Marcus O.D. Sjödin

Mining ventricular cerebrospinal fluid from patients with traumatic brain injury using hexapeptide ligand libraries to search for trauma biomarkers

Traumatic brain injury (TBI) is an acute event resulting from external force to the brain and is a major cause of death and disability associated with high health care costs in the western world. Additional injuries, originating from the secondary molecular events after the initial intensive care, may be limited by the use of objective biomarkers to provide the best treatment and patient prediction outcome. In this study, hexapeptide ligand libraries (HLL) have been used for the enrichment of suggested protein biomarkers for TBI in cerebrospinal fluid (CSF). HLL have the potential to enrich low abundant proteins and simultaneously reduce the high abundant proteins, rendering a sample with significantly reduced dynamic range. The CSF proteome from two TBI inflicted patients have been extensively mapped using a large initial sample volume obtained by extraventricular drainage. Shotgun proteomics, in combination with isoelectric focusing (IEF) and nano-LC-MS/MS, identified 339 unique proteins (MudPIT scoring p < or = 0.05) with a protein overlap of 130 between the patients. As much as 45% of the proteins reported in the literature to be associated with degenerative/regenerative processes occurring after a trauma to the head were identified. Out of the most prominent potential protein biomarkers, such as neuron specific enolase, glial fibrillary acidic protein, myelin basic protein, creatine kinase B-type and S-100beta, all except myelin basic protein were detected in the study. This study shows the possibility of using HLL as a tool for screening of low abundant protein biomarkers in human CSF.

Comparative study of label and label-free techniques using shotgun proteomics for relative protein quantification.

The analytical performance of three different strategies, iTRAQ (isobaric tag for relative and absolute quantification), dimethyl labeling (DML) and label free (LF) for relative protein quantification using shotgun proteomics have been evaluated. The methods have been explored using samples containing (i) Bovine proteins in known ratios and (ii) Bovine proteins in known ratios spiked into Escherichia coli. The latter case mimics the actual conditions in a typical biological sample with a few differentially expressed proteins and a bulk of proteins with unchanged ratios. Additionally, the evaluation was performed on both QStar and LTQ-FTICR mass spectrometers. LF LTQ-FTICR was found to have the highest proteome coverage while the highest accuracy based on the artificially regulated proteins was found for DML LTQ-FTICR (54%). A varying linearity (k: 0.55-1.16, r(2): 0.61-0.96) was shown for all methods within selected dynamic ranges. All methods were found to consistently underestimate Bovine protein ratios when matrix proteins were added. However, LF LTQ-FTICR was more tolerant toward a compression effect. A single peptide was demonstrated to be sufficient for a reliable quantification using iTRAQ. A ranking system utilizing several parameters important for quantitative proteomics demonstrated that the overall performance of the five different methods was; DML LTQ-FTICR>iTRAQ QStar>LF LTQ-FTICR>DML QStar>LF QStar.

Analysis of membrane and hydrophilic proteins simultaneously derived from the mouse brain using cloud-point extraction

In this study, a temperature-induced phase fractionation known as cloud-point extraction (CPE) with the non-ionic surfactant Triton X-114 was used to simultaneously extract, concentrate, and fractionate hydrophobic and hydrophilic proteins from mouse brain tissue. Two bottom-up proteomic techniques were used to comprehensively identify the extracted proteins. The first “shotgun”-based approach included tryptic digestion of the proteins followed by reversed-phase nanoliquid chromatography (RP-nanoLC) in combination with electrospray ionization (ESI) tandem mass spectrometry (MS/MS). In the second approach, the extracted intact proteins were first separated by one-dimensional (1D) gel electrophoresis and then in-gel digested with trypsin and analyzed with nanoLC-MS/MS. In total, 1,825 proteins were unambiguously identified and the percentage of membrane proteins was 26% which is at the reported genome expression levels of 20–30%. The protein overlap between the two approaches was high. The majority (77%) of the identifications in the first approach was also found by the second method. The protein overlap between the CPE-extracted hydrophilic and hydrophobic fractions was rather small (16–23%) for both methods, which indicates a good phase separation. A quantitative evaluation of the CPE with iTRAQ labeling and nanoLC-ESI-MS/MS analysis gave iTRAQ ratios at the expected levels and an overall variation of the entire method at 17–31%. The results indicate very reproducible sample preparation and analysis methods that readily can be applied on large-scale sample sets.

Analysis of peptides using N-methylpolyvinylpyridium as silica surface modifier for CE-ESI-MS

In this study, the N‐methylpolyvinylpyridinuim polymer has for the first time been used as a silica surface modifier for CE in combination with ESI MS (CE‐ESI‐MS). The compatibility for ESI‐MS was demonstrated by the analysis of peptides and protein digests. The N‐methylpolyvinylpyridium surface interacts electrostatically with the ionized silanol groups, giving a cationic surface with a reversed EOF. The surface modifier gave rapid and repeatable separations of peptides, proteins and protein digests at acidic pH for more than 4 h of continuous use. The CE separation yielded peak efficiencies of up to 4.3×105 plates/m. The surface coating is highly compatible with ESI and facilitates the separation and analysis of complex peptide mixtures as shown by the analysis of BSA digests.

Spinal Cord Stimulation Alters Protein Levels in the Cerebrospinal Fluid of Neuropathic Pain Patients : A Proteomic Mass Spectrometric Analysis

Electrical neuromodulation by spinal cord stimulation (SCS) is a well‐established method for treatment of neuropathic pain. However, the mechanism behind the pain relieving effect in patients remains largely unknown. In this study, we target the human cerebrospinal fluid (CSF) proteome, a little investigated aspect of SCS mechanism of action.

Quantitative subproteomic analysis of age-related changes in mouse liver peroxisomes by iTRAQ LC-MS/MS

Aging is a complex multifactorial phenomenon, which is believed to result from the accumulation of cellular damage to biological macromolecules. Peroxisomes recently emerged as another important source of reactive oxygen species (ROS) production in addition to mitochondria. However, the role of these organelles in the process of aging is still not clear. The aim of this study was to characterize the changes in protein expression profiles of young (10 weeks old) versus old (18 months old) mouse liver peroxisome-enriched fractions. We have applied shotgun proteomic approach based on liquid chromatography and tandem mass spectrometry (LC-MS/MS) combined with iTRAQ (isobaric tags for relative and absolute quantitation) labeling that allows comparative quantitative multiplex analysis. Our analysis led to identification and quantification of 150 proteins, 8 out of which were differentially expressed between two age groups at a statistically significant level (p<0.05), with folds ranging from 1.2 to 4.1. These proteins involved in peroxisomal β-oxidation, detoxification of xenobiotics and production of ROS. Noteworthy, differences in liver proteome have been observed between as well as within different age groups. In conclusion, our subproteomic quantitative study suggests that mouse liver proteome is sufficiently maintained until certain age.

De novo design and synthesis of a 30-cistron translation-factor module

Abstract Two of the many goals of synthetic biology are synthesizing large biochemical systems and simplifying their assembly. While several genes have been assembled together by modular idempotent cloning, it is unclear if such simplified strategies scale to very large constructs for expression and purification of whole pathways. Here we synthesize from oligodeoxyribonucleotides a completely de-novo-designed, 58-kb multigene DNA. This BioBrick plasmid insert encodes 30 of the 31 translation factors of the PURE translation system, each His-tagged and in separate transcription cistrons. Dividing the insert between three high-copy expression plasmids enables the bulk purification of the aminoacyl-tRNA synthetases and translation factors necessary for affordable, scalable reconstitution of an in vitro transcription and translation system, PURE 3.0.

New players in the mechanism of spinal cord stimulation for neuropathic pain

Abstract Aims The aim of this study was to uncover possible proteins involved in the mechanism for neuropathic spinal cord stimulation (SCS) pain relief in humans. Methods Using two different proteomic protocols we compared the protein concentration in cerebrospinal fluid (CSF) from 14 SCS responsive neuropathic pain patients using a shotgun proteomic approach. The comparison was made between samples from the same individual taken when the stimulator had been off for 48 h, and after the stimulator had been used as normal for three weeks. Mass spectrometry raw files from both experimental setups were analysed using MS Quant and DeCyder softwares and proteins were identified using MASCOT search against Swissprot database. After median normalization moderate paired t-test statistics were used in R limma package to find up-and down regulated proteins. Results In total, 255 and 216 proteins could be identified by the dimethyl and label free methods respectively and relatively quantified. Of these several were significantly up- and down regulated. Conclusions These novel proteins add to the SCS mechanism in patients with neuropathic pain. These results strengthen the evidence for SCS as altering extracellular matrix components and affecting central nervous system plasticity.

Proteins with potential role in analgesic effect of spinal cord stimulation on neuropathic pain

Abstract Aims We aimed to find proteins of relevance to the prolonged analgesic effect of spinal cord stimulation (SCS) for patients with neuropathic pain. Methods The proteomes of cerebrospinal fluid (CSF) from 14 neuropathic pain patients using spinal cord stimulation (SCS) was compared to the CSF proteomes of the same patients when not using the stimulator. Samples were analyzed by dimethyl label and label free shotgun proteomics approach. Samples were prepared by immunoaffinity fractionation and then separated by reversed phase nanoliquid chromatography coupled to an electrospray ionization source and analyzed by high resolution tandem mass spectrometry. The proteins were comparatively quantified on the peptide level and ranked based on numbers of regulated peptides. Then the dimethyl and label free analysis results were combined. In order to group proteins by function and interactions, a functional enrichment network analysis was performed using the String (Search Tool for the Retrieval of Interacting Genes/Proteins) database on all significantly differentially expressed proteins. Results We found 87 differentially expressed proteins. Network analysis showed a high level of enrichment in interactions between the proteins involved in platelet degranulation and wound healing with p-values 2.48E−11 and 4.58E−08. We also recognized two additional clusters related to complement and coagulation cascades and neuropeptides. None of these proteins have been implicated in SCS mechanism previously. Conclusions Up- and down-regulations of immunological proteins and neuropeptides may explain the prolonged relief of neuropathic pain obtained after SCS. These findings contribute a new basis for understanding of SCS analgesic mechanism in human neuropathic pain. Further verification studies of these initial findings are needed.

Proteomic analysis of cerebrospinal fluid gives insight into the pain relief of spinal cord stimulation

Abstract Aims Neuropathic pain is caused by a lesion or disease of the somatosensory nervous system affecting approximately 2% of the population. Current pharmacological treatments are ineffective for more than 50% of the patients and often give much adverse effects. Spinal cord stimulation (SCS) is an alternative cost-effective treatment with high efficacy, prolonged pain relief, few side effects. We have compared the cerebrospinal fluid (CSF) proteomes from neuropathic pain patients during pain relief induced by SCS and during pain sensation without SCS, to gain further insights into the mechanisms behind the obtained analgesia. Methods Paired CSF samples were taken from SCS-responsive neuropathic pain patients after the SCS had been turned off for 48 h and when the SCS had been used normally for three weeks. Thus, each patient acted as their own control. The corresponding proteomes for each patient were relatively quantified using a mass spectrometry based shotgun approach. Results In total, 419 unique proteins were simultaneously identified and relatively quantified. A panel consisting of seven proteins, 5 up-regulated and 2 down, were found to be significantly regulated by SCS in two complementary statistical tests (P ≤ 0.01). The most up-regulated protein in the SCS linked panel is a known modulator of nicotinic acetylcholine (ACh) receptor activity. Interestingly, it has a striking tertiary structural similarity and biological functionality as pain modulating prototoxins found in snake venoms. Conclusions Our findings reveal possible insights into the mechanism of spinal cord stimulation and the obtained pain relief.