Investigation of differentially expressed proteins in rat gastrocnemius muscle during denervation–reinnervation

To have a better insight into the molecular events involved in denervation-induced atrophy and reinnervation-induced regeneration of skeletal muscles, it is important to investigate the changes in expression levels of a great multitude of muscle proteins during the process of denervation–reinnervation. In this study, we employed an experimental model of rat sciatic nerve crush to examine the differentially expressed proteins in the rat gastrocnemius muscle at different time points (0, 1, 2, 3, 4 weeks) after sciatic␣nerve crush by using two-dimensional gel electrophoresis (2-DE) followed by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF-MS), collectively referred to as the modern proteomic analysis. The results showed that 16 proteins in the rat gastrocnemius muscle exhibited two distinct types of change pattern in their relative abundance: (1) The relative expression levels of 11 proteins (including alpha actin, myosin heavy chain, etc.)were decreased either within 1 or 2 weeks post-sciatic nerve injury, followed by restoration during the ensuing days until 4 weeks. (2) The other 5 proteins (including alpha enolase, beta enolase, signal peptide peptidase-like 3, etc.) displayed an up-regulation in their relative expression levels within 1 week following sciatic nerve injury, and a subsequent gradual decrease in their relative expression levels until 4 weeks. Moreover, the significance of the changes in expression levels of the 16 proteins during denervation–reinnervation has been selectively discussed.     

A comparison of the pro-inflammatory, NF-κB-dependent cytokines: TNF-alpha, IL-1-alpha, IL-6, and IL-8 in different oral fluids from oral lichen planus patients

To explore the feasibility of detection of the level of NF-κB-dependent cytokines in oral fluids from patient with oral lichen planus (OLP) for clinical application, 13 OLP subjects were enrolled in the study as were 13 age–sex-matched controls. In each subject, the whole unstimulated saliva (WUS), mixture of saliva and isotonic saline oral rinse (Saliva-NaCl), and lesion tissue transudates (TT) were collected by standard techniques. The level of cytokines, TNF-alpha, IL-1-alpha, IL-6, and IL-8 in three types of oral fluids was determined by ELISA. In the three types of oral fluids, a significantly higher level of these cytokines was detected in OLP patients than in normal controls. These results indicate that NF-κB-dependent inflammatory cytokines may be detected at increased levels in certain oral fluids which may have diagnostic and prognostic potential for monitoring disease activity and making therapeutic decisions in patients with OLP.     

运用蛋白指纹图谱技术筛选类风湿关节炎患者血清特异性标志物

目的: 用纳米磁珠与基质辅助激光解吸电离飞行时间质谱(MALDI-TOF-MS)技术检测类风湿关节炎(RA)患者血清蛋白质组,筛选候选蛋白标志物并建立诊断模型,初步探讨所建立的诊断模型在RA早期诊断中的临床意义。方法: 采用弱阳离子(WCX)纳米磁性微球捕获60例RA患者、35例骨性关节炎(OA)患者和36名健康体检者血清中的蛋白质。所获蛋白经PBSⅡ-C蛋白质芯片阅读仪绘制蛋白指纹图谱。这些蛋白指纹图谱经Ciphergen ProteinChip和Biomarker Wizard软件分析之后,再用Biomarker Patterns 软件进行识别,最终筛选出RA的特异性蛋白标志物,并优化组合建立诊断模型。结果: 在RA患者和对照组之间共找到33个差异蛋白峰(P<0.05)。其中质荷比(m/z)为15 715.5D、7 771.4D、8 959.4D、8 469.8D和8 710.8D的蛋白峰用于建立RA诊断模型。经双盲实验验证,该模型对RA诊断的敏感性为86.7%,特异性为90.0%。结论: 采用WCX纳米磁性微球联用MALDI-TOF-MS技术可检出RA患者血清中的特异性蛋白标志物,并建立敏感性和特异性均较高的RA诊断模型。     

Identification of a proteomic biomarker associated with invasive ST1, serotype VI Group B Streptococcus by MALDI-TOF MS

Background

Group B Streptococcus (GBS) is an important invasive pathogen in neonates, pregnant women and the elderly. Serotype VI GBS, which has been rarely reported globally, has emerged as a significant pathogen in Asia. However, traditional serologic latex agglutination (LA) methods may fail to type isolates that lack of or low expression of CPS.

Serologic and molecular analysis of the HLA system in Israeli Jewish patients with oral erosive lichen planus

Abstract: Oral erosive lichen planus is a distinct subtype of the common dermatosis lichen planus. Although the etiology of lichen planus is still obscure, it is known that cell-mediated immune mechanisms and genetic factors underlie its pathogenesis. Previous studies have found an association between lichen planus and HLA-DR3 or DR9 in different population groups. The present work was designed to elucidate, at the serologic and molecular levels, whether and which HLA genes are associated with oral erosive lichen planus in Israeli Jewish patients. A significant association with HLA-DR2 (RR = 4.7; p_c < 0.0013) and a decrease in DR4 (RR = 0.3; p < 0.03) among the patients were noted. Oligotyping of DR2 alleles showed the presence of all three common variants (DRB1*1501, DRB1*1502 and DRB1*1601) in the patients, although none of the variants was overrepresented significantly. Three possible explanations for the role of HLA genes in the predisposition to oral erosive lichen planus are discussed. The most attractive theory for the pathogenesis of the disease seems to include the involvement of non-classical HLA genes.     

Th1细胞/Th2细胞在口腔扁平苔藓发病机制中的作用

口腔扁平苔藓是最常见口腔黏膜疾病之一,发病机制尚不明确,因其具有癌变潜能,WHO将其列为癌前状态。研究发现,Th1细胞/Th2细胞亚群与口腔扁平苔藓的发病密切相关,尤其是Th1/Th2漂移学说与OLP的关系成为近年研究热点。下文针对Th1细胞/Th2细胞在口腔扁平苔藓中的最新研究成果做一综述和展望。     

Potential biomarkers found by protein profiling may provide insight for the macrovascular pathogenesis of diabetes mellitus

Diabetes mellitus (DM) is an alarming threat to health of mankind, yet its pathogenesis is unclear. The purpose of this study was to find potential biomarkers to serve as indicators for the pathogenesis of DM in a time course manner. Based on our previous findings that oxidative stress occurred at week 8, aorta lysate and sera of 102 streptozotocin (STZ)-induced diabetic and 85 control male Sprague-Dawley rats were obtained at the 4th, 8th and 12th week after STZ injection. The protein profiles were studied employing surface-enhanced laser desorption/ionization time-of-flight mass spectrometry technology in attomole sensitivity range. In the aorta, a multiple biomarker panel was discovered at the 4th week. At the 8th week, 4 biomarkers were found, while at the 12th week, 3 biomarkers were identified. In the sera, a triplet of 3 peaks and 2 biomarkers were all discovered to have 100% classification accuracy rate to differentiate the DM and control groups at all time intervals. Besides, 2 biomarkers were also found to have high classification value at week 12. Comparing the aorta and sera from DM and non-DM rats, a bundle of potential biomarkers with significant changes in peak intensities and high classification values were found. Two of the serum biomarkers matched with islet amyloid polypeptide and resistin in the SWISS-PROT knowledgebase. Validation has been conducted using immunoassay kits. These potential biomarkers may provide valuable insight on the pathogenesis of DM and macrovascular complications.     

Differential analysis of two-dimension gel electrophoresis profiles from the normal-metaplasia-dysplasia-carcinoma tissue of human bronchial epithelium

Processes involved in malignant transformation of the lung from preneoplasia are poorly understood. To better understand this process, two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) profiles of proteins from the normal, metaplasia, dysplasia and carcinoma tissues of human bronchial epithelia were examined by differential proteomic analysis. The selected differential protein-spots were identified by peptide mass fingerprint based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and database searching. The average spots for normal epithelium, metaplasia, dysplasia and invasive carcinoma were 1189.50 +/- 39.89, 1227.00 +/- 37.90, 1273.00 +/- 43.31 and 1326.00 +/- 66.63, respectively. Well-resolved, reproducible 2-D PAGE patterns of the normal-metaplasia-dysplasia-carcinoma tissues of bronchial epithelia were obtained. After matching, the number of spots of differential proteins between normal tissue and metaplasia, metaplasia and dysplasia, and dysplasia and invasive cancer tissues were 31.50 +/- 7.67, 41.00 +/- 9.07 and 56.00 +/- 8.96, respectively. In total, 35 differential proteins, expressed only at the later stage of a two-stage comparison, were identified, some of which are known to be involved in regulating the processes of proliferation, differentiation and signal transduction. Current data in this study, for the first time, provide the basis for identification of potential tumor markers of human lung squamous carcinoma and their involvement in the progression of malignant transformation of bronchial epithelium.     

Contemporary Mass Spectrometry and the Analysis of Synthetic Polymers: Trends,Techniques and Untapped Potential

For many decades, the capacity for mass spectrometry (MS) to analyse matter in all of its forms was shackled by an inability to ionise large molecules into the gas phase. It was only in the late 1980s, when the capabilities of the ‘soft’ ionisation protocols of matrix‐assisted laser desorption/ionisation (MALDI) and electrospray ionisation (ESI) became apparent, that these shackles were effectively removed. The emergence of soft ionisation methodologies acted as a driving force for significant advances in MS instrumentation; as a result, MS now represents one of the most potent means by which insights into the structural details of synthetic polymer samples can be obtained. However, despite MS being acknowledged to be a mainstream analytical tool in the field of polymer chemistry, the number of MS‐based studies into polymer systems remains significantly limited when compared to other analytical methods, and it would thus appear that MS is still being severely underutilised. In this Trend article, important fundamental concepts of soft ionisation MS are presented in a tutorial style fashion within the context of the analysis of polymer systems, and the remarkable breadth, power and versatility of these techniques is illustrated using selected examples. We suggest that MS‐based analyses represent one of the most promising areas of research in polymer science, and that the polymer chemistry community would be well served by utilising this analytical discipline in a more intensive manner.

     

Comparative analysis of the expression of proliferating cell nuclear antigen, p53, bax, and bcl-2 in oral lichen planus and oral squamous cell carcinoma

Several epidemiologic studies have shown the malignant transformation potential of oral lichen planus; however, this potential is subject of much controversy. To evaluate the expression of proteins related to the cell proliferation and apoptosis processes in oral lichen planus, we compared oral lichen planus with oral squamous cell carcinoma. Twenty-four cases of each lesion were submitted according to streptavidin-biotin technique to evaluate the immunohistochemical expression of proliferating cell nuclear antigen, p53, bax, and bcl-2 proteins. χ² test showed no statistically significant differences between the expression of p53, bax, and bcl-2 in oral lichen planus and oral squamous cell carcinoma (P > .05). However, the expression of proliferating cell nuclear antigen was significantly lower in oral lichen planus than in oral squamous cell carcinoma (P < .05). No statistically significant differences between the expression of p53, bax, and bcl-2 in oral lichen planus and oral squamous cell carcinoma were observed, which may be an evidence of the potential of malignant transformation of oral lichen planus.     

Identification and validation of two peptide markers for the recognition of Clostridioides difficile MLST-1 and MLST-11 by MALDI-MS

ObjectivesClostridioides difficile infection (CDI) has become the main cause of nosocomial infective diarrhoea. To survey and control the spread of different C. difficile strains, there is a need for suitable rapid tests. The aim of this study was to identify peptide/protein markers for the rapid recognition of C. difficile strains by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS).MethodsWe analysed 44 well-characterized strains, belonging to eight different multi-locus sequence types (MLST), using ultrahigh-resolution Fourier transform ion cyclotron resonance (FTICR) MS. The amino acid sequence of two peptide markers specific for MLST-1 and MLST-11 strains was elucidated by MALDI-TOF-MS/MS. The investigation of 2689 C. difficile genomes allowed the determination of the sensitivity and specificity of these markers. C18-solid-phased extraction was used to enrich the MLST-1 marker.ResultsTwo peptide markers (m/z 4927.81 and m/z 5001.84) were identified and characterized for MLST-1 and MLST-11 strains, respectively. The MLST-1 marker was found in 786 genomes of which three did not belong to MLST-1. The MLST-11 marker was found in 319 genomes, of which 14 did not belong to MLST-11. Importantly, all MLST-1 and MLST-11 genomes were positive for their respective marker. Furthermore, a peptide marker (m/z 5015.86) specific for MLST-15 was found in 59 genomes. We translated our findings into a fast and simple method that allowed the unambiguous identification of the MLST-1 marker on a MALDI-TOF-MS platform.ConclusionsMALDI-FTICR MS-based peptide profiling resulted in the identification of peptide markers for C. difficile MLST-1 and MLST-11.     

Blood culture diagnostics: a Nordic multicentre survey comparison of practices in clinical microbiology laboratories

ObjectivesAccurate and rapid microbiological diagnostics are crucial to tailor treatment and improve outcomes in patients with severe infections. This study aimed to assess blood culture diagnostics in the Nordic countries and to compare them with those of a previous survey conducted in Sweden in 2013.MethodsAn online questionnaire was designed and distributed to the Nordic clinical microbiology laboratories (CMLs) (n = 76) in January 2018.ResultsThe response rate was 64% (49/76). Around-the-clock incubation of blood cultures (BCs) was supported in 82% of the CMLs (40/49), although in six of these access to the incubators around the clock was not given to all of the cabinets in the catchment area, and 41% of the sites (20/49) did not assist with satellite incubators. Almost half (49%, 24/49) of the CMLs offered opening hours for ≥10 h during weekdays, more commonly in CMLs with an annual output ≥30 000 BCs. Still, positive BCs were left unprocessed for 60–70% of the day due to restrictive opening hours. Treatment advice was given by 23% of CMLs (11/48) in ≥75% of the phone contacts. Rapid analyses (species identification and susceptibility testing with short incubation), performed on aliquots from positive cultures, were implemented in 18% of CMLs (9/49). Compared to 2013, species identification from subcultured colonies (<6 h) had become more common.ConclusionsCMLs have taken action to improve aspects of BC diagnostics, implementing satellite incubators, rapid species identification and susceptibility testing. However, the limited opening hours and availability of clinical microbiologists are confining the advantages of these changes.     

Tubulin nitration in human gliomas

Immunohistochemical and biochemical investigations showed that significant protein nitration occurs in human gliomas, especially in grade IV glioblastomas at the level of astrocytes and oligodendrocytes and neurones. Enhanced alpha-tubulin immunoreactivity was co-present in the same elements in the glioblastomas. Proteomic methodologies were employed to identify a nitrated protein band at 55 kDa as alpha-tubulin. Peptide mass fingerprinting procedures demonstrated that tubulin is nitrated at Tyr224 in grade IV tumour samples but is unmodified in grade I samples and in non-cancerous brain tissue. These results provide the first characterisation of endogenously nitrated tubulin from human tumour samples.     

Discovery of a new biomarker for the mucopolysaccharidoses (MPS), dipeptidyl peptidase IV (DPP-IV; CD26), by SELDI-TOF mass spectrometry

Surface enhanced laser desorption/ionisation time of flight (SELDI-TOF) mass spectrometry has been used to search for new protein biomarkers in the plasma of patients with mucopolysacharidoses (MPS). Differences in the levels of some plasma proteins, particularly the apolipoprotein ApoCI, were observed between MPS patients and normal controls, using the different chromatographic surfaces (ProteinChips^®). ApoCI was identified by both its mass and by immunological techniques. In plasma, it exists in two forms, ApoCI and a truncated form which lacks two N-terminal amino acids, ApoCI′. In controls, the ratio of ApoCI′:ApoCI observed using the cation-exchange surface (CM10) was approximately 1:2 whereas in most MPS patients it varied from 1:1 to 1:0.8. The ratio of ApoCI′:ApoCI in plasma is determined by the activity of dipeptidyl peptidase IV, DPP-IV (also known as the leucocyte antigen CD26), which was found to be elevated up to 3-fold in MPS patients. The DPP-IV activity decreased in MPS I patients undergoing enzyme replacement therapy, indicating that it could be a useful biomarker for monitoring the efficacy of treatment in MPS disease. As DPP-IV has an important regulatory role in metabolism, it is possible that its elevation could cause some of the secondary pathology in MPS, and inhibition of DPP-IV might have a role in MPS therapy.     

The role of lysosomal rupture in neuronal death

Apoptosis research in the past two decades has provided an enormous insight into its role in regulating cell death. However, apoptosis is only part of the story, and inhibition of neuronal necrosis may have greater impact than apoptosis, on the treatment of stroke, traumatic brain injury, and neurodegenerative diseases. Since the “calpain–cathepsin hypothesis” was first formulated, the calpain- and cathepsin-mediated regulation of necrotic cascades observed in monkeys, has been demonstrated to be a common neuronal death mechanism occurring from simpler organisms to humans. However, the detailed mechanism inducing lysosomal destabilization still remains poorly understood. Heat-shock protein-70 (Hsp70) is known to stabilize lysosomal membrane and protect cells from oxidative stress and apoptotic stimuli in many cell death pathways. Recent proteomics approach comparing pre- and post-ischemic hippocampal CA1 neurons as well as normal and glaucoma-suffered retina of primates, suggested that the substrate protein upon which activated calpain acts at the lysosomal membrane of neurons might be Hsp70. Understanding the interaction between activated calpains and Hsp70 will help to unravel the mechanism that destabilizes the lysosomal membrane, and will provide new insights into clarifying the whole cascade of neuronal necrosis. Although available evidence is circumferential, it is hypothesized that activated calpain cleaves oxidative stress-induced carbonylated Hsp70.1 (a major human Hsp70) at the lysosomal membrane, which result in lysosomal rupture/permeabilization. This review aims at highlighting the possible mechanism of lysosomal rupture in neuronal death by a modified “calpain–cathepsin hypothesis”. As the autophagy–lysosomal degradation pathway is a target of oxidative stress, the implication of autophagy is also discussed.     

Identification of 11 new exoproteins in Corynebacterium pseudotuberculosis by comparative analysis of the exoproteome

This study involves the comparison between the exoproteomes of two different strains of Corynebacterium pseudotuberculosis, the etiologic agent of caseous lymphadenitis in small ruminants. In a previous study, based on a gel-free system (TPP-LC/MS^E), 70 exoproteins for the strain 1002 and 67 for the strain C231, totaling 93 different extracellular proteins for C. pseudotuberculosis, were identified. In the present work, we have used 2D gel electrophoresis to resolve the extracellular proteins of both strains, which were then digested with trypsin, analyzed by MALDI-TOF/TOF and identified with the software MASCOT^®. A total of 45 extracellular proteins of C. pseudotuberculosis were identified by this approach. The comparative analysis between the strains 1002 and C231 identified 13 and 3 strain-specific proteins, respectively, 11 of which are novel. These newly identified proteins may play an important role in the physiology and virulence of C. pseudotuberculosis.     

Detection of protein carbonyls in aging liver tissue: A fluorescence-based proteomic approach

Protein carbonyls are commonly used as a marker of protein oxidation in cells and tissues. Currently, 2,4-dinitrophenyl hydrazine (DNPH) is widely used (spectrophotometrically or immunologically) to quantify the global carbonyl levels in proteins and identify the specific proteins that are carbonylated. We have adapted a fluorescence-based approach using fluorescein-5-thiosemicarbazide (FTC), to quantify the global protein carbonyls as well as the carbonyl levels on individual proteins in the proteome. Protein carbonyls generated in vitro were quantified by labeling the oxidized proteins with FTC followed by separating the FTC-labeled protein from free probe by gel electrophoresis. The reaction of FTC with protein carbonyls was found to be specific for carbonyl groups. We measured protein carbonyl levels in the livers of young and old mice, and found a significant increase (two-fold) in the global protein carbonyl levels with age. Using 2-D gel electrophoresis, we used this assay to directly measure the changes in protein carbonyl levels in specific proteins. We identified 12 proteins showing a greater than two-fold increase in carbonyl content (pmoles of carbonyls/microg of protein) with age. Most of the 12 proteins contained transition metal binding sites, with Cu/Zn superoxide dismutase containing the highest molar ratio of carbonyls in old mice. Thus, the fluorescence-based assay gives investigators the ability to identify potential target proteins that become oxidized under different pathological and physiological conditions.     

Identification of N-linked carbohydrates from severe acute respiratory syndrome (SARS) spike glycoprotein

N-glycans were released from the SARS coronavirus (SARS-CoV) spike glycoprotein produced in Vero E6 cells and their structures were determined by a combination of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry, negative ion electrospray collision-induced dissociation time-of-flight mass spectrometry and normal-phase high-performance liquid chromatography with exoglycosidase digestion. Major glycans were high-mannose (Man_5-9GlcNAc₂), hybrid and bi-, tri- and tetra-antennary complex with and without bisecting GlcNAc and core fucose. Complex glycans with fewer than the full complement of galactose residues were present and sialylation was negligible. Treatment with the glucosidase inhibitor N-butyl-deoxynojirimycin (NB-DNJ) inhibited N-glycan processing as evidenced by the appearance of glycans of composition Glc₃Man_7-9GlcNAc₂. However, some complex glycans remained suggesting the presence of an α-endomannosidase. Our data in tissue culture indicate that inhibition of N-glycan processing may be considered as a therapeutic strategy against SARS CoV infections.