Leucine‐rich repeat kinase 2 and Parkinson's disease

Leucine‐rich repeat kinase 2 (LRRK2) is a large multidomain protein that is expressed in many tissues and participates in numerous biological pathways. Mutations in LRRK2 are recognized as genetic risk factors for familial Parkinson's disease (PD) and may also represent causal factors in the more common sporadic form of PD. The structure of LRRK2 comprises a combination of GTPase, kinase, and scaffolding domains. This functional diversity, combined with a potentially central role in genetic and idiopathic PD motivates significant effort to further credential LRRK2 as a therapeutic target. Here, we review the current understanding for LRRK2 function in normal physiology and PD, with emphasis on insight gained from proteomic approaches.     

泰国生物产业发展现状和趋势分析

泰国是农产品生产和出口大国,政府十分重视生物产业的发展,通过建立高层管理机构、出台优惠政策、制定发展规划,在生物农业、生物医药和生物能源等产业方面取得了较好的进展。未来泰国将更加重视政府指导作用,进一步完善法规建设,加大人才引进力度,实施产业优惠政策,加强生物资源和知识产权保护,重点发展生物农业、生物医药和生物能源产业。     

Antibody‐based proteomics and biomarker research—Current status and limitations

Antibody‐based proteomics play a very important role in biomarker discovery and validation, facilitating the high‐throughput evaluation of candidate markers. Most proteomics‐driven discovery is nowadays based on the use of MS. MS has many advantages, including its suitability for hypothesis‐free biomarker discovery, since information on protein content of a sample is not required prior to analysis. However, MS presents one main caveat which is the limited sensitivity in complex samples, especially for body fluids, where protein expression covers a huge dynamic range. Antibody‐based technologies remain the main solution to address this challenge since they reach higher sensitivity. In this article, we review the benefits and limitations of antibody‐based proteomics in preclinical and clinical biomarker research for discovery and validation in body fluids and tissue. The combination of antibodies and MS, utilizing the best of both worlds, opens new avenues in biomarker research.     

Proteomic analysis of human substantia nigra identifies novel candidates involved in Parkinson's disease pathogenesis

Parkinson's disease (PD) pathology spreads throughout the brain following a region‐specific process predominantly affecting the substantia nigra (SN) pars compacta. SN exhibits a progressive loss of dopaminergic neurons responsible for the major cardinal motor symptoms, along with the occurrence of Lewy bodies in the surviving neurons. To gain new insights into the underlying pathogenic mechanisms in PD, we studied postmortem nigral tissues dissected from pathologically confirmed PD cases (n = 5) and neurologically intact controls (n = 8). Using a high‐throughput shotgun proteomic strategy, we simultaneously identified 1795 proteins with concomitant quantitative data. To date, this represents the most extensive catalog of nigral proteins. Of them, 204 proteins displayed significant expression level changes in PD patients versus controls. These were involved in novel or known pathogenic processes including mitochondrial dysfunction, oxidative stress, or cytoskeleton impairment. We further characterized four candidates that might be relevant to PD pathogenesis. We confirmed the differential expression of ferritin‐L and seipin by Western blot and demonstrated the neuronal localization of gamma glutamyl hydrolase and nebulette by immunohistochemistry. Our preliminary findings suggest a role for nebulette overexpression in PD neurodegeneration, through mechanisms that may involve cytoskeleton dynamics disruption. All MS data have been deposited in the ProteomeXchange with identifier PXD000427 ( http://proteomecentral.proteomexchange.org/dataset/PXD000427 ).     

Urinary extracellular microvesicles: Isolation methods and prospects for urinary proteome

Extracellular microvesicles (EVs) are membranous vesicles, which are released from diverse cells. These EVs have also been found in a wide range of body fluids. The cargo of EVs, including proteins, lipids, carbohydrates, and nucleic acids, can be stably preserved in EVs. Researchers have found that EVs can mediate intercellular communication by shuttling the cargo components. Therefore, EVs can be used for the identification of disease‐specific biomarkers. As one class of EVs, urinary exosomes can reflect the status of the renal system. Moreover, urinary exosome analysis can minimize the interference of high abundant proteins in the whole urine sample. Therefore, urinary exosomes have gained much attention in recent years. In this review, we present a comprehensive summary of urinary exosome studies in recent years, including collection, storage, and isolation methods. The normal and disease proteomic analyses of urinary exosomes are also presented. Thus, this review may provide a valuable reference for future research.     

Two‐dimensional gel electrophoresis of gastric tissue in an alkaline pH range

2DE in combination with MS has facilitated the discovery of several proteins with altered abundance in gastric cancer. While acidic and wide pH ranges have been widely investigated, analysis in the alkaline pH range has not been specifically performed in gastric cancer to date. In the present study, we initially optimized the 2DE in alkaline pH range (pH 7–11) for gastric tissue samples. Using a modified lysis buffer, we analyzed pooled nontumor and tumor samples for proteins with altered abundance in gastric adenocarcinoma. We successfully identified 38 silver‐stained spots as 24 different proteins. Four of these were chosen for investigation with immunoblotting on individual paired samples to determine whether the changes seen in 2DE represent the overall abundance of the protein or possibly only a single form. While mitochondrial trifunctional protein (MTP) subunits were decreased in 2DE gels, immunoblotting identified their overall abundance as being differently dysregulated: in the gastric tumor samples, the MTP‐α subunit was decreased, and the MTP‐β subunit was increased. On the other hand, heterogenous nuclear ribonucleoprotein M and galectin‐4 were increased in the gastric tumor samples in both 2DE and immunoblotting.     

Characterization of lacrimal proline‐rich protein 4 (PRR4) in human tear proteome

This study was initiated considering the lack of comprehensive characteristics profile of PRR4 in tears of healthy subjects. Therefore, detailed characterizations of PRR4 from basal tears employing in‐gel and in‐solution digestions for MS systems are presented herein. First, pooled tear samples (n = 10) were utilized to identify PRR4‐rich region/spots in 1DE/2DE gels employing LC‐MALDI‐MS and 1DE‐LC‐ESI‐LTQ‐Orbitrap‐MS systems. PRR4‐rich region and ten spots with vast polymorphisms (M_r: 17–30 kDa, pI: 3.0–6.6) were identified in 1DE and 2DE gels, respectively. In addition, combinations of four types of PTMs, which are methylation, acetylation, oxidation, and pyroglutamate formation, were identified in these ten PRR4 spots. Furthermore, a targeted data‐acquisition approach was utilized to identify PRR4 isoforms in individual tear samples (n = 61) by in‐solution digestion combined with a LC‐ESI‐LTQ‐Orbitrap‐MS system. Importantly, a new PRR4 isoform designated as PRR4‐N3 in addition to PRR4 (gi154448886) and pHL E1F1 (gi1050983) was identified. Moreover, different combinations of these three PRR4 isoforms identified in the individual tear samples could be categorized into six distinguished groups. Conclusively, these findings provide fundamental insight into the complex characteristics profile of PRR4 isoforms and their PTMs in tears of healthy individuals.     

Proteomic differential display analysis identified upregulated astrocytic phosphoprotein PEA‐15 in human malignant pleural mesothelioma cell lines

We performed proteomic differential display analysis of human malignant pleural mesothelioma (MPM) cell lines and a human pleural mesothelial cell line by using 2‐DE and LC‐MS/MS. The human MPM cell lines were NCI‐H28, NCI‐H2052 and NCI‐H2452, and the human pleural mesothelial cell line was MeT‐5A. Between MeT‐5A and NCI‐H2052, we found 38 protein spots whose expression levels were different, from the results of 2‐DE; 28 protein spots appeared higher, and 10 other protein spots lower in NCI‐H2052 than in MeT‐5A. These spots were analyzed by LC‐MS/MS analysis and identified by a peptide sequence tag. However, from the results of 2‐DE of the other cell lines, there was only one consistently upregulated protein, astrocytic phosphoprotein PEA‐15, in all three MPM cell lines. Western blotting using specific antibodies against PEA‐15 confirmed the elevated expression level of PEA‐15 in all three MPM cell lines compared with MeT‐5A cells and normal pleura tissues from patients. PEA‐15 was knocked down in NCI‐H2052 cells, and the proliferation of PEA‐15‐silenced NCI‐H2052 cells was suppressed 7–15% compared with negative control cells. These results suggest that PEA‐15 expression is likely to be associated with the tumorigenesis of MPM.     

Characterization of peptides and proteins in commercial HSA solutions

HSA solutions account for 14% of the world market for plasma products. Albumin is indicated for reestablishing and maintaining circulatory volume in situations resulting from traumatic shock, surgery, or blood loss. Albumin is also used in extracorporeal liver support devices that perform blood dialysis against this protein. However, the protein composition of therapeutic albumin is only partially known. We performed an exhaustive analysis of albumin composition using a proteomic approach. Low abundance proteins and peptides in these samples were concentrated using a strong anion exchange resin. The absorbed material was eluted with a stepwise gradient of ammonium trifluoroacetate and the protein fraction was digested and analyzed by multidimensional liquid chromatography coupled to ESI‐MS/MS using a linear ion trap. A total of 1219 peptides corresponding to 141 proteins different from albumin were identified with a false discovery rate <1%. Near 50% of these proteins have been described previously as forming part of the albuminome. Some of these proteins are proteases (kallikrein) or protease inhibitors (kininogen and SRPK1) or have relevant functions in cell surface adhesion (selectin, cadherins, and ICAMs) or in immunity and defense (molecules of the complement system and attractin). Characterization of these proteins and peptides is crucial in order to understand the therapeutic and possible deleterious effects of albumin therapies, in which this solution is infused to treat different pathological conditions.