Molecular and pathogenic effects of endoplasmic reticulum aminopeptidases ERAP1 and ERAP2 in MHC-I-associated inflammatory disorders: Towards a unifying view

The inflammatory diseases that are most strongly associated with major histocompatibility Complex class I (MHC-I) alleles are also influenced by endoplasmic reticulum aminopeptidase (ERAP) 1 and/or 2, often in epistasis with the susceptibility MHC-I allele. This review will focus on the four major MHC-I-associated inflammatory disorders: ankylosing spondylitis, birdshot chorioretinopathy, Behçet’s disease and psoriasis. The genetics of ERAP1/ERAP2 association and the alterations induced by polymorphism of these enzymes on the risk MHC-I allotypes will be examined. A pattern emerges of analogous effects on peptide length, sequence and affinity of disparate peptidomes, suggesting that similar peptide-mediated mechanisms underlie the pathogenesis and the joint contribution of ERAP1/ERAP2 and MHC-I to distinct inflammatory diseases. Processing of specific antigens, peptide-dependent changes in global properties of the MHC-I molecules, such as folding and stability, or both may be pathogenic.     

Variations in the expressed antimicrobial peptide repertoire of northern leopard frog (Rana pipiens) populations suggest intraspecies differences in resistance to pathogens

The northern leopard frog (Rana pipiens or Lithobates pipiens) is historically found in most of the provinces of Canada and the northern and southwest states of the United States. In the last 50 years, populations have suffered significant losses, especially in the western regions of the species range. Using a peptidomics approach, we show that the pattern of expressed antimicrobial skin peptides of frogs from three geographically separated populations are distinct, and we report the presence of four peptides (brevinin-1Pg, brevinin-1Pl, ranatuerin-2Pb, and ranatuerin-2Pc) that have not previously been found in skin secretions. The differences in expressed peptides reflect differences in the distribution of alleles for the newly described Brevinin1.1 locus in the three populations. When enriched peptide mixtures were tested for their ability to inhibit growth of the pathogenic amphibian chytrid (Batrachochytrium dendrobatidis), peptides from Minnesota or Vermont frogs were more effective that peptides from Michigan frogs. Four of the purified peptides were tested for their ability to inhibit growth of two bacterial pathogens (Aeromonas hydrophila and Staphylococcus epidermidis) and B. dendrobatidis. Three of the four were effective inhibitors of B. dendrobatidis and S. epidermidis, but none inhibited A. hydrophila. We interpret these differences in expression and activity of antimicrobial peptides as evidence to suggest that each population may have been selected to express a suite of peptides that reflects current and past encounters with skin microbes.     

早产儿脑白质损伤大鼠模型海马组织差异多肽谱分析

目的 观察早产儿脑白质损伤大鼠模型海马组织多肽谱差异表达,探索早产儿脑白质损伤机制。方法 将20只新生Sprague-Dawley大鼠随机分为对照组和模型组（n=10）。模型组幼鼠在生后2 d行右侧颈总动脉永久结扎术,术后缺氧2 h;假手术组幼鼠分离右侧颈总动脉,但不行结扎和缺氧。采集两组大鼠脑组织标本并分离海马组织,采用液相色谱串联质谱联合串联质谱标记法检测两组大鼠海马组织多肽谱,将两组中差异表达多肽进行生物信息学分析,推断其在神经系统发育和功能中的作用。结果 共鉴定并量化4 164条多肽,其中262条多肽存在差异表达（倍数变化绝对值≥ 2.5）,164条多肽表达上调,98条多肽表达下调。前体蛋白ELN、PCLO、MYO15a、MAP4和MAP1b的差异表达多肽最多,可能在早产儿脑白质损伤的发病机制中具有重要意义。早产儿脑白质损伤模型大鼠的海马区CDK5信号通路被激活。结论 MAP1b等前体蛋白的差异表达多肽可能是早产儿脑白质损伤过程中参与神经系统发育和功能的关键生物活性多肽,CDK5信号通路激活可能与早产儿脑白质损伤有关。     

Classification of peptide mass fingerprint data by novel no-regret boosting method

We have developed an integrated tool for statistical analysis of large-scale LC-MS profiles of complex protein mixtures comprising a set of procedures for data processing, selection of biomarkers used in early diagnostic and classification of patients based on their peptide mass fingerprints.Here, a novel boosting technique is proposed, which is embedded in our framework for MS data analysis. Our boosting scheme is based on Hannan-consistent game playing strategies. We analyze boosting from a game-theoretic perspective and define a new class of boosting algorithms called H-boosting methods.In the experimental part of this work we apply the new classifier together with classical and state-of-the-art algorithms to classify ovarian cancer and cystic fibrosis patients based on peptide mass spectra.The methods developed here provide automatic, general, and efficient means for processing of large scale LC-MS datasets. Good classification results suggest that our approach is able to uncover valuable information to support medical diagnosis.     

Peptide screening of cerebrospinal fluid in patients with glioblastoma multiforme

Aims

To apply modern mass spectrometry based technology to identify possible CSF peptide markers of glioblastoma multiforme (GBM).

Methods

Mass spectrometry based peptidomics^® technology enables a systematic and comprehensive screening of cerebrospinal fluid (CSF) with regard to its peptide composition. Differential Peptide Display^® (DPD) allows the identification of single marker peptides for a target disease. Using both, we analyzed CSF samples of 11 patients harbouring a glioblastoma multiforme in comparison to 13 normal controls.

Results

Four CSF peptides which significantly distinguished GBM from controls in all applied statistic tests could be identified out of more than 2000 detected CSF peptides. They were specific C-terminal fragments of alpha-1-antichymotrypsin, osteopontin, and transthyretin as well as a N-terminal residue of albumin. All molecules are constituents of normal CSF, but none has previously been reported to be significantly elevated in CSF of GBM patients.

Conclusion

The study showed that peptidomics technology is able to identify possible biomarkers of neoplastic CNS disease. It remains to be determined if the identified elevated CSF peptides are specific for GBM. With regard to GBM, however, the more important role of CSF peptide biomarkers than aiding initial diagnosis might be early recognition of disease recurrence or monitoring of efficacy of adjuvant therapy protocols.     

Mass spectrometry strategies for venom mapping and peptide sequencing from crude venoms: case applications with single arthropod specimen.

Due to their complexity and diversity, animal venoms represent an extensive source of bioactive compounds such as peptides and proteins. Conventional approaches for their characterization often require large quantities of biological material. Current mass spectrometry (MS) techniques now give access to a wealth of information in a short working time frame with minute amounts of sample. Such MS approaches may now be used for the discovery of novel compounds, and once their structure has been determined they may be synthesized and tested for functional activity. Molecular mass fingerprints of venoms allow the rapid identification of known toxins as well as preliminary structural characterization of new compounds. De novo peptide sequencing by tandem mass spectrometry (MS/MS) offers rapid access to partial or total primary peptide structures. This article, written as a tutorial, also contains new material: molecular mass fingerprint analysis of Orthochirus innesi scorpion venom, and identification of components from bumblebee Bombus lapidarius venom, both collected from one single specimen. The structure of the three major peptides detected in the Bombus venom was fully characterized in one working day by de novo sequencing using an electrospray ionization hybrid quadrupole time-of-flight instrument (ESI-QqTOF) and a matrix-assisted laser desorption ionization time-of-flight instrument (MALDI-LIFT-TOF-TOF). After presenting the MS-based sequence elucidation, perspectives in using MS and MS/MS techniques in toxinology are discussed.     

Direct cellular peptidomics of hypothalamic neurons

The chemical complexity of cell-to-cell communication has emerged as a fundamental challenge to understanding brain systems. This is certainly true for the hypothalamus, where neuropeptide signals are heterogeneous, localized and dynamic. Thus far, most hypothalamic peptidomic studies have centered on the entire structure; however, recent advances in collection strategies and analytical technologies have enabled direct, high-resolution peptidomic profiles focused on two regions of interest, the suprachiasmatic and supraoptic nuclei, including their sub-regions and individual cells. Suites of peptides now can be identified and probed for function. High spatial and analytical sensitivities reveal that discrete hypothalamic nuclei have distinct peptidomic signatures. Peptidomic discovery not only reveals unanticipated complexity, but also peptides previously unknown that act as key circuit components. Analysis of tissue releasates identifies peptides secreted into the extracellular environment and available for transmitting intercellular signals. Direct sampling techniques define peptide-releasate profiles in spatial, temporal and event-dependent patterns. These approaches are providing remarkable new insights into the complexity of neuropeptidergic cell-to-cell signaling central to neuroendocrine physiology.     

基于蛋白质组学、肽组学的中药动物药活性组分的研究

动物药是我国传统中药的重要组成部分,但由于其组成复杂,分离较困难,与植物药相比动物药的研究相对落后。动物药组成中蛋白质占很大比例,目前已从动物药中发现许多蛋白质和多肽类活性组分。蛋白质组学、肽组学技术是快速发展的大规模表征蛋白质、肽的技术,借助蛋白质组学、肽组学快速、高效的特点,将蛋白质组学、肽组学技术应用于动物药中蛋白质和肽类活性组分的研究是动物药新的研究方向。本文综述了近年来应用蛋白质组学和肽组学技术研究动物药中蛋白质和肽类活性组分的进展。     

Bradykinin-related peptides and tryptophyllins in the skin secretions of the most primitive extant frog, Ascaphus truei

The tailed frog Ascaphus truei occupies a unique position in phylogeny as the most primitive extant anuran and is regarded as the sister taxon to the clade of all other living frogs. A previous study led to the isolation of eight antimicrobial peptides, termed ascaphins, from norepinephrine-stimulated skin secretions. Peptidomic analysis (HPLC separation followed by MALDI mass spectrometry and Edman degradation) of these secretions has led to the identification and structural characterization of 13 additional peptides present in relatively high concentration. In addition to bradykinin (BK; RPPGFSPFR), a C-terminally extended bradykinin (peptide RD-11; RPPGFSPFRVD), a bradykinin-like peptide (peptide AR-10; APVPGLSPFR), and a C-terminally extended form of this peptide (peptide AV-12; APVPGLSPFRVV) were obtained in pure form. These peptides produced concentration-dependent relaxation of precontracted mouse tracheal rings with a rank order of potency of BK>RD-11>AR-10>AV-12 but only RD-11 caused the same maximal relaxation as bradykinin. Four small peptides were also isolated from the skin secretions that contain the Pro-Trp motif that is a characteristic of the tryptophyllin family of peptides previously identified in skins of frogs of the family Hylidae. The data show that the synthesis of dermal peptides that may play a role in defense against predators arose early in the evolution of anurans.     

Peptidomic analysis of human peripheral monocytes persistently infected by Chlamydia trachomatis

Peptidomic analysis using Differential Peptide Display (DPD) of human peripheral blood mononuclear cells (PBMC) mock-infected or persistently infected by Chlamydia trachomatis (CT) revealed 10 peptides, expressed upon CT infection. Analysis of these 10 candidates by tandem mass spectrometry enabled the determination of seven candidates as fragments from the precursors (I) ferritin heavy chain subunit, (II) HLA class II histocompatibility antigen, (III) vimentin, (IV) indoleamine 2,3-dioxygenase, (V and VI) pre-B cell enhancing factor (PBEF), and (VII) Interleukin-8 (CXCL8). The identified candidates proved the presence of anti-bacterial and immunologically active monocytic proteins after CT infection.