bims-prodis 2018-11-11 papers

Issue of 2018–11–11
three papers selected by
Nancy Gough, Bioserendipity

J Proteomics. 2018 Nov 01. pii: S1874-3919(18)30390-7. [Epub ahead of print]

Integrated serum proteins and fatty acids analysis for putative biomarker discovery in inflammatory bowel disease.

Marcello Manfredi, Eleonora Conte, Elettra Barberis, Arianna Buzzi, Elisa Robotti, Valeria Caneparo, Daniela Cecconi, Jessica Brandi, Ester Vanni, Marco Finocchiaro, Marco Astegiano, Marisa Gariglio, Emilio Marengo, Marco De Andrea.

The diagnosis and management of Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), is still challenging. There is no definitive gold standard diagnostic test, which is made on patient history and with endoscopic and histological findings. This study analyzed serum proteins and fatty acids using mass spectrometry-based techniques. Quantitation of serum proteins was performed by depleting 14 high-abundance proteins, followed by tryptic digestion and LC-MS analysis, while fatty acids were analyzed using GC-MS. Bioinformatic tools were used to identify several new potential biomarkers for an early and non-invasive diagnosis of IBD, and to differentiate CD from UC. Moreover, the diagnostic power of the MS-identified biomarkers was also corroborated by Western Blot and ELISA assays. Hence, we identified the biological functions and pathways involved in the various subsets of IBD. Coagulation, fibrinolysis and acute phase response processes were found to be strongly involved in the condition. The involvement of several fatty acids, such as anti-inflammatory mediators, was also identified. Finally, proteomic and lipidomic data were integrated by using combinatorial and multivariate analyses to discover new combined biomarkers and to study the molecular pathways involved in IBD.

Keywords: Biomarkers; Inflammatory bowel disease; Lipidomics; Proteomics

DOI: https://doi.org/10.1016/j.jprot.2018.10.017

J Neuroimmunol. 2018 Oct 01. pii: S0165-5728(18)30391-6. [Epub ahead of print]325 54-60

Novel autoantibodies against the proteasome subunit PSMA7 in amyotrophic lateral sclerosis.

Kazuo Sugimoto, Takaki Hiwasa, Kazutomo Shibuya, Shigeki Hirano, Minako Beppu, Sagiri Isose, Kimihito Arai, Masaki Takiguchi, Satoshi Kuwabara, Masahiro Mori.

OBJECTIVE: To identify autoantibodies using sera from ALS patients and elucidate their roles in disease pathology.
METHODS: An immunological screening was performed with a phage expression library SEREX method using sera from 3 ALS patients to identify ALS-related autoantibodies. Levels of antibodies identified by SEREX were measured in 33 ALS patients and 30 normal controls (NCs) by AlphaLISA using recombinant non-full-length proteins. The results were then validated by ELISA using full-length proteins in 71 ALS patients, 30 NCs and 34 disease controls (DCs). The relationship between the titres and clinical profiles of ALS patients were examined.
RESULTS: Four autoantibodies identified by SEREX were proteasome subunit alpha type 7 (PSMA7), vimentin, hydroxymethylbilane synthase and TBC1 domain family member 2 (TBC1D2). AlphaLISA revealed that only the anti-PSMA7 and anti-TBC1D2 levels were significantly different between the ALS and NCs groups. ELISA showed that only the levels of antibody against PSMA7, involved in protein degradation by the ubiquitin-proteasome pathway (UPP), were higher in the ALS group than both the NC (P < .01) and DC (P = .034) groups. Anti-PSMA7 levels tended to be negatively correlated with the logarithm of disease duration (P = .052) and were significantly positively correlated with the logarithm of creatine kinase levels (P = .011). The anti-PSMA7 antibody levels were different between patients with and without dysphagia (P < .01).
CONCLUSIONS: Serum anti-PSMA7 antibody might be a disease-promoting factor in early-stage ALS and might be a biomarker of ALS. Anti-PSMA7 autoantibody might contribute to the pathogenesis of ALS, possibly via its role in the UPP.

Keywords: Amyotrophic lateral sclerosis; Autoantibody; Biomarker; Proteasome subunit alpha type7; Serological analysis of recombinant cDNA expression libraries

DOI: https://doi.org/10.1016/j.jneuroim.2018.09.013

Biochim Biophys Acta Proteins Proteom. 2018 Oct 31. pii: S1570-9639(18)30197-3. [Epub ahead of print]1867(2): 89-97

Analysis of cellular proteome changes in response to ZIKV NS2B-NS3 protease expression.

Chontida Tangsongcharoen, Sittiruk Roytrakul, Duncan R Smith.

The recent emergence of Zika virus (ZIKV) has caused global concern as a result of the association with neurological disorders, and brain development dysfunction in fetuses of mothers who become infected with ZIKV during pregnancy. The NS2B-NS3 protease is important for viral replication and offers an attractive drug target. In addition to processing the viral polypeptide, evidence has shown that the NS2B-NS3 protease also targets cellular proteins as part of the viral replication process. This study sought to determine new host cell protein targets of ZIKV NS2B-NS3 (zNS2B-NS3). Plasmids encoding the protease domains of zNS2B-NS3pro and an inactive zNS2B-NS3(S135A) were transfected into HEK293T/17 cells and differentially expressed proteins were detected by 2D gel electrophoresis. A total of 18 protein spots were observed as differentially expressed between zNS2B-NS3pro and zNS2B-NS3(S135A), of which 7 were selected for identification by mass spectrometry. Four proteins (protein disulfide-isomerase A3 (PDIA3), heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1), voltage-dependent anion-selective channel (VDAC) and aldolase A (ALDOA)) were selected for validation by independent transient expression and western blot analysis. Three proteins (PDIA3, hnRNP A2/B1 and ALDOA) were successfully validated, but only two proteins (PDIA3 and ALDOA) were shown to be regulated in ZIKV infection in agreement with the results of the transfection experiments. This study has identified two proteins, PDIA3 an ALDOA whose expression is modulated by the ZIKV NS2B-NS3 protease, and these proteins are involved in the ER stress response and glycolysis respectively, two critical cellular processes in ZIKV infection.

Keywords: Glycolysis; NS2B; NS3; Protease; Stress response; Zika virus

DOI: https://doi.org/10.1016/j.bbapap.2018.10.016