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Proteomics. Clinical Applications

Yogesh M Kulkarni, Sucharita Dutta, Anand Krishnan V Iyer, Clayton A Wright, Vani Ramesh, Vivek Kaushik, Oliver John Semmes, Neelam Azad
PURPOSE: Poor molecular characterization of idiopathic pulmonary fibrosis (IPF) has led to insufficient understanding of the pathogenesis of the disease, resulting in lack of effective therapies and poor prognosis. Particularly, the role of lipid imbalance due to impaired lipid metabolism in the pathogenesis of IPF has been poorly studied. EXPERIMENTAL DESIGN: We have used shotgun lipidomics in a bleomycin (BLM) mouse model of pulmonary fibrosis with vascular endothelial growth factor (VEGF)-inhibitor CBO-P11 as a therapeutic measure, to identify a comprehensive set of lipids that contribute to the pathogenesis of pulmonary fibrosis...
December 28, 2017: Proteomics. Clinical Applications
Apoorva Venkatesh, Concha Gil, Manuel Fuentes, Joshua LaBaer, Sanjeeva Srivastava
Pneumonia, HIV/AIDS, tuberculosis, malaria and several other diseases caused by pathogens largely contribute to the enormous burden of infectious diseases. Over the last few decades, the impact of infectious diseases on a population has been drastic and remains a major health concern even today. Despite advances in science and technology in this era of health and development, there is a substantial knowledge gap in our understanding of the molecular basis of these infectious diseases. The availability of valuable genomic information for a number of pathogens and their hosts has improved our understanding of disease pathogenesis but has not always been useful in addressing important biological questions...
December 28, 2017: Proteomics. Clinical Applications
Guillermo Arango Duque, Hamlet Adolfo Acevedo Ospina
Porcine diarrhea and gastroenteritis are major causes of piglet mortality that result in devastating economic losses to the industry. A plethora of pathogens can cause these diseases, with TGEV and ETEC being two of the most salient. In this issue, Xia and colleagues use comparative proteomics to shed light on how these microbes interact to cause severe disease [Xia, L., et al., Proteomics Clin. Appl. 2017, 1600137-n/a]. The authors discovered that TGEV induces an EMT-like phenotype that augments cell adhesion proteins that mediate the attachment of ETEC to intestinal epithelial cells...
December 27, 2017: Proteomics. Clinical Applications
Anders Christensson, Jessica A Ash, Robert K DeLisle, Fraser W Gaspar, Rachel Ostroff, Anders Grubb, Veronica Lindström, Laila Bruun, Steve A Williams
PURPOSE: The application of proteomics in chronic kidney disease (CKD) can potentially uncover biomarkers and pathways that are predictive of disease. EXPERIMENTAL DESIGN: Within this context, this study examined the relationship between the human plasma proteome and glomerular filtration rate (GFR) as measured by iohexol clearance in a cohort from Sweden (N = 389; GFR range: 8 - 100 mL/min/1.73m2 ). A total of 2893 proteins were quantified using a modified aptamer assay...
December 27, 2017: Proteomics. Clinical Applications
Denise Utami Putri, Po-Hao Feng, Yuu-Hueih Hsu, Kang-Yun Lee, Feng-Wen Jiang, Lu-Wei Kuo, Yu-Ju Chen, Chia-Li Han
OBJECTIVES: No study has addressed how the immune status at the molecular level is affected by first-line pemetrexed and cisplatin (PEM-CIS) combination therapy in patients with non-small-cell lung cancer (NSCLC). Thus, we aimed to identify the immune status from membrane proteome alterations in patients with NSCLC upon PEM-CIS treatment. METHODS: The paired peripheral blood mononuclear cells (PBMCs) were collected from four patients with lung adenocarcinoma before and after the first regimen of PEM-CIS treatment and applied quantitative membrane proteomics analysis...
December 26, 2017: Proteomics. Clinical Applications
Liming Shen, Kaoyuan Zhang, Chengyun Feng, Youjiao Chen, Shuiming Li, Javed Iqbal, Liping Liao, Yuxi Zhao, Jian Zhai
PURPOSE: Autism is a childhood neurological disorder with poorly understood etiology and pathology. This study is designed to identify differentially expressed proteins which might serve as potential biomarkers for autism. EXPERIMENTAL DESIGN: We performed iTRAQ (isobaric tags for relative and absolute quantitation) analysis for normal and autistic children's plasma of the same age group. RESULTS: The results showed that 24 differentially expressed proteins were identified between autistic subjects and controls...
December 23, 2017: Proteomics. Clinical Applications
Jisook Park, Ga Yeon Lee, Jin-Oh Choi, Eun-Seok Jeon, Kihyun Kim, Jung-Sun Kim, Soo-Youn Lee
Amyloidosis is caused by the extracellular deposition of insoluble fibrils and results in multiple organ dysfunctions. Accurate typing of amyloid is mandatory to decide the optimal treatment for amyloidosis. A mass spectrometry-based test combined with laser microdissection (LMD/MS) has been widely used even in the tricky cases that cannot be discriminated by immunohistochemical staining. However, shotgun proteomics analysis obligatorily requires not only expensive instruments but also highly-experienced specialists to interpret the analysis...
December 19, 2017: Proteomics. Clinical Applications
Erin K Sykes, Cassandra E McDonald, Shila Ghazanfar, Swetlana Mactier, John F Thompson, Richard A Scolyer, Jean Y Yang, Graham J Mann, Richard I Christopherson
PURPOSE: To validate differences in protein levels between good and poor prognosis AJCC stage III melanoma patients and compile a protein panel to stratify patient risk. EXPERIMENTAL DESIGN: Protein extracts from melanoma metastases within lymph nodes in patients with Stage III disease with good (n = 16, > 4 years survival) and poor survival (n = 14, < 2 years survival) were analysed by selected reaction monitoring (SRM). Diagonal Linear Discriminant Analysis was performed to generate a protein biomarker panel...
December 11, 2017: Proteomics. Clinical Applications
Mitchell Acland, Parul Mittal, Noor A Lokman, Manuela Klingler-Hoffmann, Martin K Oehler, Peter Hoffmann
Multicellular tumour spheroids (MCTS) are a powerful biological in vitro model, which closely mimics the 3D structure of primary avascularised tumours. Mass spectrometry (MS) has established itself as a powerful analytical tool, not only to better understand and describe the complex structure of MCTS, but also to monitor their response to cancer therapeutics. The first part of this review focuses on traditional mass spectrometry approaches with an emphasis on elucidating the molecular characteristics of these structures...
December 11, 2017: Proteomics. Clinical Applications
Katja Walpurgis, Andreas Thomas, Frank Dellanna, Wilhelm Schänzer, Mario Thevis
PURPOSE: Inhibitors of the ActRII signaling pathways represent promising therapeutics for the treatment of muscular diseases, but also pose risks as performance-enhancing agents in sports. Bimagrumab is a human anti-ActRII antibody which was found to increase muscle mass and function by blocking ActRII signaling. As it has considerable potential for being misused as doping agent in sports, the aim of this study was to develop a mass spectrometric detection assay for doping control serum samples...
December 11, 2017: Proteomics. Clinical Applications
Swati Patankar, Shobhona Sharma, Pradipsinh K Rathod, Manoj Duraisingh
Plasmodium vivax is a protozoan parasite that is one of the causative agents of human malaria. Due to several occult features of its life cycle, P. vivax threatens to be a problem for the recent efforts towards elimination of malaria globally. With an emphasis on malaria elimination goals, we summarize the major gaps in P. vivax diagnosis and describe how proteomics technologies have begun to contribute towards the discovery of antigens that could be used for various technology platforms and applications. We suggest areas where, in the future, proteomics technologies could fill in gaps in P...
November 29, 2017: Proteomics. Clinical Applications
Claudia Vincenza Fiumara, Domenica Scumaci, Anna Iervolino, Angela Mena Perri, Antonio Concolino, Laura Tammè, Federica Petrillo, Giovambattista Capasso, Giovanni Cuda
PURPOSE: Dicer, an RNase III type endonuclease, is a key enzyme involved in miRNA biogenesis. It has been shown that this enzyme is essential for several aspects of postnatal kidney functions and homeostasis. In this study, we have examined conditional knockout (cKO) mice for Dicer in Pax8 (Paired-box gene 8) expressing cells to investigate the kidney protein profile. This specific model develops a glomerulocystic phenotype coupled with urinary concentration impairment, proteinuria and severe renal failure...
November 21, 2017: Proteomics. Clinical Applications
Maurizio Bruschi, Laura Santucci, Silvia Ravera, Martina Bartolucci, Andrea Petretto, Daniela Calzia, Gianmarco Ghiggeri, Luca A Ramenghi, Giovanni Candiano, Isabella Panfoli
PURPOSE: Microvesicles, 200-1000 nm bodies budding from the cell plasma membrane, are a promising source of biomarkers. This study aimed at comparing the proteome of Microvesicles collected by ultracentrifugation from cultured Mesenchymal Stem Cells from Human Umbilical Cord of Preterm newborns(<34-weeks gestational age) in comparison to infants at Term(≥37 weeks). This discovery study was designed to establish the signature of prematurity. EXPERIMENTAL DESIGN: Orbitrap mass spectrometry, statistical, bioinformatics and biochemical analyses were employed...
November 16, 2017: Proteomics. Clinical Applications
Robert Moulder, Domitille Schvartz, David R Goodlett, Loïc Dayon
No abstract text is available yet for this article.
November 16, 2017: Proteomics. Clinical Applications
Yanmei Zhu, Yuehua Gong, Aodi Li, Moye Chen, Dan Kang, Jun Liu, Yuan Yuan
PURPOSE: Though Helicobacter pylori (H. pylori) has been classified as class I carcinogen, key virulence factor generated by H. pylori that causes gastric cancer remains to be fully determined. Recently, we identified a gastric cancer-associated H. pylori gene, peptidylprolyl isomerase-FK506 binding protein (PPIase-FKBP), and showed that PPIase-FKBP was capable of inducing oncogenic transformation of gastric epithelial cells. But its mechanism was unclear. EXPERIMENTAL DESIGN: We carried out a comparative proteomic analysis of human gastric epithelial cells that either express PPIase-FKBP or green fluorescent protein (GFP) using two-dimensional (2-D) gel electrophoresis and then matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS/MS)...
November 16, 2017: Proteomics. Clinical Applications
Dhanya Madhu, Maha Hammad, Sina Kavalakatt, Abdelkrim Khadir, Ali Tiss
PURPOSE: Glucagon-like peptide-1 (GLP-1) analogues reduce ER stress and inflammation in key metabolic organs, including the liver. However, their effects on heat shock response (HSR) and mitogen-activated protein kinases (MAPKs) have not yet been elucidated. In the present study, we investigated whether the GLP-1 analogue, exendin-4, triggers the expression of HSR and increases MAPK activity under metabolic stress. EXPERIMENTAL DESIGN: The effects of exendin-4 in the presence or absence of palmitic acid (PA; 400 μM) or glucose (30 mM) in the HepG2 liver cell line were assessed using Western blots, quantitative real-time PCR and label-free proteomics...
November 3, 2017: Proteomics. Clinical Applications
Lu Xia, Lei Dai, Liqi Zhu, Weiwei Hu, Qian Yang
Piglet diarrhea causes large economic losses to the swine industry. Epidemiological investigations show that piglet diarrhea is often caused by mixed infections, but the mechanisms by which multiple microorganisms cause disease are unclear. Because transmissible gastroenteritis virus (TGEV) and enterotoxigenic Escherichia coli K88 (ETEC K88) are important contributors to piglet diarrhea, coinfection experiments were conducted using porcine intestinal columnar epithelial cells (IPEC-J2) as a model system. LC-MS/MS coupled to iTRAQ was used to profile expressed proteins in IPEC-J2 cells infected by TGEV alone, ETEC K88 alone, and by both agents together...
November 1, 2017: Proteomics. Clinical Applications
Birgit Knebel, Simon Göddeke, Sonja Hartwig, Tina Hörbelt, Pia Fahlbusch, Hadi Al-Hasani, Sylvia Jacob, Cornelia Koellmer, Ulrike Nitzgen, Martina Schiller, Stefan Lehr, Jorg Kotzka
PURPOSE: MetS consist of five risk factors: elevated blood pressure and fasting glucose, visceral obesity, dyslipidemia and hypercholesterinemia. The physiological impact of lipid metabolism indicated as visceral obesity and hepatic lipid accumulation on MetS is still under debate. One major cause of disturbed lipid metabolism might be dysfunction of cellular organelles controlling energy homeostasis, i.e. mitochondria and peroxisomes. EXPERIMENTAL DESIGN: The New Zealand Obese (NZO) mouse model exhibits a polygenic syndrome of obesity, insulin resistance, triglyceridemia and hypercholesterolemia that resembles human metabolic syndrome...
October 25, 2017: Proteomics. Clinical Applications
Mario Bonomini
Adsorption of plasma proteins onto the membrane surface during the hemodialysis session represents a key feature of membranes used for chronic dialysis therapy. In this issue of Proteomics - Clinical Applications, Han et al. [Proteomics - Clinical Applications 2017, XX] originally describe how, by using proteomic technologies, the adsorptive properties of two membranes made from the same biomaterial (Polyamix) may have different flux characteristics (low-flux and high-flux, the former having smaller pore size)...
October 24, 2017: Proteomics. Clinical Applications
Andreas Roos, Rachel Thompson, Rita Horvath, Hanns Lochmüller, Albert Sickmann
Despite recent rapid advances in sequencing technologies, a significant proportion of patients with rare genetic disorders do not receive a genetic diagnosis after exhaustive testing, and even fewer have a potential therapeutic target identified. Taking rare neuromuscular and neurodegenerative disorders as a paradigm that can be extended to other rare Mendelian disorders, this viewpoint explores the opportunities that are brought about by the integration of genomics and proteomics, as well as the limitations and remaining challenges of this newly emerging field of proteogenomics...
October 23, 2017: Proteomics. Clinical Applications
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