Post-translational modifications*; Protein Identification*; fetuin

DOI:  https://doi.org/10.1074/mcp.RA119.001411
Breast J. 2019 May 12.

The role of circulating extracellular vesicles in breast cancer classification and molecular subtyping.

Khrystyna Platko, Sandor Haas-Neill, Tariq Aziz, Khalid Al-Nedawi.

  Currently, tumor biopsies are used for breast cancer molecular subtyping. Biopsies are associated with various pathological changes and are thought to contribute to the dissemination of tumor cells. Extracellular vesicles shed by tumor cells into circulation exhibit the molecular signature of the parent cells. Herein, we show that proteomic analysis of circulating EV can discriminate BC patients from healthy subjects and indicate stage of the disease. Also, we performed a correlation between the BC molecular subtype using plasma EV and immunohistochemistry of tumor biopsies. Circulating EV may represent a useful, non-invasive tool to study the molecular makeup of BC tumors.

Keywords:  breast cancer; extracellular vesicles; molecular subtyping

DOI:  https://doi.org/10.1111/tbj.13309
EBioMedicine. 2019 May 08. pii: S2352-3964(19)30301-9. [Epub ahead of print]

Treatment of keratinocytes with 4-phenylbutyrate in epidermolysis bullosa: Lessons for therapies in keratin disorders.

Marina Spörrer, Ania Prochnicki, Regine C Tölle, Alexander Nyström, Philipp R Esser, Melanie Homberg, Ioannis Athanasiou, Eleni Zingkou, Achim Schilling, Richard Gerum, Ingo Thievessen, Lilli Winter, Leena Bruckner-Tuderman, Ben Fabry, Thomas M Magin, Jörn Dengjel, Rolf Schröder, Dimitra Kiritsi.

   BACKGROUND: Missense mutations in keratin 5 and 14 genes cause the severe skin fragility disorder epidermolysis bullosa simplex (EBS) by collapsing of the keratin cytoskeleton into cytoplasmic protein aggregates. Despite intense efforts, no molecular therapies are available, mostly due to the complex phenotype of EBS, comprising cell fragility, diminished adhesion, skin inflammation and itch.
METHODS: We extensively characterized KRT5 and KRT14 mutant keratinocytes from patients with severe generalized EBS following exposure to the chemical chaperone 4-phenylbutyrate (4-PBA).
FINDINGS: 4-PBA diminished keratin aggregates within EBS cells and ameliorated their inflammatory phenotype. Chemoproteomics of 4-PBA-treated and untreated EBS cells revealed reduced IL1β expression- but also showed activation of Wnt/β-catenin and NF-kB pathways. The abundance of extracellular matrix and cytoskeletal proteins was significantly altered, coinciding with diminished keratinocyte adhesion and migration in a 4-PBA dose-dependent manner.
INTERPRETATION: Together, our study reveals a complex interplay of benefits and disadvantages that challenge the use of 4-PBA in skin fragility disorders.

Keywords:  4-PBA; Epidermolysis bullosa; Keratinocyte; Keratins; Skin blistering

DOI:  https://doi.org/10.1016/j.ebiom.2019.04.062
Orthopedics. 2019 May 01. 42(3): 149-157

Analysis of Retrieved Unicompartmental Knee Implants and Tissue: Third-Body Wear as a Potential Contributor to Progression of Arthritis to Adjacent Compartments.

Lige M Kaplan, Matthew P Siljander, James J Verner, Kevin C Baker, Corinn K Gehrke, Meagan R Salisbury, Erin A Baker.

Unicompartmental knee arthroplasty (UKA) for the treatment of single-compartment osteoarthritis has been associated with polyethylene wear and progression of osteoarthritis into adjacent compartments, leading to revision. In this study, damage and clinical failure modes of retrieved UKA implants were investigated and protein expression profiles between articular cartilage adjacent to UKA and primary osteoarthritic cartilage were compared. Fifty retrieved UKA implants were analyzed for various damage. Records review and radiographic analysis were performed to collect clinical data and implant characteristics. Cartilage harvested from revision UKA and primary total knee arthroplasty surgeries was characterized with a proteome profiling array detecting levels of 36 different cytokines, chemokines, and acute phase inflammatory proteins. Progression of osteoarthritis (n=18, 36%) and component loosening (n=17, 34%) were the most common reasons for revision. Liners exhibited the highest frequency of damage modes. Progression of arthritis positively correlated with radiographic presence of extruded bone cement and burnishing of liner components. A protein-level profile between revision UKA and primary total knee arthroplasty cartilage showed 12 differentially expressed cytokines. Failure of UKA may be secondary to the effects of wear debris particulate migration into the adjacent compartment, suggesting an additional pathway of cartilage damage manifesting as traditional clinical symptoms. [Orthopedics. 2019; 42(3):149-157.].

DOI: https://doi.org/10.3928/01477447-20190424-06