Proteomics in pathology, research and practice

Serum Proteomic Analysis by Tandem Mass Tag-Based Quantitative Proteomics in Pediatric Obstructive Sleep Apnea

Pediatric obstructive sleep apnea (OSA) is a frequent respiratory disorder with an estimated prevalence of 3–6% in the general population. However, the underlying pathophysiology of OSA remains unclear. Recently, proteomic analysis using high-resolution and high-throughput mass spectrometry has been widely used in the field of medical sciences. In the present study, tandem mass tag (TMT)-based proteomic analysis was performed in the serum of patients with OSA. The proteomic analysis revealed a set of differentially expressed proteins that may be associated with the pathophysiology of OSA. The differentially expressed proteins in patients with OSA were enriched in pathways including phagosome and glycan synthesis/degradation, immune response, and the hedgehog signaling pathway, indicating that such functions are key targets of OSA. Moreover, the experimental validation studies revealed that four proteins including ANTXR1, COLEC10, NCAM1, and VNN1 were reduced in the serum from patients with moderate and severe OSA, while MAN1A1 and CSPG4 protein levels were elevated in the serum from patients with severe OSA. The protein levels of ANTXR1, COLEC10, NCAM1, and VNN1 were inversely correlated with apnea-hypopnea index (AHI) in the recruited subjects, while the protein level of MAN1A1 was positively correlated with AHI, and no significant correlation was detected between CSPG4 protein and AHI. In summary, the present study for the first time identified differentially expressed proteins in the serum from OSA patients with different severities by using TMT-based proteomic analysis. The functional enrichment studies suggested that several signaling pathways may be associated with the pathophysiology of OSA. The experimental validation results indicated that six proteins including ANTXR1, COLEC10, NCAM1, VNN1, CGPG4, and MAN1A1 may play important roles in the pathophysiology of OSA, which requires further mechanistic investigation.

Using Omics Approaches in the Discovery of Biomarkers for Early Diagnosis of Johne's Disease in Sheep and Goats

Simple Summary

Johne’s disease (JD) is caused by Mycobacterium avium subsp. paratuberculosis (MAP) and is an important and emerging problem in livestock. Most JD research has been carried out on cattle, but interest in the pathogenesis and diagnosis of this disease in sheep and goats is greatest in developing countries. Sheep and goats are also a relevant part of livestock production in Europe and Australia, and these species provide an excellent resource to study and better understand the mechanism of survival of MAP and gain insights into possible approaches to control this disease. This review gives an overview of the literature on paratuberculosis in sheep and goats, highlighting the immunological aspects and the potential for “omics” approaches to identify effective biomarkers for the early detection of infection.

Abstract

Johne’s disease (JD) is caused by Mycobacterium avium subsp. paratuberculosis (MAP) and is an important and emerging problem in livestock; therefore, its control and prevention is a priority to reduce economic losses and health risks. Most JD research has been carried out on cattle, but interest in the pathogenesis and diagnosis of this disease in sheep and goats is greatest in developing countries. Sheep and goats are also a relevant part of livestock production in Europe and Australia, and these species provide an excellent resource to study and better understand the mechanism of survival of MAP and gain insights into possible approaches to control this disease. This review gives an overview of the literature on paratuberculosis in sheep and goats, highlighting the immunological aspects and the potential for “omics” approaches to identify effective biomarkers for the early detection of infection. As JD has a long incubation period before the disease becomes evident, early diagnosis is important to control the spread of the disease.

Protein Biomarkers in Uveitis

The diseases affecting the retina or uvea (iris, ciliary body, or choroid) generate changes in the biochemical or protein composition of ocular fluids/tissues due to disruption of blood-retinal barrier. Ocular infections and inflammations are sight-threatening diseases associated with various infectious and non-infectious etiologies. Several etiological entities cause uveitis, a complex intraocular inflammatory disease. These causes of uveitis differ in different populations due to geographical, racial, and socioeconomic variations. While clinical appearance is sufficiently diagnostic in many diseases, some of the uveitic entities manifest nonspecific or atypical clinical presentation. Identification of biomarkers in such diseases is an important aid in their diagnostic armamentarium. Different diseases and their different severity states release varying concentrations of proteins, which can serve as biomarkers. Proteomics is a high throughput technology and a powerful screening tool for serum biomarkers in various diseases that identifies proteins by mass spectrometry and helps to improve the understanding of pathogenesis of a disease. Proteins determine the biological state of a cell. Once identified as biomarkers, they serve as future diagnostic and pharmaceutical targets. With a potential to redirect the diagnosis of idiopathic uveitis, ocular proteomics provide a new insight into the pathophysiology and therapeutics of various ocular inflammatory diseases. Tears, aqueous and vitreous humor represent potential repositories for proteomic biomarkers discovery in uveitis. With an extensive proteomics work done on animal models of uveitis, various types of human uveitis are being subjected to proteome analysis for biomarker discovery in different ocular fluids (vitreous, aqueous, or tears).

Application of Proteomics to Inflammatory Bowel Disease Research: Current Status and Future Perspectives

Inflammatory bowel disease (IBD) is a chronic relapsing/remitting inflammatory illness of the gastrointestinal tract of unknown aetiology. Despite recent advances in decoding the pathophysiology of IBD, many questions regarding disease pathogenesis remain. Genome-wide association studies (GWAS) and knockout mouse models have significantly advanced our understanding of genetic susceptibility loci and inflammatory pathways involved in IBD pathogenesis. Despite their important contribution to a better delineation of the disease process in IBD, these genetic findings have had little clinical impact to date. This is because the presence of a given gene mutation does not automatically correspond to changes in its expression or final metabolic or structural effect(s). Furthermore, the existence of these gene susceptibility loci in the normal population suggests other driving prerequisites for the disease manifestation. Proteins can be considered the main functional units as almost all intracellular physiological functions as well as intercellular interactions are dependent on them. Proteomics provides methods for the large-scale study of the proteins encoded by the genome of an organism or a cell, to directly investigate the proteins and pathways involved. Understanding the proteome composition and alterations yields insights into IBD pathogenesis as well as identifying potential biomarkers of disease activity, mucosal healing, and cancer progression. This review describes the state of the art in the field with respect to the study of IBD and the potential for translation from biomarker discovery to clinical application.

Discovery of gastric cancer specific biomarkers by the application of serum proteomics

Current diagnostic markers for gastric cancer are not sufficiently specific or sensitive for use in clinical practice. The aims of this study are to compare the proteomes of serum samples from patients with gastric cancers and normal controls, and to develop useful tumor markers of gastric cancer by quantitative proteomic analysis. We identified a total of 388 proteins with a ≤1% FDR and with at least two unique peptides from the sera of each group. Among them, 215, 251, and 260 proteins were identified in serum samples of patients in an advanced cancer group, early cancer group, and normal control group, respectively. We selected differentially expressed proteins in cancer patients compared with those of normal controls via semiquantitative analyses comparing the spectral counts of identified proteins. These differentially expressed proteins were successfully verified using an MS-based quantitative assay, multiple reactions monitoring analysis. Four proteins (vitronectin, clusterin isoform 1, thrombospondin 1, and tyrosine-protein kinase SRMS) were shown to have significant changes between the cancer groups and the normal control group. These four serum proteins were able to discriminate gastric cancer patients from normal controls with sufficient specificity and selectivity.

Potential Serum Markers for Monitoring the Progression of Hepatitis B Virus-Associated Chronic Hepatic Lesions to Liver Cirrhosis

BACKGROUND/AIMS

To screen for serum protein/peptide biomarkers of hepatitis B virus (HBV)-associated chronic hepatic lesions in an attempt to profile the progression of HBV-associated chronic hepatic lesions using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) techniques.

METHODS

Using SELDI-TOF MS, serum protein/peptide profiles on the CM10 ProteinChip arrays were obtained from a training group including 26 HBV-associated hepatocellular carcinoma patients with liver cirrhosis (LC), 30 HBV-associated LC patients, 85 patients at different stages of liver fibrosis, and 30 asymptomatic HBV carriers. The most valuable SELDI peak for predicting the progression to LC in HBV-infected patients was identified.

RESULTS

A SELDI peak of M/Z 5805 with value for predicting LC in HBV-infected patients was found and was identified as a peptide of the C-terminal fraction of the fibrinogen a-chain precursor, isoform 1.

CONCLUSIONS

The peptide of the C-terminal fraction of the fibrinogen α-chain precursor, isoform 1 with M/Z 5805, may be a serological biomarker for progression to LC in HBV-infected patients.

Comparative Proteomic Analysis of Mature and Immature Oocytes of the Swamp Buffalo (Bubalus bubalis)

Maternal protein components change markedly during mammalian oogenesis. Many of these proteins have yet to be characterized and verified. In this study, a proteomics approach was used to evaluate changes in proteins during oogenesis in the Swamp Buffalo (Bubalus bubalis). Proteins from 500 immature oocytes and 500 in vitro matured oocytes were subjected to two-dimensional electrophoresis, and more than 400 spots were detected. Image analysis indicated that 17 proteins were differentially expressed between the two groups. Eight proteins were identified by mass spectrometry. In mature oocytes, three proteins were down-regulated: major vault protein (MVP), N-acetyllactosaminide β-1,6-N-acetylglucosaminyl-transferase (GCNT-2), and gem-associated protein (GEMIN)8, whereas five other proteins, heat shock protein (HSP)60, Ras-responsive element-binding protein 1 (RREB-1), heat shock cognate 71 kDa protein (HSC71), hemoglobin subunit α (HBA), and BMP-2-inducible protein kinase (BMP-2K), were up-regulated. The expression profiles of HSP60 and GEMIN8 were further verified by Western blotting. The changes in HSP60 protein expression demonstrate the increasing need for mitochondrial protein importation to facilitate macromolecular assembly during oocyte maturation. The down-regulation of GEMIN8 production implies that RNA splicing is impaired in mature oocytes.

Differential Expression of Proteins Associated with the Hair Follicle Cycle - Proteomics and Bioinformatics Analyses

Hair follicle cycling can be divided into the following three stages: anagen, catagen, and telogen. The molecular signals that orchestrate the follicular transition between phases are still unknown. To better understand the detailed protein networks controlling this process, proteomics and bioinformatics analyses were performed to construct comparative protein profiles of mouse skin at specific time points (0, 8, and 20 days). Ninety-five differentially expressed protein spots were identified by MALDI-TOF/TOF as 44 proteins, which were found to change during hair follicle cycle transition. Proteomics analysis revealed that these changes in protein expression are involved in Ca2+-regulated biological processes, migration, and regulation of signal transduction, among other processes. Subsequently, three proteins were selected to validate the reliability of expression patterns using western blotting. Cluster analysis revealed three expression patterns, and each pattern correlated with specific cell processes that occur during the hair cycle. Furthermore, bioinformatics analysis indicated that the differentially expressed proteins impacted multiple biological networks, after which detailed functional analyses were performed. Taken together, the above data may provide insight into the three stages of mouse hair follicle morphogenesis and provide a solid basis for potential therapeutic molecular targets for this hair disease.

Apolipoprotein AII levels are associated with the UP/UCr levels in idiopathic steroid-sensitive nephrotic syndrome

BACKGROUND

Various humoral factors have been proposed as causal agents of idiopathic steroid-sensitive nephrotic syndrome (ISSNS), resulting in varying data. We used mass spectrometry (MS) to analyze serum proteins in a search for proteins that might be involved in ISSNS pathophysiology.

METHODS

Serial serum samples were obtained from 33 children with ISSNS. Samples were collected during Phase A1 [the acute phase prior to steroid treatment (STx)], Phase A2 (remission with STx), and Phase A3 (remission without any medication). We also included age- and sex-matched two control groups comprising children with normal urinalysis (Group B) and children with a nephrotic syndrome other than ISSNS (Group C). The urinary protein/urinary creatinine (UP/UCr) ratios were not statistically different between Phase A1 and Group C. Samples were analyzed using surface-enhanced laser desorption/ionization time of flight MS.

RESULTS

A total of 207 peptide ion peaks were detected in the range of m/z 2000-10000. Four peptide ions (m/z 6444, 6626, 8695, and 8915) were detected at significant elevation during Phase A1 compared with Phase A2, Phase A3, and Group C. The intensities of m/z 6444 and 8695 were higher in Phase A3 than in Group B. There were significant correlations between the intensities of m/z 6626, 8695, and 8915 and UP/UCr levels. The m/z 8695 was identified as apolipoprotein AII.

CONCLUSIONS

Apolipoprotein AII was detected as a protein associated with the UP/UCr levels in pediatric ISSNS. Our findings present an interesting starting point for further investigation into the pathophysiology of ISSNS.

Oocyte cryopreservation: searching for novel improvement strategies

PURPOSE

To highlight emerging techniques aimed at improving oocyte cryopreservation.

METHODS

Review of available and relevant literature through Pubmed and Medline searches.

RESULTS

Oocyte cryopreservation is an increasingly common procedure utilized for assisted reproduction and may benefit several patient populations. Therefore, improving efficiency is paramount in realizing the tremendous promise of this approach. However, in addition to numerous studies looking to improve oocyte cryopreservation efficacy via examination of variables involved with protocol methodology, such as type/concentration of cryoprotectant (CPA), type of storage device, or cooling/warming rates, there are more novel approaches for improvement. These alternate approaches include utilizing different the stages of oocytes, examining alteration of basal media and buffer composition, optimizing CPA exchange protocols and device loading through use of automated technology, as well as examination/manipulation of oocyte cellular composition to improve cryotolerance. Finally, elucidating more accurate or insightful indicators of "success" is crucial for continued improvement of oocyte cryopreservation.

CONCLUSION

Oocyte cryopreservation has improved dramatically in recent years and is receiving widespread clinical use. Novel approaches to further improve success, as well as improved methods to assess this success will aid in continued improvement.

Identification of serum CCL15 in hepatocellular carcinoma

Background:

Early serum detection is of critical importance to improve the therapy for hepatocellular carcinoma (HCC), one of the most deadly cancers. Hepatitis infection is a leading cause of HCC.

Methods:

In the present study, we collected total serum samples with informed consent from 80 HCC patients with HBV (+)/cirrhosis (+), 80 patients with benign diseases (50 liver cirrhosis patients and 30 HBV-infected patients) and 60 healthy controls. Analysis was by using surface-enhanced laser desorption/ionisation-time-of-flight mass spectroscopy (SELDI-TOF-MS) to find new serum markers of HCC. SELDI peaks were isolated by SDS–PAGE, identified by LC-MS/MS and validated by immunohistochemistry (IHC) in liver tissues. Migration and invasion assay were performed to test the ability of cell migration and invasion in vitro.

Results:

SELDI-TOF-MS revealed a band at 7777 M/Z in the serum samples from HCC patients but not from healthy controls or patients with benign diseases. The protein (7777.27 M/Z) in the proteomic signature was identified as C-C motif chemokine 15 (CCL15) by peptide mass fingerprinting. A significant increase in serum CCL15 was detected in HCC patients. Functional analysis showed that HCC cell expressed CCL15, which in turn promoted HCC cell migration and invasion.

Conclusion:

CCL15 may be a specific proteomic biomarker of HCC, which has an important role in tumorigenesis and tumour invasion.

Increased α1-antitrypsin levels in acute-phase Kawasaki disease as shown by SELDI-TOF MS analysis

Various agents have been suggested as causal or associated factors in the pathogenesis of Kawasaki disease (KD); however, the underlying factors of KD remain unknown. Plasma exchange is one of the most effective treatments for the acute phase of KD. This indicates that plasma may contain factors associated with the pathogenesis of KD. To search for proteins that may be involved in KD pathogenesis, we analyzed serum proteins with surface-enhanced laser desorption/ionization time of flight mass spectrometry (SELDI-TOF MS). Serum samples were obtained from 17 KD patients. Serum from six of the patients was collected during acute phase before acetylsalicylic acid (ASA) and intravenous immunoglobulin administration (phase A1), during remission with ASA (phase A2), and during remission without any medication (phase A3). Serum from the remaining 11 patients was collected for phases A1 and A2 only. There were two age- and sex-matched control groups comprising 8 afebrile healthy children (group B) and 8 febrile children with several infectious diseases (group C). There were no statistical differences in laboratory examination between phase A1 and group C except for albumin level, alanine aminotransferase, or sodium level. Serum samples were analyzed by SELDI-TOF MS after purification. We detected five peaks, i.e., those were specifically increased or decreased during phase A1, and identified 1 of these as α1-antitrypsin (α1-AT). α1-AT can inhibit neutrophil elastase activity. This elastase is thought to play a role in coronary artery damage. Our findings present an interesting starting point for further investigations into the pathophysiology of KD.

Novel prognostic protein markers of resectable pancreatic cancer identified by coupled shotgun and targeted proteomics using formalin-fixed paraffin-embedded tissues

Pancreatic cancer is among the most lethal malignancies worldwide. We aimed to identify novel prognostic markers by applying mass spectrometry (MS)-based proteomic analysis to formalin-fixed paraffin-embedded (FFPE) tissues. Resectable, node positive pancreatic ductal adenocarcinoma (PDAC) with poor (n = 4) and better (n = 4) outcomes, based on survival duration, with essentially the same clinicopathological backgrounds, and noncancerous pancreatic ducts (n = 5) were analyzed. Cancerous and noncancerous cells collected from FFPE tissue sections by laser microdissection (LMD) were processed for liquid chromatography (LC)-tandem MS (MS/MS). Candidate proteins were identified by semiquantitative comparison and then analyzed quantitatively using selected reaction monitoring (SRM)-based MS. To confirm the associations between candidate proteins and outcomes, we immunohistochemically analyzed a cohort of 87 cases. In result, totally 1,229 proteins were identified and 170 were selected as candidate proteins for SRM-based targeted proteomics. Fourteen proteins overexpressed in cancerous as compared to noncancerous tissue showed different expressions in the poor and better outcome groups. Among these proteins, we found that three novel proteins ECH1, OLFM4 and STML2 were overexpressed in poor group than in better group, and that one known protein GTR1 was expressed reciprocally. Kaplan-Meier analysis showed high expressions of all four proteins to correlate with significantly worse overall survival (p < 0.05). In conclusion, we identified four proteins as candidates of prognostic marker of PDAC. The combination of shotgun proteomics verified by SRM and validated by immunohistochemistry resulted in the prognostic marker discovery that will contribute the understanding of PDAC biology and therapeutic development.

Proteomic analysis of serum of workers occupationally exposed to arsenic, cadmium, and lead for biomarker research: a preliminary study

The main factor of environmental contamination is the presence of the heavy metals lead, cadmium, and arsenic. The aim of serum protein profile analysis of people chronically exposed to heavy metals is to find protein markers of early pathological changes. The study was conducted in a group of 389 healthy men working in copper foundry and 45 age-matched non-exposed healthy men. Toxicological test samples included whole blood, serum, and urine. Thirty-seven clinical parameters were measured. Based on the parameters values of the healthy volunteers, the centroid in 37-dimensional space was calculated. The individuals in the metal-exposed and control groups were ordered based on the Euclidean distance from the centroid defined by the first component according to Principal Component Analysis (PCA). Serum samples of two individuals, one from the control and one from the metal-exposed group, were chosen for proteomic analysis. In optimized conditions of two-dimensional gel electrophoresis (2-DE), two protein maps were obtained representing both groups. Twenty-eight corresponding protein spots from both protein maps were chosen and identified based on PDQuest analysis and the SWISS-2DPAGE database. From a panel of six proteins with differences in expression greater than a factor of two, three potential markers with the highest differences were selected: hemoglobin-spot 26 (pI 7.05, Mw 10.53), unidentified protein-spot 27 (pI 6.73, Mw 10.17), and unidentified protein-spot 25 (pI 5.75, Mw 12.07). Further studies are required to prove so far obtained results. Identified proteins could serve as potential markers of preclinical changes and could be in the future included in biomonitoring of people exposed to heavy metals.

Protein expression profile of the mouse metaphase-II oocyte

The mature oocyte contains the full complement of maternal proteins required for fertilization, the transition to zygotic transcription, and the beginning stages of embryogenesis. Many of these proteins have yet to be characterized. In this study, two-dimensional electrophoresis (2-DE) of mouse metaphase-II (MII) oocyte proteins, stained with silver staining or Pro-Q Diamond dye, was performed to describe the proteome and phosphoproteome of the mouse oocyte derived from ICR mice. A total of 869 selected protein spots, corresponding to 380 unique proteins, were identified successfully by mass spectrometry, in which 90 protein spots representing 53 unique proteins have been stained with Pro-Q Diamond, indicating that they are in phosphorylated forms. All identified proteins were bioinformatically annotated in detail and compared with the embryonic stem cell (ESC) proteome. A proteome reference database for the mouse oocyte was established from the protein data generated in this study, which can be accessed over the Internet ( http://reprod.njmu.edu.cn/2d). This database is the most detailed mouse oocyte proteomic database to date. It should be valuable in expanding our knowledge of the regulation of signaling in oogenesis, fertilization, and embryo development, while revealing potential mechanisms for epigenetic reprogramming.

Proteomic profiling of ovine serum by SELDI-TOF MS: optimisation, reproducibility and feasibility of biomarker discovery using routinely collected samples

The diagnosis of infectious diseases in animals may be enhanced by study of the serum proteome in which myriad components are influenced by physiological and pathological processes. Surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI-TOF MS) has the capacity to detect known and unknown immunologically relevant molecules in the serum proteome. Optimum combinations of ProteinChip array surfaces, energy absorbing molecules, sample dilutions and instrument settings were determined for spectral generation from whole ovine sera. The coefficient of variation for within and between chip mass/charge and peak intensity were <0.03% and <23%, respectively. There were minor alterations in spectra associated with storage of chips or machine drift. Clotting times of 30 min to 3h did not greatly alter protein spectra although storage of sera at -20 degrees C led to alterations. However, routinely collected serum samples stored at -20 degrees C were useful for identification of biomarkers associated with vaccination with a bacterial antigen. This information will inform future studies on serum proteome profiling in livestock, but independent assessments are recommended for each species.

Proteomics of pancreatic cancer

Pancreatic cancer is a devastating disease, with a mortality rate almost identical with its incidence. Late diagnosis and limited therapeutic options make early detection of pancreatic cancer a pressing clinical problem. In this context, the investigation of the pancreatic cancer proteome has recently gained considerable attention because profiles of proteins may be able to more accurately identify disease states, such as cancer. Recent pancreatic cancer proteome studies may be categorized into basic studies cataloguing the pancreatic proteome, studies investigating differential protein expression patterns, and studies searching for proteome-based biomarkers for early cancer detection and differentiation. Although these studies clearly demonstrate that a range of biological samples are suitable for proteomic analyses, comparison of different studies is problematic due to the diversity of methodologies, sample sources, and characterization of patient populations. Reproducibility between studies has rarely been investigated, and no investigation has compared the different methods of proteomic research. The results of this review have shown that more stringent requirements concerning the design and the analysis of future studies should be implemented. These include an adequate patient number, obligatory histological examination of tissues, appropriate control groups, identification of proteins and peaks, validation of differential expression using independent cohorts and/or a second methodology, and, finally, demonstration of result reproducibility. This will hopefully lead to the discovery of prognostic and predictive biomarkers that help to improve prognosis of pancreatic cancer patients.

Detection and identification of NAP-2 as a biomarker in hepatitis B-related hepatocellular carcinoma by proteomic approach

BACKGROUND

A lack of sensitive and specific biomarkers is a major reason for the high rate of Primary hepatocellular carcinoma (HCC)-related mortality. The aim of this study was to investigate potential proteomic biomarkers specific for HCC.

METHODS

81 patients with hepatitis B-related HCC and 33 healthy controls were randomly divided into a training set (33 HCC, 33 controls) and a testing set (48 HCC, 33 controls). Serum proteomic profiles were measured using Surface-enhanced laser desorption/ionization-time-of-flight mass spectroscopy (SELDI-TOF-MS).) A classification tree was established by Biomarker Pattern Software (BPS). Candidate SELDI peaks were isolated by tricine-SDS-PAGE, identified by HPLC-MS/MS and validated by immunohistochemistry (IHC) in liver tissues.

RESULTS

A total of 6 proteomic peaks (3157.33 m/z, 4177.02 m/z, 4284.79 m/z, 4300.80 m/z, 7789.87 m/z, and 7984.14 m/z) were chosen by BPS to establish a classification tree with the highest discriminatory power in the training set. The sensitivity and specificity of this classification tree were 95.92%, and 100% respectively in the testing set. A candidate marker of about 7984 m/z was isolated and identified as neutrophil-activating peptide 2 (NAP-2). IHC staining showed that NAP-2 signals were positive in HCC tissues but negative in adjacent tissues.

CONCLUSION

The NAP-2 may be a specific proteomic biomarker of hepatitis B-related HCC.

Fractionation of proteins by heparin chromatography

Heparins are negatively charged polydispersed linear polysaccharides which have the ability to bind a wide range of biomolecules including enzymes, serine protease inhibitors, growth factors, extracellular matrix proteins, DNA modification enzymes and hormone receptors. In this chromatography, heparin is not only an affinity ligand but also an ion exchanger with high charge density and distribution. Heparin chromatography is an adsorption chromatography in which biomolecules can be specifically and reversibly adsorbed by heparins immobilized on an insoluble support. An advantage of this chromatography is that heparin-binding proteins can be conveniently enriched using its concentration effect. This is especially important for separating low abundance proteins for the analysis in two-dimensional electrophoresis (2DE) or other proteomics approaches. Heparin chromatography is a powerful sample-pretreatment technology that has been widely used to fractionate proteins from extracts of prokaryotic organism or eukaryotic cells. As an example, the fractionation of fibroblast growth factors (FGFs) from the extract of mouse brain microvascular endothelial cells (MVEC) is now introduced to demonstrate the procedure of heparin chromatography.

Discovery of distinct protein profiles for polycystic ovary syndrome with and without insulin resistance by surface-enhanced laser adsorption/ionization time of flight mass spectrometry

OBJECTIVE

To screen the serum protein expression profiles in patients having polycystic ovary syndrome (PCOS) with or without insulin resistance (IR) and search for discriminatory proteins.

DESIGN

Cross-sectional study.

SETTING

Reproductive Center of Peking University Third Hospital.

PATIENT(S)

Thirty patients with PCOS with IR, 30 patients with PCOS without IR, and 30 control individuals.

INTERVENTION(S)

Fasting serum samples.

MAIN OUTCOME MEASURE(S)

Serum protein peak spectrum.

RESULT(S)

There were 27 differential protein peaks between patients with PCOS and IR and controls, 17 between patients with PCOS without IR and controls, and 19 between patients with PCOS and IR and patients without IR. Marker proteins from differentially expressed proteins were screened out with use of a support vector machine and were used to establish three diagnostic models for PCOS IR, PCOS non-IR, and IR, respectively.

CONCLUSION(S)

There were statistically significantly different serum proteomic patterns in different types of PCOS. With use of ProteinChip combined with the support vector machine, computer diagnostic models for PCOS with and without IR were set up quickly and efficiently. These discriminatory proteins may help us understand the proteomic changes in serum and find out potential biomarkers of PCOS and IR.

Proteomic analysis of human ovaries from normal and polycystic ovarian syndrome

Polycystic ovary syndrome (PCOS) is the most common cause of anovulatory infertility, affecting 5-10% of females of reproductive age. Currently, little is known about the changes in whole proteins between PCOS and normal ovaries. In the present study, a proteomic approach comprised two-dimensional gel electrophoresis (2DE) analysis and mass spectroscopy was used to identify proteins and examine expression patterns in three PCOS and normal ovaries. One hundred and ten protein spots were separated and showed different intensities between PCOS and normal ovaries. Sixty-nine proteins associated with cellular metabolism and physiological process were identified from 72 spots. Fifty-four proteins were up-regulated in PCOS ovaries and 15 other proteins were up-regulated in normal ovaries. These data demonstrate, for the first time, the complexity in the regulation of ovarian protein expression in human PCOS, and will provide important insight for a better understanding of the pathogenetic mechanisms underlying this clinical disorder.

Emerging technologies for the molecular study of infertility, and potential clinical applications

The techniques currently used to treat infertility cases are quite limited in their capabilities, due to an incomplete understanding of the molecular activities of germ cells. Fortunately, several technologies are presently being researched that should aid the understanding of the various molecular causes of germ cell pathologies. This review discusses microarray technology, proteomics, metabolic profiling, the PolScope, atomic force microscopy and microfluidics. These technologies have all seen success in preliminary studies, and promise directly or indirectly to improve the low success rates of IVF and other related therapies. However, their widespread use in laboratories and clinics may not be seen until preliminary studies confirming their safety and effectiveness are published, and until standardized protocols for their utilization are established.

Analysis of oocyte physiology to improve cryopreservation procedures

In contrast to the preimplantation mammalian embryo, it has been notoriously difficult to cryopreserve the metaphase II oocyte. The ability to store oocytes successfully at -196 degrees C has numerous practical and financial advantages, together with ethical considerations, and will positively impact animal breeding programs and assisted conception in the human. Differences in membrane permeability and in physiology are two main reasons why successful oocyte cryopreservation has remained elusive. It is proposed, therefore, that rather than relying on technologies already established for the preimplantation embryo, the development of cryopreservation techniques suitable for the mammalian oocyte needs to take into account the idiosyncratic physiology of this cell. Analysis of intracellular calcium, for example, has revealed that exposure to conventional permeating cryoprotectants, such as propanediol, ethylene glycol and DMSO, all independently result in an increase in calcium, which in turn has the potential to initiate oocyte activation, culminating in zona hardening. Quantification of the metabolome and proteome of the oocyte has revealed that whereas slow freezing has a dramatic effect on cell physiology, vitrification appears to have limited effect. This is plausibly achieved by the limited exposure to cryoprotectants. Analysis of meiotic spindle dynamics and embryo development following IVF, also indicate that vitrification is less traumatic than slow freezing, and therefore has the greatest potential for successful oocyte cryopreservation.

Nanopatterning proteins and peptides

A variety of techniques have been developed to site-specifically immobilize biomolecules onto surfaces with resolutions below one micron. The ability to pattern proteins and peptides in particular has great potential for applications in biosensors, biomaterials, and tissue engineering. For example, immobilizing proteins at the nanoscale could lead to the development of diagnostic protein nanoarrays, while patterning peptides could lead to greater control over the cell/biomaterial interface. This review discusses the methods that have been reported for patterning proteins and peptides with submicron and nanometer resolutions.

A path or a new road in laboratory diagnostics? Biological mass spectrometry: Facts and perspectives

Proteins in tissues and biofluids and their many attributes define the proteome. Proteome can be directly correlated to known diseases and histological regions allowing the diagnosis and monitoring of disease progression as well predicting the patient's response to specific treatments. Proteomics performs large-scale, high-throughput characterization of the human proteome, among others by biological mass spectrometry. Proteinchip technology coupled with bioinformatics is able to screen any protein source for putative disease biomarkers from a small sample volume (microliter range) by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS). This article discusses on a basic level both the technology and reliability of these methods.

Molecular screening of gastric cancer by proteome analysis

Gastric cancer affects annually more than 800,000 individuals worldwide and remains a challenge for clinicians and oncologists. Most patients with gastric cancer are diagnosed in advanced stages, when a curative resection is impossible, which leads to an overall poor prognosis. Finding new diagnostic and treatment procedures is of paramount importance to improve patient prognosis, which will be improved most dramatically by techniques that allow the detection of gastric cancer in its early stages. So far the value of conventional tumour markers such as Ca72-4 or carcinoembryonic antigen is limited, and even markers developed from molecular biological studies on the carcinogenesis of gastric cancer, such as E-cadherin and others, have not proved to be of adequate sensitivity and specificity to allow the early detection of gastric cancer. With the development of innovative diagnostic tools, such as proteome analysis, new biomarkers may be identified that may allow early diagnosis and thus screening for gastric cancer, particularly in at-risk patient populations. Recent studies have indicated that these biomarkers may be derived from the tumour itself or reflect a specific metabolic or immunological response to cancer that can be used to find gastric cancer patients at an early and putatively curative stage of the disease.

Identification of protein biomarkers for schizophrenia and bipolar disorder in the postmortem prefrontal cortex using SELDI-TOF-MS ProteinChip profiling combined with MALDI-TOF-PSD-MS analysis

This paper describes the high-throughput proteomic analysis of the dorsolateral prefrontal cortex (DLPFC) from schizophrenia (SCHIZ), bipolar (BD), and normal control cohorts from the Harvard Brain Tissue Resource Center performed using ProteinChip technology based on the surface-enhanced laser desorption/ionization time of flight mass spectrometry (SELDI-TOF-MS). The resultant profiles were utilized in classification-tree algorithms for selection of protein biomarker peaks contributing maximally to the differentiation between the examined diagnostic cohorts. Twenty-four such protein biomarker peaks were identified. All of them had lower levels in the SCHIZ cohort as compared to the BD cohort. Also, 21 of these peaks were down-regulated in the SCHIZ cohort vs. the control cohort, and 7 peaks were up-regulated in the BD cohort vs. the control cohort. The proteins constituting these biomarker peaks were recognized via matrix-assisted laser desorption time of flight/postsource decay mass spectrometry (MALDI-TOF-PSD-MS). These proteins represent a wide range of functional groups involved in cell metabolism, signaling cascades, regulation of gene transcription, protein and RNA chaperoning, and other aspects of cellular homeostasis. Finally, after statistical evaluation suggesting that the selected protein biomarkers are not significantly impacted by epidemiological/tissue storage parameters (although, influence of antipsychotic and mood stabilizing drugs could not be fully excluded), the ProteinChip-based profiling was engaged again to demonstrate that the detected SCHIZ-associated changes in the levels of our protein biomarkers could also be seen in DLPFC samples from the brain collection of the Mount Sinai Medical School/Bronx Veteran Affairs Medical Center. This study demonstrates the usefulness of ProteinChip-based SELDI-TOF protein profiling in gaining insight into the molecular pathology of SCHIZ and BD as it points to changes in protein levels characterizing these diseases.

Proteomic Profiling in the Sera of Workers Occupationally Exposed to Arsenic and Lead: Identification of Potential Biomarkers

Arsenic (As) and lead (Pb) are important inorganic toxicants in the environment. Frequently, humans are exposed to the mixtures of As and Pb, but little is known about the expression of biomarkers resulting from such mixed exposures. In this study, we analyzed serum proteomic profiles in a group of smelter workers with the aim of identifying protein biomarkers of mixed As and Pb exposure. Forty-six male workers co-exposed to As and Pb were studied. Forty-five age-matched male office workers were chosen as controls. Urine As and blood Pb concentrations were determined. Serum proteomic profiles were analyzed by Surface-Enhanced Laser Desorption/Ionization Time-Of-Flight (SELDI-TOF) mass spectrometer on the WCX2 ProteinChip. Using Recursive support vector machine (RSVM) algorithm, a panel of five peptides/proteins (2097 Da, 2953 Da, 3941 Da, 5338 Da, and 5639 Da) was selected based on their collective contribution to the optional separation between higher metal mixture exposure and non-exposure controls. Among these five selected markers, the 3941 Da was down-regulated and the four other proteins were up-regulated. Descriptive statistics confirmed that these five proteins differed significantly between metal exposure and non-exposure. Interestingly, the combined use of the five selected biomarkers could achieve higher discriminative power than single marker. These results demonstrated that proteomic technology, in conjunction with bioinformatics tools, could facilitate the discovery of new and better biomarkers of mixed metal exposure.

Proteomic analysis of childhood leukemia

Childhood acute lymphoblastic and myeloid leukemias are stratified into molecular and cytogenetic subgroups important for prognosis and therapy. Studies have shown that gene expression profiles can discriminate between leukemia subtypes. Thus, proteome analysis similarly holds the potential for characterizing different subtypes of childhood leukemia. We used surface-enhanced laser desorption/ionization time-of-flight mass spectrometry to analyze cell lysates from childhood leukemia cell lines as well as pretreatment leukemic bone marrow derived from childhood leukemia cases. Comparison of the acute myeloid leukemia (AML) cell line, Kasumi, and the biphenotypic myelomonocytic cell line, MV4;11, with the acute lymphoblastic leukemia (ALL) cell lines, 697 and REH, revealed many differentially expressed proteins. In particular, one 8.3 kDa protein has been identified as a C-terminal truncated ubiquitin. Analysis of childhood leukemia bone marrow showed differentially expressed proteins between AML and ALL, including a similar peak at 8.3 kDa, as well as several proteins that differentiate between the ALL t(12;21) and hyperdiploid subtypes. These results demonstrate the potential for proteome analysis to distinguish between various forms of childhood leukemia. Future analyses are warranted to validate these findings and to investigate the role of the C-terminal truncated ubiquitin in the etiology of ALL.

Overexpression of cathepsin B in gastric cancer identified by proteome analysis

We aimed to validate an analytical approach based on proteomics on gastric cancer specimens for the identification of new putative diagnostic or prognostic markers. Primary screening was performed on gastrectomy specimens obtained from ten consecutive patients with gastric cancer. Gastric epithelial cells were obtained with an epithelial cell enrichment technique, homogenized and then separated by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). The differential protein expression pattern was verified stepwise by Western blotting and immunohistochemistry on samples from 28 and 46 cancer patients, respectively. The putative clinical applicability and prognostic use were tested by an enzyme-linked immunoabsorbent assay on serum samples obtained from 149 cancer patients. One hundred-ninety-one differentially expressed protein spots were found by 2-D PAGE and identified by mass spectrometry, including cathepsin B, which was over-expressed in six (60%) patients. Western blotting confirmed that the active form of cathepsin B is over-expressed, while immunohistochemistry showed strong cytoplasmic staining in cancer tissues of 45 (98%) patients. The serum level of cathepsin B was increased in patients with gastric cancer compared to healthy controls (P = 0.0026) and correlated with T-category and the presence of distant metastases (P < 0.05). Serum levels above 129 pmol x L(-1) were associated with a reduced survival rate (P = 0.0297). Proteome analysis is a valuable tool for the identification of prognostic markers in gastric cancer: Increased cathepsin B serum levels are associated with advanced tumor stages and progressive disease, which enables the classification of some gastric cancer patients into a subgroup that should undergo aggressive therapy.