人血清蛋白质组学方法的比较和优化

目的:对人未做处理的血清以及去除白蛋白和免疫球蛋白G(IgG)血清的蛋白质组学方法进行比较和优化。方法:应用双向电泳(2-DE)方法分离了未做处理的以及去除白蛋白和免疫球蛋白G(IgG)的血清,比较优化了高温变性、水化液成份组成及泡胀方式等影响血清2-DE分离效果的因素,并用质谱分析鉴定未做处理和已处理血清的2-DE谱图中部分差异蛋白点。结果:得到了分辨率和重复性较好的2-DE谱图,未做处理的血清、去除白蛋白及IgG血清的平均蛋白质点分别为(482±18)个和(523±29)个,质谱分析了9个差异蛋白点,鉴定为8种蛋白质,其中7种为功能蛋白质。仅出现在未做处理血清中的蛋白有4种,分别是维生素A结合蛋白、可溶性尿激酶血纤维蛋白溶酶原激活剂受体、蛋白激酶1抗原、血清白蛋白。4种蛋白仅出现在去除白蛋白和IgG的血清中,分别是NADH脱氢酶辅酶β亚基、肌动蛋白结合蛋白M1、T细胞活性受体β链、血小板生长因子C。结论:去除高丰度蛋白可增加一些低丰度蛋白质的检出,但非特异性吸附会导致部分功能蛋白质的丢失。     

外固定支架及开放手术治疗肘关节严重异位骨化疗效分析

目的:探讨外固定支架及开放手术治疗治疗肘关节严重异位骨化的方法及疗效。方法:自2007年9月至2012年9月,对18例(其中男13例女5例,平均年龄33.5岁)创伤后严重异位骨化性肘关节僵硬患者进行开放手术及外固定支架治疗。所有患者均采用相同的手术方式,即取出原有内固定,前置尺神经,松解关节囊粘连,清除异位骨化。对患者肘关节屈伸范围术前及术后均评估,采用Mayo肘关节评分肘关节功能(MEPI)评估疗效。术后予以指导康复锻炼。结果:术后患者的屈伸分别平均增加到125°和10°,MEPI评分由术前的平均50分提高到术后的90分。结论:外固定支架及开放手术治疗治疗严重异位骨化性肘关节僵硬具有确切的疗效。     

III度膝关节内侧副韧带损伤缝合锚重建术后异位骨化8例临床分析

目的:分析8例III度膝关节内侧副韧带损伤的患者行缝合锚重建术后异位骨化发生与损伤的关系。方法:回顾性收集8例Ⅲ度膝关节内侧副韧带损伤行缝合锚重建术后发生异位骨化的患者,对其临床一般资料、损伤程度及部位、膝关节活动度及异位骨化程度等进行分析。结果:8位中Ⅰ度异位骨化4例,膝关节活动度73.75°~176.25°,平均125°,Ⅱ°异位骨化4例,膝关节活动度78.75°~157.25°,平均117.4°。在发生内侧副韧带异位骨化的8名患者中,仅有1名为单纯内侧副韧带损伤导致,其余7名患者中5名合并前叉或前、后叉韧带损伤,1例伴有胫骨髁间棘的撕脱骨折,1例合并胫骨平台骨折,4例合并胫骨或股骨髁骨折。结论:膝关节内侧异位骨化是异位骨化的好发部位,其发生与膝关节多发韧带损伤有关。     

Comparative Proteomic Analysis of Supportive and Unsupportive Extracellular Matrix Substrates for Human Embryonic Stem Cell Maintenance

Human embryonic stem cells (hESCs) are pluripotent cells that have indefinite replicative potential and the ability to differentiate into derivatives of all three germ layers. hESCs are conventionally grown on mitotically inactivated mouse embryonic fibroblasts (MEFs) or feeder cells of human origin. In addition, feeder-free culture systems can be used to support hESCs, in which the adhesive substrate plays a key role in the regulation of stem cell self-renewal or differentiation. Extracellular matrix (ECM) components define the microenvironment of the niche for many types of stem cells, but their role in the maintenance of hESCs remains poorly understood. We used a proteomic approach to characterize in detail the composition and interaction networks of ECMs that support the growth of self-renewing hESCs. Whereas many ECM components were produced by supportive and unsupportive MEF and human placental stromal fibroblast feeder cells, some proteins were only expressed in supportive ECM, suggestive of a role in the maintenance of pluripotency. We show that identified candidate molecules can support attachment and self-renewal of hESCs alone (fibrillin-1) or in combination with fibronectin (perlecan, fibulin-2), in the absence of feeder cells. Together, these data highlight the importance of specific ECM interactions in the regulation of hESC phenotype and provide a resource for future studies of hESC self-renewal.     

The Hippocampal Proteomic Analysis of Senescence-Accelerated Mouse: Implications of Uchl3 and Mitofilin in Cognitive Disorder and Mitochondria Dysfunction in SAMP8

Senescence-accelerated mouse prone 8 (SAMP8) is considered as a useful animal model for age-related learning and memory impairments. Hippocampus, a critical brain region associated with cognitive decline during normal aging and various neurodegenerative diseases, appeared a series of abnormalities in SAMP8. To investigate the molecular mechanisms underlying age-related cognitive disorders, we used 2-DE coupled with MALDI TOF/TOF MS to analyze the differential protein expression of the hippocampus of SAMP8 at 6-month-old compared with the age-matched SAM/resistant 1 (SAMR1) which shows normal aging process. Two proteins were found to be markedly changed in SAMP8 as compared to SAMR1: ubiquitin carboxyl-terminal hydrolase L3 (Uchl3), implicating in cytosolic proteolysis of oxidatively damaged proteins, was down-regulated while mitofilin, a vital protein for normal mitochondria function, exhibited four isoforms with a consistent basic shift of isoelectric point among the soluble hippocampal proteins in SAMP8 compared with SAMR1. The alterations were confirmed by Western blotting analysis. The analysis of their expression changes may shed light on the mechanisms of learning and memory deficits and mitochondrial dysfunction as observed in SAMP8.     

Protein Extraction From Leaves of Aloe vera L., A Succulent and Recalcitrant Plant, for Proteomic Analysis

An improved method for extracting proteins from leaf tissues of Aloe vera L., a recalcitrant plant species, for proteomic analysis is presented. In this protocol, the following critical components are included. A washing step is added prior to homogenization of the tissue to eliminate contaminants, and a concentrated 2× extraction buffer (pH 7.5) is used to increase protein yield. Compared to classical trichloroacetic acid–acetone and phenol extraction methods, this novel protocol has yielded two-dimensional electrophoresis gels with minimal (if any) streaking and provided high-quality protein samples. This protocol is expected to be applicable to other recalcitrant plant tissues.     

A Pilot Clinical Study of Hyperacute Serum Treatment in Osteoarthritic Knee Joint: Cytokine Changes and Clinical Effects

The serum fraction of platelet-rich fibrin (hyperacute serum) has been shown to improve cartilage cell proliferation in in vitro osteoarthritic knee joint models. We hypothesize that hyperacute serum may be a potential regenerative therapeutic for osteoarthritic knees. In this study, the cytokine milieu at the synovial fluid of osteoarthritic knee joints exposed to hyperacute serum intraarticular injections was investigated. Patients with knee osteoarthritis received three injections of autologous hyperacute serum; synovial fluid was harvested before each injection and clinical monitoring was followed-up for 6 months. Forty osteoarthritic-related cytokines, growth factors and structural proteins from synovial fluid were quantified and analysed by Multivariate Factor Analysis. Hyperacute serum provided symptomatic relief regarding pain and joint stability for OA patients. Both patients “with” and “without effusion knees” had improved VAS, KOOS and Lysholm-Tegner scores 6 months after of hyperacute serum treatment. Synovial fluid analysis revealed two main clusters of proteins reacting together as a group, showing strong and significant correlations with their fluctuation patterns after hyperacute serum treatment. In conclusion, hyperacute serum has a positive effect in alleviating symptoms of osteoarthritic knees. Moreover, identified protein clusters may allow the prediction of protein expression, reducing the number of investigated proteins in future studies.     

BrcaSeg: A Deep Learning Approach for Tissue Quantification and Genomic Correlations of Histopathological Images

Epithelial and stromal tissues are components of the tumor microenvironment and play a major role in tumor initiation and progression. Distinguishing stroma from epithelial tissues is critically important for spatial characterization of the tumor microenvironment. Here, we propose BrcaSeg, an image analysis pipeline based on a convolutional neural network (CNN) model to classify epithelial and stromal regions in whole-slide hematoxylin and eosin (H&E) stained histopathological images. The CNN model is trained using well-annotated breast cancer tissue microarrays and validated with images from The Cancer Genome Atlas (TCGA) Program. BrcaSeg achieves a classification accuracy of 91.02%, which outperforms other state-of-the-art methods. Using this model, we generate pixel-level epithelial/stromal tissue maps for 1000 TCGA breast cancer slide images that are paired with gene expression data. We subsequently estimate the epithelial and stromal ratios and perform correlation analysis to model the relationship between gene expression and tissue ratios. Gene Ontology (GO) enrichment analyses of genes that are highly correlated with tissue ratios suggest that the same tissue is associated with similar biological processes in different breast cancer subtypes, whereas each subtype also has its own idiosyncratic biological processes governing the development of these tissues. Taken all together, our approach can lead to new insights in exploring relationships between image-based phenotypes and their underlying genomic events and biological processes for all types of solid tumors. BrcaSeg can be accessed at https://github.com/Serian1992/ImgBio.     

The Effects of Prenatal Iron Deficiency and Risperidone Treatment on the Rat Frontal Cortex: A Proteomic Analysis

Prenatal iron deficiency (pID) has been described to increase the risk for neurodevelopmental disorders such as autism and schizophrenia; however, the precise molecular mechanisms are still unknown. Here, we utilized high‐throughput MS to examine the proteomic effects of pID in adulthood on the rat frontal cortex area (FCA). In addition, the FCA proteome was examined in adulthood following risperidone treatment in adolescence to see if these effects could be prevented. We identified 1501 proteins of which 100 were significantly differentially expressed in the FCA at postnatal day 90. Pathway analysis of proteins affected by pID revealed changes in metabolic processes, including the tricyclic acid cycle, mitochondrial dysfunction, and P13K/Akt signaling. Interestingly, most of these protein changes were not present in the adult pID offspring who received risperidone in adolescence. Considering the link between pID and several neurodevelopmental disorders such as autism and schizophrenia these presented results bring new perspectives to understand the role of iron in metabolic pathways and provide novel biomarkers for future studies of pID.     

Use of SILAC for exploring sheddase and matrix degradation of fibroblasts in culture by the PIII SVMP atrolysin A: identification of two novel substrates with functional relevance

Snake venom metalloproteinases (SVMPs) in Viperid venoms primarily function to give rise to local and systemic hemorrhage following snake envenomation. Years of research on these toxins, both in vitro and in vivo, indicate that they function by disrupting capillary basement membranes, stromal matrix and cell-cell and cell-matrix contacts to allow escape of capillary contents under pressure. However, most of these studies used either defined substrates in vitro or were limited by relevant antibodies for detection of sites of action in vivo. In this investigation we use stable isotope-labeled amino acids in culture (SILAC) to determine novel proteolytic activities for exogenously added atrolysin A, a hemorrhagic PIII SVMP isolated from Crotalus atrox venom. When comparing the solubilized products of SILAC-labeled cultured human fibroblasts treated with atrolysin A to that of untreated fibroblasts using LC/MS/MS, several proteins were identified as being released into the culture media specifically due to atrolysin A proteolytic activity. These included collagen VI, fibronectin, fibulin 2 and annexin V. Of particular interest was the observation of collagen VI and annexin V in that the release of these substrates could play a role in altering hemostasis and promote hemorrhage caused by the more typical actions of atrolysin A. In summary, this study demonstrates the utility of SILAC for exploring sheddase activity with cells in culture and suggests the presence of two novel substrates for SVMPs that may play a pathological role in altering host hemostasis during envenomation.     

Monoclonal Antibody-Based Dipstick Assay: A Reliable Field Applicable Technique for Diagnosis of Schistosoma mansoni Infection Using Human Serum and Urine Samples

A field applicable diagnostic technique, the dipstick assay, was evaluated for its sensitivity and specificity in diagnosing human Schistosoma mansoni infection. A monoclonal antibody (mAb) against S. mansoni adult worm tegumental antigen (AWTA) was employed in dipstick and sandwich ELISA for detection of circulating schistosome antigen (CSA) in both serum and urine samples. Based on clinical and parasitological examinations, 60 S. mansoni-infected patients, 30 patients infected with parasites other than schistosomiasis, and 30 uninfected healthy individuals were selected. The sensitivity and specificity of dipstick assay in urine samples were 86.7% and 90.0%, respectively, compared to 90.0% sensitivity and 91.7% specificity of sandwich ELISA. In serum samples, the sensitivity and specificity were 88.3% and 91.7% for dipstick assay vs. 91.7% and 95.0% for sandwich ELISA, respectively. The diagnostic efficacy of dipstick assay in urine and serum samples was 88.3% and 90.0%, while it was 90.8% and 93.3% for sandwich ELISA, respectively. The diagnostic indices of dipstick assay and ELISA either in serum or in urine were statistically comparable (P>0.05). In conclusion, the dipstick assay offers an alternative simple, rapid, non-invasive technique in detecting CSA or complement to stool examinations especially in field studies.     

小豆VaDREB1A基因克隆及其应答锈菌侵染的表达分析

为明确小豆VaDREB1A在抗锈菌侵染过程中的作用,本研究分别从小豆基因组DNA及cDNA中克隆了该基因,测序结果表明VaDREB1A无内含子,全长660 bp编码219个氨基酸,氨基酸序列包含1个AP2结构域,序列特征及系统发育分析表明VaDREB1A属于DREB/CBF亚家族A1亚类。启动子顺式元件分析发现,VaDREB1A启动子包含乙烯、水杨酸及生物和非生物胁迫等响应元件。对该基因响应豇豆单胞锈菌(Uromyces vignae)侵染的表达分析发现,与不接种对照相比,VaDREB1A在抗病品种中于接种后24 h和120 h显著下调,而在感病品种中于接种后120 h和192 h显著上调。在1-氨基环丙烷-1-羧酸(ACC)诱导小豆抗锈病过程中,VaDREB1A的表达与其在抗病品种中的表达相似,分别于ACC处理并接种后24 h和192 h显著下调。上述结果说明VaDREB1A可能参与小豆对锈病的抗性。     

Mass Spectrometry-based Structural Analysis and Systems Immunoproteomics Strategies for Deciphering the Host Response to Endotoxin

One cause of sepsis is systemic maladaptive immune response of the host to bacteria and specifically, to Gram-negative bacterial outer-membrane glycolipid lipopolysaccharide (LPS). On the host myeloid cell surface, proinflammatory LPS activates the innate immune system via Toll-like receptor-4/myeloid differentiation factor-2 complex. Intracellularly, LPS is also sensed by the noncanonical inflammasome through caspase-11 in mice and 4/5 in humans. The minimal functional determinant for innate immune activation is the membrane anchor of LPS called lipid A. Even subtle modifications to the lipid A scaffold can enable, diminish, or abolish immune activation. Bacteria are known to modify their LPS structure during environmental stress and infection of hosts to alter cellular immune phenotypes. In this review, we describe how mass spectrometry-based structural analysis of endotoxin helped uncover major determinations of molecular pathogenesis. Through characterization of LPS modifications, we now better understand resistance to antibiotics and cationic antimicrobial peptides, as well as how the environment impacts overall endotoxin structure. In addition, mass spectrometry-based systems immunoproteomics approaches can assist in elucidating the immune response against LPS. Many regulatory proteins have been characterized through proteomics and global/targeted analysis of protein modifications, enabling the discovery and characterization of novel endotoxin-mediated protein translational modifications.