Immunofluorescence identifies distinct subsets of endothelial cells in the human liver.

As well as systemic vascular endothelial cells, the liver has specialised sinusoidal endothelial cells (LSEC). LSEC dysfunction has been documented in many diseased states yet their phenotype in normal human liver has not been comprehensively assessed. Our aim was to improve characterisation of subsets of endothelial cells and associated pericytes in the human liver. Immunofluorescence microscopy was performed on normal human liver tissue samples to assess endothelial and structural proteins in a minimum of three donors. LSEC are distributed in an acinar pattern and universally express CD36, but two distinctive subsets of LSEC can be identified in different acinar zones. Type 1 LSEC are CD36hiCD32-CD14-LYVE-1- and are located in acinar zone 1 of the lobule, while Type 2 LSEC are LYVE-1+CD32hiCD14+CD54+CD36mid-lo and are located in acinar zones 2 and 3 of the lobule. Portal tracts and central veins can be identified using markers for systemic vascular endothelia and pericytes, none of which are expressed by LSEC. In areas of low hydrostatic pressure LSEC are lined by stellate cells that express the pericyte marker CD146. Our findings identify distinctive populations of LSEC and distinguish these cells from adjacent stellate cells, systemic vasculature and pericytes in different zones of the liver acinus.

In vitro comparison between gamma-irradiated cryopreserved and Day 7 liquid-stored buffy coat-derived platelet components.

BACKGROUND: Cryopreserved platelet (PLT) components stored at -80°C in 5% to 6% dimethyl sulfoxide (DMSO) demonstrate enhanced hemostatic activity. Alterations in PLT surface glycoprotein expression and release of procoagulant microparticles during the freeze/thaw cycle result in PLT activation. Nothing is known of the effect of gamma irradiation on the in vitro quality of reconstituted cryopreserved PLTs. STUDY DESIGN AND METHODS: Gamma-irradiated (25-50 Gy) buffy coat-derived PLT components were either stored at room temperature for 7 days (the current expiry in New Zealand) or cryopreserved at -80°C using 5% to 6% DMSO. Cryopreserved PLTs were thawed at 37°C and reconstituted in ABO-identical plasma or PAS-E and compared to Day 7 gamma-irradiated liquid-stored PLTs. In vitro assays were performed to assess glycoprotein expression, PLT functionality and soluble cytokine release. RESULTS: Cryopreserved PLTs after thawing and reconstitution in ABO-matched plasma or PAS-E displayed differing recoveries (82.7 and 75.9%, respectively). Key expression levels of glycoproteins GPIbα (CD42b) and GPIIb (CD41a) were reduced. Cryopreserved PLTs retained the ability to form an effective functional clot, while showing accelerated initiation of clot formation (R-time) compared to Day 7 gamma-irradiated liquid-stored PLTs. CONCLUSION: Gamma-irradiated buffy coat-derived liquid-stored and cryopreserved PLTs have distinctly differing phenotypes. Cryopreserved PLTs reconstituted in ABO plasma have enhanced clot strength driven by coagulation factors and fibrinogen levels not present in PAS-E. Irradiated cryopreserved PLTs maintain a similar in vitro quality profile and hemostatic behavior to previously published, nonirradiated cryopreserved PLTs.

Identifying and quantifying metabolites by scoring peaks of GC-MS data.

BACKGROUND: Metabolomics is one of most recent omics technologies. It has been applied on fields such as food science, nutrition, drug discovery and systems biology. For this, gas chromatography-mass spectrometry (GC-MS) has been largely applied and many computational tools have been developed to support the analysis of metabolomics data. Among them, AMDIS is perhaps the most used tool for identifying and quantifying metabolites. However, AMDIS generates a high number of false-positives and does not have an interface amenable for high-throughput data analysis. Although additional computational tools have been developed for processing AMDIS results and to perform normalisations and statistical analysis of metabolomics data, there is not yet a single free software or package able to reliably identify and quantify metabolites analysed by GC-MS. RESULTS: Here we introduce a new algorithm, PScore, able to score peaks according to their likelihood of representing metabolites defined in a mass spectral library. We implemented PScore in a R package called MetaBox and evaluated the applicability and potential of MetaBox by comparing its performance against AMDIS results when analysing volatile organic compounds (VOC) from standard mixtures of metabolites and from female and male mice faecal samples. MetaBox reported lower percentages of false positives and false negatives, and was able to report a higher number of potential biomarkers associated to the metabolism of female and male mice. CONCLUSIONS: Identification and quantification of metabolites is among the most critical and time-consuming steps in GC-MS metabolome analysis. Here we present an algorithm implemented in a R package, which allows users to construct flexible pipelines and analyse metabolomics data in a high-throughput manner.

Sphingosine-1-phosphate lyase is expressed by CD68+ cells on the parenchymal side of marginal reticular cells in human lymph nodes.

Lymph nodes (LNs) form the intersection between the vascular and lymphatic systems. Lymphocytes and antigen-presenting cells (APCs) traffic between these systems, but the barriers crossed during this trafficking in human LNs are poorly defined. We identified a population of cells in human LNs that lines the boundary between the parenchyma and lymphatic sinuses, consistent with descriptions of marginal reticular cells (MRCs) in murine LNs. Human MRCs are CD141(high) podoplanin(+), CD90(+), ICAM1(+), and VCAM1(+) but lack endothelial and hematopoietic cell markers, or alpha-smooth muscle actin. We then examined expression of the enzyme sphingosine-1-phosphate (S1P) lyase (SGPL1) relative to the boundary defined by MRCs. SGPL1 expression was almost exclusively restricted to cells on the parenchymal side of MRCs, consistent with a role in maintaining the S1P gradient between the sinuses and the parenchyma. Surprisingly the cells expressing SGPL1 in the parenchyma were CD68(+) APCs. CD68(+) APCs generated from human monocytes were able to internalize and irreversibly degrade S1P, and this activity was inhibited by the S1P analogue FTY720. This work provides a map of the key structures at the boundary where human lymphocytes egress into sinuses, and identifies a novel potential mechanism for the activity of S1P analogues in humans.

Metab: an R package for high-throughput analysis of metabolomics data generated by GC-MS.

MOTIVATION: The Automated Mass Spectral Deconvolution and Identification System (AMDIS) is freeware extensively applied in metabolomics. However, datasets processed by AMDIS require extensive data correction, filtering and reshaping to create reliable datasets for further downstream analysis. Performed manually, these processes are laborious and extremely time consuming. Furthermore, manual corrections increase the chance of human error and can introduce additional technical variability to the data. Thus, an automated pipeline for curating GC-MS data is urgently needed. RESULTS: We present the Metab R package designed to automate the pipeline for analysis of metabolomics GC-MS datasets processed by AMDIS. AVAILABILITY: The Metab package, the AMDIS library and the reference ion library are available at www.metabolomics.auckland.ac.nz/index.php/downloads. CONTACT: k.ruggiero@auckland.ac.nz.

Pathway Activity Profiling (PAPi): from the metabolite profile to the metabolic pathway activity.

MOTIVATION: Metabolomics is one of the most recent omics-technologies and uses robust analytical techniques to screen low molecular mass metabolites in biological samples. It has evolved very quickly during the last decade. However, metabolomics datasets are considered highly complex when used to relate metabolite levels to metabolic pathway activity. Despite recent developments in bioinformatics, which have improved the quality of metabolomics data, there is still no straightforward method capable of correlating metabolite level to the activity of different metabolic pathways operating within the cells. Thus, this kind of analysis still depends on extremely laborious and time-consuming processes. RESULTS: Here, we present a new algorithm Pathway Activity Profiling (PAPi) with which we are able to compare metabolic pathway activities from metabolite profiles. The applicability and potential of PAPi was demonstrated using a previously published data from the yeast Saccharomyces cerevisiae. PAPi was able to support the biological interpretations of the previously published observations and, in addition, generated new hypotheses in a straightforward manner. However, PAPi is time consuming to perform manually. Thus, we also present here a new R-software package (PAPi) which implements the PAPi algorithm and facilitates its usage to quickly compare metabolic pathways activities between different experimental conditions. Using the identified metabolites and their respective abundances as input, the PAPi package calculates pathways' Activity Scores, which represents the potential metabolic pathways activities and allows their comparison between conditions. PAPi also performs principal components analysis and analysis of variance or t-test to investigate differences in activity level between experimental conditions. In addition, PAPi generates comparative graphs highlighting up- and down-regulated pathway activity. AVAILABILITY: These datasets are available in http://www.4shared.com/file/hTWyndYU/extra.html and http://www.4shared.com/file/VbQIIDeu/intra.html. PAPi package is available in: http://www.4shared.com/file/s0uIYWIg/PAPi_10.html CONTACT: s.villas-boas@auckland.ac.nz SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Mice lacking the neuropeptide alpha-calcitonin gene-related peptide are protected against diet-induced obesity.

Alpha-calcitonin gene-related peptide (alphaCGRP) is a neuropeptide that is expressed in motor and sensory neurons. It is a powerful vasodilator and has been implicated in diverse metabolic roles. However, its precise physiological function remains unclear. In this study, we investigated the role of alphaCGRP in lipid metabolism by chronically challenging alphaCGRP-specific knockout (alphaCGRP(-/-)) and control mice with high-fat diet regimens. At the start of the study, both animal groups displayed similar body weights, serum lipid markers, and insulin sensitivity. However, alphaCGRP(-/-) mice displayed higher core temperatures, increased energy expenditures, and a relative daytime (nonactive) depression in respiratory quotients, which indicated increased beta-oxidation. In response to fat feeding, alphaCGRP(-/-) mice were comparatively protected against diet-induced obesity with an attenuated body weight gain and an overall reduction in adiposity across all the three diets examined. AlphaCGRP(-/-) mice also displayed improved glucose handling and insulin sensitivity, lower im and hepatic lipid accumulation, and improved overall metabolic health. These findings define a new role for alphaCGRP as a mediator of energy metabolism and opens up therapeutic opportunities to target CGRP action in obesity.

Pharmacokinetics, pharmacodynamics, and metabolism of triethylenetetramine in healthy human participants: an open-label trial.

The selective Cu(II)-chelator, triethylenetetramine (TETA), is undergoing clinical trials for the treatment of heart failure in patients with diabetes. Recently, the authors showed that 2 acetylated metabolites, N(1)-acetyltriethylenetetramine (MAT) and N(1),N(10)-diacetyltriethylenetetramine (DAT), are formed in humans following oral TETA administration. Thus, it became necessary to determine whether the N-acetyltransferase (NAT) 2 phenotype has any effects on the pharmacological properties and safety profile of TETA. Twelve fast and 12 slow NAT2-phenotype healthy participants were recruited. After oral drug administration, the authors collected plasma and urine samples, measured plasma concentrations of TETA and its 2 metabolites along with concomitant urinary copper concentrations, and performed safety tests. They present, for the first time, the complete 24-hour pharmacokinetic profiles of TETA, MAT, and DAT in humans. There was no evidence for clear-cut differences in pharmacokinetic profiles between fast and slow acetylators. Pharmacodynamic analysis showed no significant differences in cupruresis between the 2 NAT2 phenotypes. Safety results were consistent with TETA being well tolerated, and no significant differences in safety profiles were observed between the 2 phenotypes. Based on these data, NAT2 phenotype does not affect TETA's pharmacokinetic, pharmacodynamic, or safety profiles. TETA may be acetylated via an alternative mechanism, such as that catalyzed by spermidine/spermine N(1)-acetyltranferase.

Changes in the mesenteric lymph proteome induced by hemorrhagic shock.

Biologically active factors produced by the intestine and transported by the aqueous and protein fraction of mesenteric lymph are now thought to contribute significantly to the development of distant organ failure in hemorrhagic shock. Despite the likely relevance of the protein composition of mesenteric lymph conditioned by hemorrhagic shock, there is no detailed description of its proteome. The aim of this study was to provide the first comprehensive description of the proteome of hemorrhagic shock-conditioned mesenteric lymph. Mesenteric lymph was collected from 16 male Wistar rats randomized to group 1 (n = 8) sham control and group 2 (n = 8) with hemorrhagic shock. The lymph was subjected to proteomic analysis using iTRAQ and liquid chromatography-tandem mass spectrometry. Sixty of the 245 proteins had a significant increase in their relative abundance in the hemorrhagic shock group. A bioinformatics approach highlighted the importance of the key gene ontology pathways relating to response to injury and metabolic responses as changing most significantly in shock. Using an interactome, we identified several highly connected proteins: 14-3-3 Zeta, 14-3-3 epsilon, actin, aldolase A, calmodulin, cofilin 1, cystatin C, fatty acid-binding protein 4, profilin 1, prolyl 4-hydrolase, peptidylprolyl isomerase, and transgelin. This study provides the first detailed description of protein changes in hemorrhagic shock-conditioned mesenteric lymph, and using a bioinformatics approach, we identified several targets for possible further research.

Quantitative proteomic profiling identifies new renal targets of copper(II)-selective chelation in the reversal of diabetic nephropathy in rats.

This study aimed to identify new diabetic nephropathy (DN)-related proteins and renal targets of the copper(II)-selective chelator, triethylenetetramine (TETA) in streptozotocin-diabetic rats. We used the recently developed iTRAQ technology to compare renal protein profiles among non-diabetic, diabetic, and TETA-treated diabetic rats. In diabetic kidneys, tubulointerstitial nephritis antigen (TINag), voltage-dependent anion-selective channel (VDAC) 1, and VDAC2 were up-regulated in parallel with alterations in expression of proteins with functions in oxidative stress and oxidative phosphorylation (OxPhos) pathways. By contrast, mitochondrial HSP 60, Cu/Zn-superoxide dismutase, glutathione S-transferase alpha3 and aquaporin-1 were down-regulated in diabetic kidneys. Following TETA treatment, levels of D-amino acid oxidase-1, epoxide hydrolase-1, aquaporin-1, and a number of mitochondrial proteins were normalized, with concomitant amelioration of albuminuria. Changes in levels of TINag, collagen VIalpha1, actinin 4alpha, apoptosis-inducing factor 1, cytochrome C, histone H3, VDAC1, and aquaporin-1 were confirmed by Western blotting or immunohistochemistry. Changes in expression of proteins related to tubulointerstitial function, podocyte structure, and mitochondrial apoptosis are implicated in the mechanism of DN and their reversal by TETA. These findings are consistent with the hypothesis that this new experimental therapy may be useful for treatment of DN.

The proteome of mesenteric lymph during acute pancreatitis and implications for treatment.

CONTEXT: The protein fraction of mesenteric lymph during acute pancreatitis and other critical illness is thought to contain toxic factors. However, we do not have a complete description of the mesenteric lymph proteome during acute pancreatitis. OBJECTIVE: The aim of this study was to define the proteomic changes in mesenteric lymph during acute pancreatitis. SETTING: Animal Laboratory, University of Auckland, New Zealand. DESIGN: Mesenteric lymph was collected from sixteen male Wistar rats randomised to Group 1 (n=8) with taurocholate induced acute pancreatitis and Group 2 (n=8) sham control. The lymph was subjected to proteomic analysis using iTRAQ (Applied Biosystems, Foster City, CA, USA) and liquid chromatography-tandem mass spectrometry. RESULTS: Two hundred and forty-five proteins including 35 hypothetical proteins were identified in mesenteric lymph. Eight of the 245 proteins had a significant increase in their relative abundance in acute pancreatitis conditioned mesenteric lymph, and 7 of these were pancreatic catabolic enzymes (pancreatic amylase 2, pancreatic lipase, carboxypeptidase A2, chymotrypsinogen B, carboxypeptidase B1, cationic trypsinogen, ribonuclease 1). CONCLUSIONS: This is the first comprehensive description of the proteome of mesenteric lymph during acute pancreatitis and has demonstrated a significantly increased relative abundance of 7 secreted pancreatic catabolic enzymes in acute pancreatitis conditioned mesenteric lymph. This study provides a clear rationale for further research to investigate the efficacy of enteral protease inhibitors in the treatment of acute pancreatitis.

The proteome of rodent mesenteric lymph.

Mesenteric lymph contributes to normal homeostasis and has an emerging role in the pathogenesis of multiple organ dysfunction syndrome. The aim of this study was to define the proteome of normal rodent mesenteric lymph in the fasted and fed states. Eight male Wistar rats fed a standard rodent diet were randomized to two groups. Group 1 (fasted, n = 4) were fasted for 24 h before anesthetized collection of mesenteric lymph. Group 2 (fed, n = 4) were allowed ad libitum access to food before lymph collection. Mesenteric lymph was subjected to proteomic analysis using iTRAQ and liquid chromatography-tandem mass spectrometry (LC-MS/MS). One hundred fifty proteins, including 26 hypothetical proteins, were identified in this study. All proteins were identified in lymph from both the fasted and fed states. The relative distribution profiles of protein functional classes in the mesenteric lymph differed significantly from that reported for plasma. The most abundant classes identified in lymph were protease inhibitors (16%) and proteins related to innate immunity (12%). In conclusion, this study provides the first detailed description of the normal mesenteric lymph proteome in the fed and fasted states using iTRAQ and LC-MS/MS.

Design and analysis of two-phase experiments for gene expression microarrays-part I.

Gene expression microarray experiments are intrinsically two-phase experiments. Messenger RNA (mRNA), required for the microarray experiment, must first be derived from plants or animals that are exposed to a set of treatments in a previous experiment (Phase 1). The mRNA is then used in the subsequent laboratory-based microarray experiment (Phase 2) from which gene expression is measured and ultimately analyzed. We show that obtaining a valid test for the effects of treatments on gene expression depends on the design of both the Phase 1 and Phase 2 experiments. Examples show that the multiple dye-swap design at Phase 2 is more robust than the alternating loop design in the absence of prior knowledge of the relative size of variation in the Phase 1 and Phase 2 experiments.

Laser capture microdissection and cDNA microarrays used to generate gene expression profiles of the rapidly expanding fibre initial cells on the surface of cotton ovules.

Cotton (Gossypium hirsutum L.) fibre initial cells undergo a rapid cellular re-programming around anthesis to form the long cellulose fibres prized for textile manufacture. On the day of anthesis the cotton fibre initial cells balloon out from the ovule surface and so are clearly distinguished from adjacent epidermal pavement cells. To enhance our understanding of the molecular processes that determine which cells become fibres and why adjacent epidermal cells remain in a different developmental state we studied the expression profiles of the two respective cell types. Using laser-capture microdissection, coupled with an in vitro RNA amplification system, we used cDNA microarray slides to profile the gene expression in expanding fibre initials compared to the non-expanding epidermal cells at an early stage just after the fibre initials are discernable. Except for a few regulatory genes, the genes that are up-regulated in the cotton fibre initials relative to epidermal cells predominantly encode proteins involved in generating the components for the extra cell membrane and primary cell wall needed for the rapid cell expansion of the initials. This includes synthesis of enzymes and cell wall proteins, carbohydrates, and lipids. An analysis of single channel fluorescence levels confirmed that these classes of genes were also the most highly expressed genes in fibre initials. Genes involved in DNA metabolism were also well represented in the expanding fibre cell, consistent with the limited endoreduplication we previously reported to occur in fibre initial cells.

Cycloheximide treatment of cotton ovules alters the abundance of specific classes of mRNAs and generates novel ESTs for microarray expression profiling.

Fibres of cotton (Gossypium hirsutum L.) are single elongated epidermal cells that start to develop on the outer surface of cotton ovules on the day of anthesis. Little is known about the control of fibre initiation and development. As a first step towards discovering important genes involved in fibre initiation and development using a genomics approach, we report technical advances aimed at reducing redundancy and increasing coverage for anonymous cDNA microarrays in this study. Cotton ovule cDNA libraries (both normalised and un-normalised) from around the time of fibre initial formation have been prepared and partially characterised by sequencing. Re-association-based normalisation partially reduced library redundancy and increased representation of novel sequences. However, another library generated from in vitro cultured cotton ovules treated with the protein synthesis inhibitor, cycloheximide, showed a significantly altered gene representation including a greater proportion of protein phosphorylation genes, transport genes and transcription factors and a much reduced proportion of protein synthesis genes than were identified in the conventional types of libraries. Over 10,000 expressed sequence tag (EST) clones randomly selected from the three libraries were printed on microarray slides and used to assess gene expression in tissue cultured ovules with and without cycloheximide treatment. The microarray results showed that cycloheximide had a dramatic effect in modifying the pattern of the gene expression in cultured ovules, affecting the same types of genes identified in the preliminary analysis on relative EST abundance in the different ovule cDNA libraries. Cycloheximide clearly provided a simple and useful method for enriching novel gene sequences for genomic studies.